Nextflow lint results

Generated: 2026-03-13T00:23:27.201999737Z
Nextflow version: 26.02.0-edge
Summary: 119 errors, 549 warnings

❌ Errors

Error: conf/modules/aligner.config:19:17: Unexpected input: ':'
```
        withName: 'BWAMEM1_MEM' {
                ^
```

Error: conf/modules/annotate.config:20:17: Unexpected input: ':'

        withName: 'SNPEFF_SNPEFF' {
                ^

Error: conf/modules/freebayes.config:75:17: Unexpected input: ':'

        withName: '.*:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_FREEBAYES:FREEBAYES' {
                ^

Error: conf/modules/haplotypecaller.config:60:17: Unexpected input: ':'

        withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:(MERGE_BAM|INDEX_MERGE_BAM)' {
                ^

Error: conf/modules/joint_germline.config:36:17: Unexpected input: ':'

        withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:BCFTOOLS_SORT' {
                ^

Error: conf/modules/lofreq.config:19:17: Unexpected input: ':'

        withName: "LOFREQ_CALLPARALLEL" {
                ^

Error: conf/modules/manta.config:18:17: Unexpected input: ':'

        withName: 'MANTA_GERMLINE|MANTA_TUMORONLY|MANTA_SOMATIC' {
                ^

Error: conf/modules/markduplicates.config:122:9: If statements cannot be mixed with config statements

        if (params.tools && params.tools.split(',').contains('sentieon_dedup')) {
        ^

Error: conf/modules/modules.config:78:17: Unexpected input: ':'

        withName: 'NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH' {
                ^

Error: conf/modules/mpileup.config:56:17: Unexpected input: ':'

        withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_MPILEUP:SAMTOOLS_MPILEUP' {
                ^

Error: conf/modules/mutect2.config:19:17: Unexpected input: ':'

        withName: 'GATK4_MUTECT2' {
                ^

Error: conf/modules/prepare_recalibration.config:19:9: If statements cannot be mixed with config statements
```
        if (params.use_gatk_spark) {
        ^
```

Error: conf/modules/recalibrate.config:47:17: Unexpected input: ':'

        withName: 'NFCORE_SAREK:SAREK:FASTQ_PREPROCESS_GATK:(BAM_APPLYBQSR|BAM_APPLYBQSR_SPARK):CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM' {
                ^

Error: conf/modules/sentieon_dedup.config:44:17: Unexpected input: ':'

        withName: 'NFCORE_SAREK:SAREK:FASTQ_PREPROCESS_GATK:BAM_SENTIEON_DEDUP:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS' {
                ^

Error: conf/modules/sentieon_dnascope_joint_germline.config:28:17: Unexpected input: ':'

        withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_SENTIEON:BCFTOOLS_SORT' {
                ^

Error: conf/modules/sentieon_haplotyper.config:48:17: Unexpected input: ':'

        withName: '.*:SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES' {
                ^

Error: conf/modules/sentieon_haplotyper_joint_germline.config:27:17: Unexpected input: ':'

        withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_SENTIEON:BCFTOOLS_SORT' {
                ^

Error: conf/modules/tiddit.config:40:17: Unexpected input: ':'

        withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_TIDDIT:TIDDIT_NORMAL:TABIX_BGZIP_TIDDIT_SV' {
                ^

Error: conf/modules/umi.config:38:17: Unexpected input: ':'

        withName: 'NFCORE_SAREK:SAREK:FASTQ_PREPROCESS_GATK:FASTQ_CREATE_UMI_CONSENSUS_FGBIO:ALIGN_UMI:BWAMEM.*_MEM' {
                ^

Error: main.nf:76:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/sarek/subworkflows/local/prepare_intervals/main.nf'

include { PREPARE_INTERVALS               } from './subworkflows/local/prepare_intervals'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: main.nf:131:5: PREPARE_INTERVALS is not defined

    PREPARE_INTERVALS(PREPARE_GENOME.out.fasta_fai, params.intervals, params.no_intervals, params.nucleotides_per_second, params.outdir, params.step)
    ^^^^^^^^^^^^^^^^^

Error: main.nf:135:72: PREPARE_INTERVALS is not defined

    intervals_bed_combined = params.no_intervals ? Channel.value([]) : PREPARE_INTERVALS.out.intervals_bed_combined
                                                                       ^^^^^^^^^^^^^^^^^

Error: main.nf:136:79: PREPARE_INTERVALS is not defined

    intervals_bed_gz_tbi_combined = params.no_intervals ? Channel.value([]) : PREPARE_INTERVALS.out.intervals_bed_gz_tbi_combined
                                                                              ^^^^^^^^^^^^^^^^^

Error: main.nf:137:50: PREPARE_INTERVALS is not defined

    intervals_bed_combined_for_variant_calling = PREPARE_INTERVALS.out.intervals_bed_combined
                                                 ^^^^^^^^^^^^^^^^^

Error: main.nf:144:17: PREPARE_INTERVALS is not defined

    intervals = PREPARE_INTERVALS.out.intervals_bed
                ^^^^^^^^^^^^^^^^^

Error: main.nf:146:28: PREPARE_INTERVALS is not defined

    intervals_bed_gz_tbi = PREPARE_INTERVALS.out.intervals_bed_gz_tbi
                           ^^^^^^^^^^^^^^^^^

Error: main.nf:171:29: PREPARE_INTERVALS is not defined

    versions = versions.mix(PREPARE_INTERVALS.out.versions)
                            ^^^^^^^^^^^^^^^^^

Error: subworkflows/local/bam_baserecalibrator/main.nf:26:21: cram is already declared

        .map{ meta, cram, crai, intervals, num_intervals -> [ meta + [ num_intervals:num_intervals ], cram, crai, intervals ] }
                    ^^^^

Error: subworkflows/local/bam_baserecalibrator/main.nf:26:33: intervals is already declared

        .map{ meta, cram, crai, intervals, num_intervals -> [ meta + [ num_intervals:num_intervals ], cram, crai, intervals ] }
                                ^^^^^^^^^

Error: subworkflows/local/bam_baserecalibrator_spark/main.nf:26:21: cram is already declared

        .map{ meta, cram, crai, intervals, num_intervals -> [ meta + [ num_intervals:num_intervals ], cram, crai, intervals ] }
                    ^^^^

Error: subworkflows/local/bam_baserecalibrator_spark/main.nf:26:33: intervals is already declared

        .map{ meta, cram, crai, intervals, num_intervals -> [ meta + [ num_intervals:num_intervals ], cram, crai, intervals ] }
                                ^^^^^^^^^

Error: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:74:26: fasta is already declared
```
        fasta.map{ meta, fasta -> [ fasta ] },
                         ^^^^^
```
Error: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:75:24: fai is already declared
```
        fai.map{ meta, fai -> [ fai ] },
                       ^^^
```
Error: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:76:25: dict is already declared
```
        dict.map{ meta, dict -> [ dict ] })
                        ^^^^
```
Error: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:83:26: fasta is already declared
```
        fasta.map{ meta, fasta -> [ fasta ] },
                         ^^^^^
```
Error: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:84:24: fai is already declared
```
        fai.map{ meta, fai -> [ fai ] },
                       ^^^
```
Error: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:85:25: dict is already declared
```
        dict.map{ meta, dict -> [ dict ] })
                        ^^^^
```
Error: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:100:26: fasta is already declared
```
        fasta.map{ meta, fasta -> [ fasta ] },
                         ^^^^^
```
Error: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:101:24: fai is already declared
```
        fai.map{ meta, fai -> [ fai ] },
                       ^^^
```
Error: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:102:25: dict is already declared
```
        dict.map{ meta, dict -> [ dict ] })
                        ^^^^
```
Error: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:114:26: fasta is already declared
```
        fasta.map{ meta, fasta -> [ fasta ] },
                         ^^^^^
```
Error: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:115:24: fai is already declared
```
        fai.map{ meta, fai -> [ fai ] },
                       ^^^
```
Error: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:116:25: dict is already declared
```
        dict.map{ meta, dict -> [ dict ] })
                        ^^^^
```
Error: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:137:9: Variables in a closure should be declared with def
```
        vcf_out = recal_vcf ?: joint_vcf
        ^^^^^^^
```
Error: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:145:9: Variables in a closure should be declared with def
```
        tbi_out = recal_tbi ?: joint_tbi
        ^^^^^^^
```
Error: subworkflows/local/bam_joint_calling_germline_sentieon/main.nf:125:13: Variables in a closure should be declared with def
```
            vcf_out = recal_vcf ?: joint_vcf
            ^^^^^^^
```
Error: subworkflows/local/bam_joint_calling_germline_sentieon/main.nf:133:13: Variables in a closure should be declared with def
```
            tbi_out = recal_tbi ?: joint_tbi
            ^^^^^^^
```

Error: subworkflows/local/bam_markduplicates/main.nf:22:48: fasta is already declared

    GATK4_MARKDUPLICATES(bam, fasta.map{ meta, fasta -> [ fasta ] }, fasta_fai.map{ meta, fasta_fai -> [ fasta_fai ] })
                                               ^^^^^

Error: subworkflows/local/bam_markduplicates/main.nf:22:91: fasta_fai is already declared

    GATK4_MARKDUPLICATES(bam, fasta.map{ meta, fasta -> [ fasta ] }, fasta_fai.map{ meta, fasta_fai -> [ fasta_fai ] })
                                                                                          ^^^^^^^^^

Error: subworkflows/local/bam_markduplicates_spark/main.nf:25:53: fasta is already declared

    GATK4SPARK_MARKDUPLICATES(bam, fasta.map{ meta, fasta -> [ fasta ] }, fasta_fai.map{ meta, fasta_fai -> [ fasta_fai ] }, dict.map{ meta, dict -> [ dict ] })
                                                    ^^^^^

Error: subworkflows/local/bam_markduplicates_spark/main.nf:25:96: fasta_fai is already declared

    GATK4SPARK_MARKDUPLICATES(bam, fasta.map{ meta, fasta -> [ fasta ] }, fasta_fai.map{ meta, fasta_fai -> [ fasta_fai ] }, dict.map{ meta, dict -> [ dict ] })
                                                                                               ^^^^^^^^^

Error: subworkflows/local/bam_markduplicates_spark/main.nf:25:142: dict is already declared

    GATK4SPARK_MARKDUPLICATES(bam, fasta.map{ meta, fasta -> [ fasta ] }, fasta_fai.map{ meta, fasta_fai -> [ fasta_fai ] }, dict.map{ meta, dict -> [ dict ] })
                                                                                                                                             ^^^^

Error: subworkflows/local/bam_markduplicates_spark/main.nf:37:59: fasta is already declared

    GATK4_ESTIMATELIBRARYCOMPLEXITY(bam, fasta.map{ meta, fasta -> [ fasta ] }, fasta_fai.map{ meta, fasta_fai -> [ fasta_fai ] }, dict.map{ meta, dict -> [ dict ] })
                                                          ^^^^^

Error: subworkflows/local/bam_markduplicates_spark/main.nf:37:102: fasta_fai is already declared

    GATK4_ESTIMATELIBRARYCOMPLEXITY(bam, fasta.map{ meta, fasta -> [ fasta ] }, fasta_fai.map{ meta, fasta_fai -> [ fasta_fai ] }, dict.map{ meta, dict -> [ dict ] })
                                                                                                     ^^^^^^^^^

Error: subworkflows/local/bam_markduplicates_spark/main.nf:37:148: dict is already declared

    GATK4_ESTIMATELIBRARYCOMPLEXITY(bam, fasta.map{ meta, fasta -> [ fasta ] }, fasta_fai.map{ meta, fasta_fai -> [ fasta_fai ] }, dict.map{ meta, dict -> [ dict ] })
                                                                                                                                                   ^^^^

Error: subworkflows/local/bam_sentieon_dedup/main.nf:19:26: bam is already declared

    bam = bam.map{ meta, bam -> [ meta - meta.subMap('data_type'), bam ] }
                         ^^^

Error: subworkflows/local/bam_sentieon_dedup/main.nf:20:26: bai is already declared

    bai = bai.map{ meta, bai -> [ meta - meta.subMap('data_type'), bai ] }
                         ^^^

Error: subworkflows/local/bam_variant_calling_deepvariant/main.nf:26:21: cram is already declared

        .map{ meta, cram, crai, intervals, num_intervals -> [ meta + [ num_intervals:num_intervals ], cram, crai, intervals ]}
                    ^^^^

Error: subworkflows/local/bam_variant_calling_deepvariant/main.nf:26:33: intervals is already declared

        .map{ meta, cram, crai, intervals, num_intervals -> [ meta + [ num_intervals:num_intervals ], cram, crai, intervals ]}
                                ^^^^^^^^^

Error: subworkflows/local/bam_variant_calling_germline_all/main.nf:98:29: cram is already declared

            cram.map{ meta, cram, crai -> [ meta, [], cram ] },
                            ^^^^

Error: subworkflows/local/bam_variant_calling_germline_all/main.nf:127:29: cram is already declared

            cram.map{ meta, cram, crai -> [ meta, cram, crai, [], [] ] },
                            ^^^^

Error: subworkflows/local/bam_variant_calling_germline_all/main.nf:181:38: fasta is already declared

                    fasta.map{ meta, fasta -> [ fasta ] },
                                     ^^^^^

Error: subworkflows/local/bam_variant_calling_germline_all/main.nf:182:42: fasta_fai is already declared

                    fasta_fai.map{ meta, fasta_fai -> [ fasta_fai ] },
                                         ^^^^^^^^^

Error: subworkflows/local/bam_variant_calling_germline_all/main.nf:183:37: dict is already declared

                    dict.map{ meta, dict -> [ dict ] },
                                    ^^^^

Error: subworkflows/local/bam_variant_calling_germline_all/main.nf:334:37: dict is already declared

                    dict.map{ meta, dict -> [ dict ] },
                                    ^^^^

Error: subworkflows/local/bam_variant_calling_germline_all/main.nf:354:30: fasta is already declared

            fasta.map{ meta, fasta -> [ fasta ] },
                             ^^^^^

Error: subworkflows/local/bam_variant_calling_germline_all/main.nf:355:34: fasta_fai is already declared

            fasta_fai.map{ meta, fasta_fai -> [ fasta_fai ] },
                                 ^^^^^^^^^

Error: subworkflows/local/bam_variant_calling_germline_manta/main.nf:22:9: Variables in a closure should be declared with def
```
        bed_gz = it.size() > 3 ? it[3] : []
        ^^^^^^
```
Error: subworkflows/local/bam_variant_calling_germline_manta/main.nf:23:9: Variables in a closure should be declared with def
```
        bed_tbi = it.size() > 3 ? it[4] : []
        ^^^^^^^
```

Error: subworkflows/local/bam_variant_calling_haplotypecaller/main.nf:31:21: cram is already declared

        .map{ meta, cram, crai, intervals, num_intervals -> [ meta + [ interval_name:intervals.baseName, num_intervals:num_intervals, variantcaller:'haplotypecaller' ], cram, crai, intervals, [] ] }
                    ^^^^

Error: subworkflows/local/bam_variant_calling_haplotypecaller/main.nf:31:33: intervals is already declared

        .map{ meta, cram, crai, intervals, num_intervals -> [ meta + [ interval_name:intervals.baseName, num_intervals:num_intervals, variantcaller:'haplotypecaller' ], cram, crai, intervals, [] ] }
                                ^^^^^^^^^

Error: subworkflows/local/bam_variant_calling_haplotypecaller/main.nf:45:32: cram is already declared

        .map{ meta, gvcf, tbi, cram, crai, intervals, dragstr_model -> [ meta, gvcf, tbi, intervals ] }
                               ^^^^

Error: subworkflows/local/bam_variant_calling_haplotypecaller/main.nf:45:44: intervals is already declared

        .map{ meta, gvcf, tbi, cram, crai, intervals, dragstr_model -> [ meta, gvcf, tbi, intervals ] }
                                           ^^^^^^^^^

Error: subworkflows/local/bam_variant_calling_haplotypecaller/main.nf:49:19: vcf is already declared

            meta, vcf -> [ meta - meta.subMap('interval_name'), vcf]
                  ^^^

Error: subworkflows/local/bam_variant_calling_haplotypecaller/main.nf:76:68: vcf is already declared

    MERGE_HAPLOTYPECALLER(haplotypecaller_vcf.intervals.map{ meta, vcf -> [ groupKey(meta, meta.num_intervals), vcf ] }.groupTuple(), dict)
                                                                   ^^^

Error: subworkflows/local/bam_variant_calling_haplotypecaller/main.nf:98:42: vcf is already declared

    vcf = haplotypecaller_vcf.map{ meta, vcf -> [ meta - meta.subMap('num_intervals'), vcf ] }
                                         ^^^

Error: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:36:21: cram is already declared
```
        .map{ meta, cram, crai, intervals, num_intervals -> [
                    ^^^^
```

Error: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:36:33: intervals is already declared

        .map{ meta, cram, crai, intervals, num_intervals -> [
                                ^^^^^^^^^

Error: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:66:25: gvcf is already declared

            .map{ meta, gvcf, tbi, cram, crai, intervals -> [ meta, gvcf, tbi, intervals ] }
                        ^^^^

Error: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:66:36: cram is already declared

            .map{ meta, gvcf, tbi, cram, crai, intervals -> [ meta, gvcf, tbi, intervals ] }
                                   ^^^^

Error: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:66:48: intervals is already declared

            .map{ meta, gvcf, tbi, cram, crai, intervals -> [ meta, gvcf, tbi, intervals ] }
                                               ^^^^^^^^^

Error: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:71:19: vcf is already declared

            meta, vcf -> [ meta - meta.subMap('interval_name'), vcf]
                  ^^^

Error: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:87:19: gvcf is already declared

            meta, gvcf -> [ meta - meta.subMap('interval_name'), gvcf]
                  ^^^^

Error: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:103:15: vcf is already declared
```
        meta, vcf -> [ groupKey(meta, meta.num_intervals), vcf ]}
              ^^^
```
Error: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:106:15: vcf is already declared
```
        meta, vcf -> [
              ^^^
```

Error: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:123:35: vcf is already declared

    vcf = dnascope_vcf.map{ meta, vcf -> [ meta - meta.subMap('num_intervals'), vcf ] }
                                  ^^^

Error: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:129:15: vcf is already declared
```
        meta, vcf -> [groupKey(meta, meta.num_intervals), vcf]}
              ^^^
```
Error: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:132:15: vcf is already declared
```
        meta, vcf -> [ meta - meta.subMap('intervals_name'), vcf ]
              ^^^
```
Error: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:34:21: cram is already declared
```
        .map{ meta, cram, crai, intervals, num_intervals -> [
                    ^^^^
```

Error: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:34:33: intervals is already declared

        .map{ meta, cram, crai, intervals, num_intervals -> [
                                ^^^^^^^^^

Error: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:50:48: cram is already declared

        cram_intervals_for_sentieon.map{ meta, cram, crai, intervals -> [ meta, cram, crai, intervals, [] ]},
                                               ^^^^

Error: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:50:60: intervals is already declared

        cram_intervals_for_sentieon.map{ meta, cram, crai, intervals -> [ meta, cram, crai, intervals, [] ]},
                                                           ^^^^^^^^^

Error: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:62:25: gvcf is already declared

            .map{ meta, gvcf, tbi, cram, crai, intervals -> [ meta, gvcf, tbi, intervals ] }
                        ^^^^

Error: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:62:36: cram is already declared

            .map{ meta, gvcf, tbi, cram, crai, intervals -> [ meta, gvcf, tbi, intervals ] }
                                   ^^^^

Error: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:62:48: intervals is already declared

            .map{ meta, gvcf, tbi, cram, crai, intervals -> [ meta, gvcf, tbi, intervals ] }
                                               ^^^^^^^^^

Error: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:67:19: vcf is already declared

            meta, vcf -> [ meta - meta.subMap('interval_name'), vcf]
                  ^^^

Error: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:83:19: gvcf is already declared

            meta, gvcf -> [ meta - meta.subMap('interval_name'), gvcf]
                  ^^^^

Error: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:99:15: vcf is already declared
```
        meta, vcf -> [ groupKey(meta, meta.num_intervals), vcf ]}
              ^^^
```
Error: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:102:15: vcf is already declared
```
        meta, vcf -> [
              ^^^
```

Error: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:119:37: vcf is already declared

    vcf = haplotyper_vcf.map{ meta, vcf -> [ meta - meta.subMap('num_intervals'), vcf ] }
                                    ^^^

Error: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:125:15: vcf is already declared
```
        meta, vcf -> [groupKey(meta, meta.num_intervals), vcf]}
              ^^^
```
Error: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:128:15: vcf is already declared
```
        meta, vcf -> [ meta - meta.subMap('intervals_name'), vcf ]
              ^^^
```

Error: subworkflows/local/bam_variant_calling_single_strelka/main.nf:25:21: cram is already declared

        .map{ meta, cram, crai, intervals, intervals_index, num_intervals -> [ meta + [ num_intervals:num_intervals ], cram, crai, intervals, intervals_index ] }
                    ^^^^

Error: subworkflows/local/bam_variant_calling_single_strelka/main.nf:25:33: intervals is already declared

        .map{ meta, cram, crai, intervals, intervals_index, num_intervals -> [ meta + [ num_intervals:num_intervals ], cram, crai, intervals, intervals_index ] }
                                ^^^^^^^^^

Error: subworkflows/local/bam_variant_calling_somatic_manta/main.nf:21:9: Variables in a closure should be declared with def
```
        bed_gz = it.size() > 5 ? it[5] : []
        ^^^^^^
```
Error: subworkflows/local/bam_variant_calling_somatic_manta/main.nf:22:9: Variables in a closure should be declared with def
```
        bed_tbi = it.size() > 5 ? it[6] : []
        ^^^^^^^
```

Error: subworkflows/local/bam_variant_calling_somatic_strelka/main.nf:25:93: intervals is already declared

        .map{ meta, normal_cram, normal_crai, tumor_cram, tumor_crai, manta_vcf, manta_tbi, intervals, intervals_index, num_intervals -> [ meta + [ num_intervals:num_intervals ], normal_cram, normal_crai, tumor_cram, tumor_crai, manta_vcf, manta_tbi, intervals, intervals_index ] }
                                                                                            ^^^^^^^^^

Error: subworkflows/local/bam_variant_calling_tumor_only_lofreq/main.nf:18:45: intervals is already declared

        .map {meta, tumor_cram, tumor_crai, intervals, num_intervals -> [meta + [ num_intervals:num_intervals ], tumor_cram, tumor_crai, intervals]}
                                            ^^^^^^^^^

Error: subworkflows/local/bam_variant_calling_tumor_only_manta/main.nf:22:9: Variables in a closure should be declared with def
```
        bed_gz = it.size() > 3 ? it[3] : []
        ^^^^^^
```
Error: subworkflows/local/bam_variant_calling_tumor_only_manta/main.nf:23:9: Variables in a closure should be declared with def
```
        bed_tbi = it.size() > 3 ? it[4] : []
        ^^^^^^^
```
Error: subworkflows/local/channel_variant_calling_create_csv/main.nf:13:13: Variables in a closure should be declared with def
```
            patient       = meta.patient
            ^^^^^^^
```
Error: subworkflows/local/channel_variant_calling_create_csv/main.nf:14:13: Variables in a closure should be declared with def
```
            sample        = meta.id
            ^^^^^^
```
Error: subworkflows/local/channel_variant_calling_create_csv/main.nf:15:13: Variables in a closure should be declared with def
```
            variantcaller = meta.variantcaller
            ^^^^^^^^^^^^^
```

Error: subworkflows/local/prepare_intervals/main.nf:77:34: Unexpected input: '='

                    final fields = line.split('\t')
                                 ^

Error: subworkflows/local/vcf_variant_filtering_gatk/main.nf:20:61: vcf is already declared

    cnn_in = vcf.combine(intervals_bed_combined).map{ meta, vcf, tbi, intervals -> [ meta, vcf, tbi, [], intervals ] }
                                                            ^^^

Error: subworkflows/local/vcf_variant_filtering_gatk/main.nf:28:21: vcf is already declared

        .map{ meta, vcf -> [ meta - meta.subMap('num_intervals'), vcf ] }
                    ^^^

Error: tests/nextflow.config:22:1: If statements cannot be mixed with config statements
```
if (System.getenv('SENTIEON_LICSRVR_IP')) {
^
```
Error: tests/nextflow.config:26:1: If statements cannot be mixed with config statements
```
if (System.getenv('SENTIEON_AUTH_MECH')) {
^
```
Error: tests/nextflow.config:29:1: If statements cannot be mixed with config statements
```
if (secrets.SENTIEON_AUTH_DATA) {
^
```

⚠️ Warnings

Warning: conf/modules/aligner_parabricks.config:31:44: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            saveAs: { params.save_mapped ? it : null }
                                           ^^
```
Warning: conf/modules/aligner_parabricks.config:41:44: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            saveAs: { params.save_mapped ? it : null }
                                           ^^
```
Warning: conf/modules/aligner_parabricks.config:50:44: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            saveAs: { params.save_mapped ? it : null }
                                           ^^
```
Warning: conf/modules/aligner_parabricks.config:60:51: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            saveAs: { params.save_output_as_bam ? it : null }
                                                  ^^
```

Warning: conf/modules/contamination.config:17:55: Implicit closure parameter is deprecated, declare an explicit parameter instead

                saveAs: { params.save_bbsplit_reads ? it : null }
                                                      ^^

Warning: conf/modules/deepvariant.config:29:81: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { meta.num_intervals > 1 ? null : "deepvariant/${meta.id}/${it}" }
                                                                                ^^

Warning: conf/modules/markduplicates.config:32:52: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { !params.save_output_as_bam ? it : null }
                                                   ^^

Warning: conf/modules/markduplicates.config:59:52: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { !params.save_output_as_bam ? it : null }
                                                   ^^

Warning: conf/modules/markduplicates.config:88:56: Implicit closure parameter is deprecated, declare an explicit parameter instead

                saveAs: { !params.save_output_as_bam ? it : null }
                                                       ^^

Warning: conf/modules/markduplicates.config:94:145: Implicit closure parameter is deprecated, declare an explicit parameter instead

                saveAs: { !(params.skip_tools && params.skip_tools.split(',').contains('markduplicates_report')) ? "markduplicates/${meta.id}/${it}" : null}
                                                                                                                                                ^^

Warning: conf/modules/markduplicates.config:107:52: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { !params.save_output_as_bam ? it : null }
                                                   ^^

Warning: conf/modules/markduplicates.config:116:52: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { !params.save_output_as_bam ? it : null }
                                                   ^^

Warning: conf/modules/prepare_genome.config:21:74: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { params.save_reference || params.build_only_index ? it : null }
                                                                         ^^

Warning: conf/modules/prepare_genome.config:31:74: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { params.save_reference || params.build_only_index ? it : null }
                                                                         ^^

Warning: conf/modules/prepare_genome.config:40:74: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { params.save_reference || params.build_only_index ? it : null }
                                                                         ^^

Warning: conf/modules/prepare_genome.config:50:84: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { params.save_reference || params.build_only_index ? "cnvkit/${it}" : null }
                                                                                   ^^

Warning: conf/modules/prepare_genome.config:61:84: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { params.save_reference || params.build_only_index ? "cnvkit/${it}" : null }
                                                                                   ^^

Warning: conf/modules/prepare_genome.config:70:74: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { params.save_reference || params.build_only_index ? it : null }
                                                                         ^^

Warning: conf/modules/prepare_genome.config:79:74: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { params.save_reference || params.build_only_index ? it : null }
                                                                         ^^

Warning: conf/modules/prepare_genome.config:88:74: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { params.save_reference || params.build_only_index ? it : null }
                                                                         ^^

Warning: conf/modules/prepare_genome.config:97:74: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { params.save_reference || params.build_only_index ? it : null }
                                                                         ^^

Warning: conf/modules/prepare_genome.config:106:74: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { params.save_reference || params.build_only_index ? it : null }
                                                                         ^^

Warning: conf/modules/prepare_genome.config:115:74: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { params.save_reference || params.build_only_index ? it : null }
                                                                         ^^

Warning: conf/modules/prepare_genome.config:124:74: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { params.save_reference || params.build_only_index ? it : null }
                                                                         ^^

Warning: conf/modules/prepare_genome.config:133:74: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { params.save_reference || params.build_only_index ? it : null }
                                                                         ^^

Warning: conf/modules/prepare_genome.config:142:74: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { params.save_reference || params.build_only_index ? it : null }
                                                                         ^^

Warning: conf/modules/prepare_genome.config:151:74: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { params.save_reference || params.build_only_index ? it : null }
                                                                         ^^

Warning: conf/modules/prepare_genome.config:160:74: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { params.save_reference || params.build_only_index ? it : null }
                                                                         ^^

Warning: conf/modules/prepare_genome.config:175:78: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { (params.save_reference || params.build_only_index) && !it.equals('versions.yml') ? it : null }
                                                                             ^^

Warning: conf/modules/prepare_genome.config:175:106: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { (params.save_reference || params.build_only_index) && !it.equals('versions.yml') ? it : null }
                                                                                                         ^^

Warning: conf/modules/prepare_genome.config:186:74: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { params.save_reference || params.build_only_index ? it : null }
                                                                         ^^

Warning: conf/modules/prepare_intervals.config:28:87: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { params.save_reference || params.build_only_index ? "intervals/${it}" : null }
                                                                                      ^^

Warning: conf/modules/prepare_intervals.config:37:87: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { params.save_reference || params.build_only_index ? "intervals/${it}" : null }
                                                                                      ^^

Warning: conf/modules/prepare_intervals.config:47:87: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { params.save_reference || params.build_only_index ? "intervals/${it}" : null }
                                                                                      ^^

Warning: conf/modules/prepare_recalibration.config:27:81: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { meta.num_intervals > 1 ? null : "recal_table/${meta.id}/${it}" }
                                                                                ^^

Warning: conf/modules/sentieon_dnascope.config:25:87: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { meta.num_intervals > 1 ? null : "sentieon_dnascope/${meta.id}/${it}" }
                                                                                      ^^

Warning: conf/modules/sentieon_tnscope.config:28:86: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { meta.num_intervals > 1 ? null : "sentieon_tnscope/${meta.id}/${it}" }
                                                                                     ^^

Warning: conf/modules/strelka.config:26:77: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { meta.num_intervals > 1 ? null : "strelka/${meta.id}/${it}" }
                                                                            ^^

Warning: main.nf:93:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```

Warning: main.nf:135:52: The use of Channel to access channel factories is deprecated -- use channel instead

    intervals_bed_combined = params.no_intervals ? Channel.value([]) : PREPARE_INTERVALS.out.intervals_bed_combined
                                                   ^^^^^^^

Warning: main.nf:136:59: The use of Channel to access channel factories is deprecated -- use channel instead

    intervals_bed_gz_tbi_combined = params.no_intervals ? Channel.value([]) : PREPARE_INTERVALS.out.intervals_bed_gz_tbi_combined
                                                          ^^^^^^^

Warning: main.nf:142:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        : Channel.value([[id: 'null'], []])
          ^^^^^^^
```

Warning: main.nf:158:32: The use of Channel to access channel factories is deprecated -- use channel instead

            cnvkit_reference = Channel.fromPath(params.cnvkit_reference).collect()
                               ^^^^^^^

Warning: main.nf:167:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
        cnvkit_reference = Channel.value([])
                           ^^^^^^^
```

Warning: main.nf:182:27: The use of Channel to access channel factories is deprecated -- use channel instead

        ensemblvep_info = Channel.of([[id: "${params.vep_cache_version}_${params.vep_genome}"], params.vep_genome, params.vep_species, params.vep_cache_version])
                          ^^^^^^^

Warning: main.nf:183:23: The use of Channel to access channel factories is deprecated -- use channel instead

        snpeff_info = Channel.of([[id: "${params.snpeff_db}"], params.snpeff_db])
                      ^^^^^^^

Warning: main.nf:268:21: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_snpsift_db = Channel.value([[], [], [], [], []])
                    ^^^^^^^
```

Warning: main.nf:290:35: The use of Channel to access channel factories is deprecated -- use channel instead

        params.bcftools_columns ? Channel.fromPath(params.bcftools_columns).collect() : Channel.value([]),
                                  ^^^^^^^

Warning: main.nf:290:89: The use of Channel to access channel factories is deprecated -- use channel instead

        params.bcftools_columns ? Channel.fromPath(params.bcftools_columns).collect() : Channel.value([]),
                                                                                        ^^^^^^^

Warning: main.nf:291:40: The use of Channel to access channel factories is deprecated -- use channel instead

        params.bcftools_header_lines ? Channel.fromPath(params.bcftools_header_lines).collect() : Channel.empty(),
                                       ^^^^^^^

Warning: main.nf:291:99: The use of Channel to access channel factories is deprecated -- use channel instead

        params.bcftools_header_lines ? Channel.fromPath(params.bcftools_header_lines).collect() : Channel.empty(),
                                                                                                  ^^^^^^^

Warning: main.nf:292:31: The use of Channel to access channel factories is deprecated -- use channel instead

        params.cf_chrom_len ? Channel.fromPath(params.cf_chrom_len).collect() : [],
                              ^^^^^^^

Warning: main.nf:297:29: The use of Channel to access channel factories is deprecated -- use channel instead

        params.dbsnp_vqsr ? Channel.value(params.dbsnp_vqsr) : Channel.empty(),
                            ^^^^^^^

Warning: main.nf:297:64: The use of Channel to access channel factories is deprecated -- use channel instead

        params.dbsnp_vqsr ? Channel.value(params.dbsnp_vqsr) : Channel.empty(),
                                                               ^^^^^^^

Warning: main.nf:310:36: The use of Channel to access channel factories is deprecated -- use channel instead

        params.known_indels_vqsr ? Channel.value(params.known_indels_vqsr) : Channel.empty(),
                                   ^^^^^^^

Warning: main.nf:310:78: The use of Channel to access channel factories is deprecated -- use channel instead

        params.known_indels_vqsr ? Channel.value(params.known_indels_vqsr) : Channel.empty(),
                                                                             ^^^^^^^

Warning: main.nf:315:34: The use of Channel to access channel factories is deprecated -- use channel instead

        params.known_snps_vqsr ? Channel.value(params.known_snps_vqsr) : Channel.empty(),
                                 ^^^^^^^

Warning: main.nf:315:74: The use of Channel to access channel factories is deprecated -- use channel instead

        params.known_snps_vqsr ? Channel.value(params.known_snps_vqsr) : Channel.empty(),
                                                                         ^^^^^^^

Warning: main.nf:316:30: The use of Channel to access channel factories is deprecated -- use channel instead

        params.mappability ? Channel.fromPath(params.mappability).collect() : Channel.value([]),
                             ^^^^^^^

Warning: main.nf:316:79: The use of Channel to access channel factories is deprecated -- use channel instead

        params.mappability ? Channel.fromPath(params.mappability).collect() : Channel.value([]),
                                                                              ^^^^^^^

Warning: main.nf:319:35: The use of Channel to access channel factories is deprecated -- use channel instead

        params.ngscheckmate_bed ? Channel.value(params.ngscheckmate_bed) : Channel.empty(),
                                  ^^^^^^^

Warning: main.nf:319:76: The use of Channel to access channel factories is deprecated -- use channel instead

        params.ngscheckmate_bed ? Channel.value(params.ngscheckmate_bed) : Channel.empty(),
                                                                           ^^^^^^^

Warning: main.nf:322:42: The use of Channel to access channel factories is deprecated -- use channel instead

        params.sentieon_dnascope_model ? Channel.fromPath(params.sentieon_dnascope_model).collect() : Channel.value([]),
                                         ^^^^^^^

Warning: main.nf:322:103: The use of Channel to access channel factories is deprecated -- use channel instead

        params.sentieon_dnascope_model ? Channel.fromPath(params.sentieon_dnascope_model).collect() : Channel.value([]),
                                                                                                      ^^^^^^^

Warning: main.nf:323:50: The use of Channel to access channel factories is deprecated -- use channel instead

        params.varlociraptor_scenario_germline ? Channel.fromPath(params.varlociraptor_scenario_germline).map { it -> [[id: it.baseName - '.yte'], it] }.collect() : Channel.fromPath("${projectDir}/assets/varlociraptor_germline.yte.yaml").collect(),
                                                 ^^^^^^^

Warning: main.nf:323:166: The use of Channel to access channel factories is deprecated -- use channel instead

        params.varlociraptor_scenario_germline ? Channel.fromPath(params.varlociraptor_scenario_germline).map { it -> [[id: it.baseName - '.yte'], it] }.collect() : Channel.fromPath("${projectDir}/assets/varlociraptor_germline.yte.yaml").collect(),
                                                                                                                                                                     ^^^^^^^

Warning: main.nf:324:49: The use of Channel to access channel factories is deprecated -- use channel instead

        params.varlociraptor_scenario_somatic ? Channel.fromPath(params.varlociraptor_scenario_somatic).map { it -> [[id: it.baseName - '.yte'], it] }.collect() : Channel.fromPath("${projectDir}/assets/varlociraptor_somatic.yte.yaml").collect(),
                                                ^^^^^^^

Warning: main.nf:324:164: The use of Channel to access channel factories is deprecated -- use channel instead

        params.varlociraptor_scenario_somatic ? Channel.fromPath(params.varlociraptor_scenario_somatic).map { it -> [[id: it.baseName - '.yte'], it] }.collect() : Channel.fromPath("${projectDir}/assets/varlociraptor_somatic.yte.yaml").collect(),
                                                                                                                                                                   ^^^^^^^

Warning: main.nf:325:52: The use of Channel to access channel factories is deprecated -- use channel instead

        params.varlociraptor_scenario_tumor_only ? Channel.fromPath(params.varlociraptor_scenario_tumor_only).map { it -> [[id: it.baseName - '.yte'], it] }.collect() : Channel.fromPath("${projectDir}/assets/varlociraptor_tumor_only.yte.yaml").collect(),
                                                   ^^^^^^^

Warning: main.nf:325:170: The use of Channel to access channel factories is deprecated -- use channel instead

        params.varlociraptor_scenario_tumor_only ? Channel.fromPath(params.varlociraptor_scenario_tumor_only).map { it -> [[id: it.baseName - '.yte'], it] }.collect() : Channel.fromPath("${projectDir}/assets/varlociraptor_tumor_only.yte.yaml").collect(),
                                                                                                                                                                         ^^^^^^^

Warning: modules/local/consensus_from_sites/main.nf:27:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/bcftools/concat/main.nf:32:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def input = vcfs.sort{it.toString()}.join(" ")
                          ^^
```
Warning: modules/nf-core/bcftools/isec/main.nf:35:9: Variable was declared but not used
```
    def args = task.ext.args   ?: ''
        ^^^^
```

Warning: modules/nf-core/bcftools/merge/main.nf:28:58: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def input = (vcfs.collect().size() > 1) ? vcfs.sort{ it.name } : vcfs
                                                         ^^

Warning: modules/nf-core/bcftools/norm/main.nf:56:65: Implicit closure parameter is deprecated, declare an explicit parameter instead

        if (['--write-index=tbi', '-W=tbi'].any { args.contains(it) }  && extension == 'vcf.gz') {
                                                                ^^

Warning: modules/nf-core/bcftools/norm/main.nf:58:126: Implicit closure parameter is deprecated, declare an explicit parameter instead

        } else if (['--write-index=tbi', '-W=tbi', '--write-index=csi', '-W=csi', '--write-index', '-W'].any { args.contains(it) }) {
                                                                                                                             ^^

Warning: modules/nf-core/cat/cat/main.nf:23:40: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def file_list = files_in.collect { it.toString() }
                                       ^^
```
Warning: modules/nf-core/cat/cat/main.nf:58:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def file_list   = files_in.collect { it.toString() }
                                         ^^
```

Warning: modules/nf-core/cat/fastq/main.nf:22:60: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def readList = reads instanceof List ? reads.collect { it.toString() } : [reads.toString()]
                                                           ^^

Warning: modules/nf-core/cat/fastq/main.nf:58:60: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def readList = reads instanceof List ? reads.collect { it.toString() } : [reads.toString()]
                                                           ^^

Warning: modules/nf-core/cnvkit/batch/main.nf:40:9: Variable was declared but not used

    def tumor_bam = tumor_exists && tumor.Extension == "bam" ? true : false
        ^^^^^^^^^

Warning: modules/nf-core/cnvkit/batch/main.nf:41:9: Variable was declared but not used

    def normal_bam = normal_exists && normal.Extension == "bam" ? true : false
        ^^^^^^^^^^

Warning: modules/nf-core/fgbio/fastqtobam/main.nf:58:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/gatk4/baserecalibrator/main.nf:29:60: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def sites_command = known_sites.collect{"--known-sites $it"}.join(' ')
                                                           ^^

Warning: modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf:26:47: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def input_list = input.collect(){"--INPUT $it"}.join(" ")
                                              ^^
```

Warning: modules/nf-core/gatk4/filtermutectcalls/main.nf:29:113: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def orientationbias_command = orientationbias ? orientationbias.collect{"--orientation-bias-artifact-priors $it"}.join(' ') : ''
                                                                                                                ^^

Warning: modules/nf-core/gatk4/filtermutectcalls/main.nf:30:96: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def segmentation_command    = segmentation    ? segmentation.collect{"--tumor-segmentation $it"}.join(' ')                  : ''
                                                                                               ^^

Warning: modules/nf-core/gatk4/filtermutectcalls/main.nf:32:90: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def table_command           = table           ? table.collect{"--contamination-table $it"}.join(' ')                        : ''
                                                                                         ^^

Warning: modules/nf-core/gatk4/filtervarianttranches/main.nf:30:55: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def resource_list = resources.collect{"--resource $it"}.join(' ')
                                                      ^^
```
Warning: modules/nf-core/gatk4/gatherbqsrreports/main.nf:23:45: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def input_list = table.collect{"--input $it"}.join(' ')
                                            ^^
```
Warning: modules/nf-core/gatk4/gatherpileupsummaries/main.nf:25:43: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def input_list = pileup.collect{ "--I $it" }.join(' ')
                                          ^^
```

Warning: modules/nf-core/gatk4/genomicsdbimport/main.nf:30:90: Implicit closure parameter is deprecated, declare an explicit parameter instead

    input_command = input_map ? "--sample-name-map ${vcf[0]}" : vcf.collect(){"--variant $it"}.join(' ')
                                                                                         ^^

Warning: modules/nf-core/gatk4/learnreadorientationmodel/main.nf:23:44: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def input_list = f1r2.collect{"--input $it"}.join(' ')
                                           ^^
```
Warning: modules/nf-core/gatk4/markduplicates/main.nf:33:47: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def input_list = bam.collect { "--INPUT ${it}" }.join(' ')
                                              ^^
```
Warning: modules/nf-core/gatk4/mergemutectstats/main.nf:23:48: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def input_list = stats.collect{ "--stats ${it}"}.join(' ')
                                               ^^
```
Warning: modules/nf-core/gatk4/mergevcfs/main.nf:25:44: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def input_list = vcf.collect{ "--INPUT $it"}.join(' ')
                                           ^^
```
Warning: modules/nf-core/gatk4/mutect2/main.nf:33:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def inputs = input.collect{ "--input $it"}.join(" ")
                                         ^^
```

Warning: modules/nf-core/gatk4spark/baserecalibrator/main.nf:29:64: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def sites_command = known_sites.collect { "--known-sites ${it}" }.join(' ')
                                                               ^^

Warning: modules/nf-core/gatk4spark/markduplicates/main.nf:28:47: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def input_list = bam.collect { "--input ${it}" }.join(' ')
                                              ^^
```

Warning: modules/nf-core/gawk/main.nf:26:54: Implicit closure parameter is deprecated, declare an explicit parameter instead

    suffix    = task.ext.suffix ?: "${input.collect{ it.getExtension()}.get(0)}" // use the first extension of the input files
                                                     ^^

Warning: modules/nf-core/gawk/main.nf:29:37: Implicit closure parameter is deprecated, declare an explicit parameter instead

    lst_gz     = input.findResults{ it.getExtension().endsWith("gz") ? it.toString() : null }
                                    ^^

Warning: modules/nf-core/gawk/main.nf:29:72: Implicit closure parameter is deprecated, declare an explicit parameter instead

    lst_gz     = input.findResults{ it.getExtension().endsWith("gz") ? it.toString() : null }
                                                                       ^^

Warning: modules/nf-core/gawk/main.nf:31:34: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    input_cmd  = input.collect { it.toString() - ~/\.gz$/ }.join(" ")
                                 ^^
```

Warning: modules/nf-core/gawk/main.nf:34:49: Implicit closure parameter is deprecated, declare an explicit parameter instead

    cleanup    = lst_gz ? "rm ${lst_gz.collect{ it - ~/\.gz$/ }.join(" ")}" : ""
                                                ^^

Warning: modules/nf-core/gawk/main.nf:37:16: Implicit closure parameter is deprecated, declare an explicit parameter instead

        assert it.name != "${prefix}.${suffix}" : "Input and output names are the same, set prefix in module configuration to disambiguate!"
               ^^

Warning: modules/nf-core/goleft/indexcov/main.nf:31:36: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def input_files = bams.findAll{it.name.endsWith(".bam")} + indexes.findAll{it.name.endsWith(".crai")}
                                   ^^

Warning: modules/nf-core/goleft/indexcov/main.nf:31:80: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def input_files = bams.findAll{it.name.endsWith(".bam")} + indexes.findAll{it.name.endsWith(".crai")}
                                                                               ^^

Warning: modules/nf-core/goleft/indexcov/main.nf:32:42: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def extranormalize = input_files.any{it.name.endsWith(".crai")} ? " --extranormalize " : ""
                                         ^^

Warning: modules/nf-core/goleft/indexcov/main.nf:52:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/gunzip/main.nf:43:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/lofreq/callparallel/main.nf:29:9: Variable was declared but not used

    def alignment_bam = bam.Extension == "bam" ? true : false
        ^^^^^^^^^^^^^

Warning: modules/nf-core/manta/germline/main.nf:33:46: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def input_files = input.collect{"--bam ${it}"}.join(' ')
                                             ^^
```
Warning: modules/nf-core/ngscheckmate/ncm/main.nf:28:29: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def unzip = files.any { it.toString().endsWith(".vcf.gz") }
                            ^^
```
Warning: modules/nf-core/ngscheckmate/ncm/main.nf:51:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/sentieon/dedup/main.nf:36:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def input_list = bam.collect { "-i ${it}" }.join(' ')
                                         ^^
```

Warning: modules/nf-core/sentieon/haplotyper/main.nf:37:68: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def input_list = input instanceof List ? input.collect { "-i ${it}" }.join(' ') : "-i ${input}"
                                                                   ^^

Warning: modules/nf-core/sentieon/tnscope/main.nf:38:40: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def inputs = input.collect { "-i ${it}" }.join(" ")
                                       ^^
```

Warning: modules/nf-core/svdb/merge/main.nf:38:53: Implicit closure parameter is deprecated, declare an explicit parameter instead

            def pairs = vcfs.indices.collect { [vcfs[it], input_priority[it]] }
                                                    ^^

Warning: modules/nf-core/svdb/merge/main.nf:38:73: Implicit closure parameter is deprecated, declare an explicit parameter instead

            def pairs = vcfs.indices.collect { [vcfs[it], input_priority[it]] }
                                                                        ^^

Warning: modules/nf-core/svdb/merge/main.nf:40:36: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            vcfs = pairs.collect { it[0] }
                                   ^^
```
Warning: modules/nf-core/svdb/merge/main.nf:41:40: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            priority = pairs.collect { it[1] }
                                       ^^
```

Warning: modules/nf-core/svdb/merge/main.nf:55:74: Implicit closure parameter is deprecated, declare an explicit parameter instead

        input = (vcfs.collect().size() > 1 && sort_inputs) ? vcfs.sort { it.name } : vcfs
                                                                         ^^

Warning: modules/nf-core/unzip/main.nf:38:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/vcftools/main.nf:97:26: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    args_list.removeIf { it.contains('--bed') }
                         ^^
```
Warning: modules/nf-core/vcftools/main.nf:98:26: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    args_list.removeIf { it.contains('--exclude-bed') }
                         ^^
```
Warning: modules/nf-core/vcftools/main.nf:99:26: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    args_list.removeIf { it.contains('--hapcount') }
                         ^^
```
Warning: modules/nf-core/vcftools/main.nf:100:26: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    args_list.removeIf { it.contains('--positions') }
                         ^^
```
Warning: modules/nf-core/vcftools/main.nf:101:26: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    args_list.removeIf { it.contains('--exclude-positions') }
                         ^^
```
Warning: modules/nf-core/vcftools/main.nf:106:26: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    args_list.removeIf { it.contains('--diff') }
                         ^^
```
Warning: modules/nf-core/vcftools/main.nf:107:26: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    args_list.removeIf { it.contains('--gzdiff') }
                         ^^
```
Warning: modules/nf-core/vcftools/main.nf:108:26: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    args_list.removeIf { it.contains('--diff-bcf') }
                         ^^
```

Warning: subworkflows/local/annotation_cache_initialisation/main.nf:37:24: The use of Channel to access channel factories is deprecated -- use channel instead

        snpeff_cache = Channel.fromPath(file("${snpeff_cache}/${snpeff_annotation_cache_key}"), checkIfExists: true)
                       ^^^^^^^

Warning: subworkflows/local/annotation_cache_initialisation/main.nf:58:28: The use of Channel to access channel factories is deprecated -- use channel instead

        ensemblvep_cache = Channel.fromPath(file("${vep_cache}/${vep_annotation_cache_key}"), checkIfExists: true).collect()
                           ^^^^^^^

Warning: subworkflows/local/bam_baserecalibrator/main.nf:21:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_baserecalibrator/main.nf:41:19: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        single:   it[0].num_intervals <= 1
                  ^^
```
Warning: subworkflows/local/bam_baserecalibrator/main.nf:42:19: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        multiple: it[0].num_intervals > 1
                  ^^
```
Warning: subworkflows/local/bam_baserecalibrator_spark/main.nf:21:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```

Warning: subworkflows/local/bam_baserecalibrator_spark/main.nf:29:60: Parameter was not used -- prefix with _ to suppress warning

    GATK4SPARK_BASERECALIBRATOR(cram_intervals, fasta.map{ meta, it -> [ it ] }, fasta_fai.map{ meta, it -> [ it ] }, dict.map{ meta, it -> [ it ] }, known_sites, known_sites_tbi)
                                                           ^^^^

Warning: subworkflows/local/bam_baserecalibrator_spark/main.nf:29:97: Parameter was not used -- prefix with _ to suppress warning

    GATK4SPARK_BASERECALIBRATOR(cram_intervals, fasta.map{ meta, it -> [ it ] }, fasta_fai.map{ meta, it -> [ it ] }, dict.map{ meta, it -> [ it ] }, known_sites, known_sites_tbi)
                                                                                                ^^^^

Warning: subworkflows/local/bam_baserecalibrator_spark/main.nf:29:129: Parameter was not used -- prefix with _ to suppress warning

    GATK4SPARK_BASERECALIBRATOR(cram_intervals, fasta.map{ meta, it -> [ it ] }, fasta_fai.map{ meta, it -> [ it ] }, dict.map{ meta, it -> [ it ] }, known_sites, known_sites_tbi)
                                                                                                                                ^^^^

Warning: subworkflows/local/bam_baserecalibrator_spark/main.nf:34:19: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        single:   it[0].num_intervals <= 1
                  ^^
```
Warning: subworkflows/local/bam_baserecalibrator_spark/main.nf:35:19: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        multiple: it[0].num_intervals > 1
                  ^^
```
Warning: subworkflows/local/bam_convert_samtools/main.nf:22:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:34:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:74:20: Parameter was not used -- prefix with _ to suppress warning
```
        fasta.map{ meta, fasta -> [ fasta ] },
                   ^^^^
```
Warning: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:75:18: Parameter was not used -- prefix with _ to suppress warning
```
        fai.map{ meta, fai -> [ fai ] },
                 ^^^^
```
Warning: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:76:19: Parameter was not used -- prefix with _ to suppress warning
```
        dict.map{ meta, dict -> [ dict ] })
                  ^^^^
```
Warning: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:83:20: Parameter was not used -- prefix with _ to suppress warning
```
        fasta.map{ meta, fasta -> [ fasta ] },
                   ^^^^
```
Warning: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:84:18: Parameter was not used -- prefix with _ to suppress warning
```
        fai.map{ meta, fai -> [ fai ] },
                 ^^^^
```
Warning: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:85:19: Parameter was not used -- prefix with _ to suppress warning
```
        dict.map{ meta, dict -> [ dict ] })
                  ^^^^
```
Warning: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:100:20: Parameter was not used -- prefix with _ to suppress warning
```
        fasta.map{ meta, fasta -> [ fasta ] },
                   ^^^^
```
Warning: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:101:18: Parameter was not used -- prefix with _ to suppress warning
```
        fai.map{ meta, fai -> [ fai ] },
                 ^^^^
```
Warning: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:102:19: Parameter was not used -- prefix with _ to suppress warning
```
        dict.map{ meta, dict -> [ dict ] })
                  ^^^^
```
Warning: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:114:20: Parameter was not used -- prefix with _ to suppress warning
```
        fasta.map{ meta, fasta -> [ fasta ] },
                   ^^^^
```
Warning: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:115:18: Parameter was not used -- prefix with _ to suppress warning
```
        fai.map{ meta, fai -> [ fai ] },
                 ^^^^
```
Warning: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:116:19: Parameter was not used -- prefix with _ to suppress warning
```
        dict.map{ meta, dict -> [ dict ] })
                  ^^^^
```

Warning: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:123:58: Parameter was not used -- prefix with _ to suppress warning

    merge_vcf_for_join = MERGE_GENOTYPEGVCFS.out.vcf.map{meta, vcf -> [[id: 'joint_variant_calling'] , vcf]}
                                                         ^^^^

Warning: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:124:58: Parameter was not used -- prefix with _ to suppress warning

    merge_tbi_for_join = MERGE_GENOTYPEGVCFS.out.tbi.map{meta, tbi -> [[id: 'joint_variant_calling'] , tbi]}
                                                         ^^^^

Warning: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:127:78: Parameter was not used -- prefix with _ to suppress warning

    vqsr_vcf_for_join = GATK4_APPLYVQSR_INDEL.out.vcf.ifEmpty([[:], []]).map{meta, vcf -> [[id: 'joint_variant_calling'] , vcf]}
                                                                             ^^^^

Warning: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:128:78: Parameter was not used -- prefix with _ to suppress warning

    vqsr_tbi_for_join = GATK4_APPLYVQSR_INDEL.out.tbi.ifEmpty([[:], []]).map{meta, tbi -> [[id: 'joint_variant_calling'] , tbi]}
                                                                             ^^^^

Warning: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:135:9: Parameter was not used -- prefix with _ to suppress warning
```
        meta, joint_vcf, recal_vcf ->
        ^^^^
```
Warning: subworkflows/local/bam_joint_calling_germline_gatk/main.nf:143:9: Parameter was not used -- prefix with _ to suppress warning
```
        meta, joint_tbi, recal_tbi ->
        ^^^^
```
Warning: subworkflows/local/bam_joint_calling_germline_sentieon/main.nf:33:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```

Warning: subworkflows/local/bam_joint_calling_germline_sentieon/main.nf:54:50: Parameter was not used -- prefix with _ to suppress warning

    merged_vcf = MERGE_GENOTYPEGVCFS.out.vcf.map{meta, vcf -> [[id: 'joint_variant_calling'] , vcf]}
                                                 ^^^^

Warning: subworkflows/local/bam_joint_calling_germline_sentieon/main.nf:55:50: Parameter was not used -- prefix with _ to suppress warning

    merged_tbi = MERGE_GENOTYPEGVCFS.out.tbi.map{meta, tbi -> [[id: 'joint_variant_calling'] , tbi]}
                                                 ^^^^

Warning: subworkflows/local/bam_joint_calling_germline_sentieon/main.nf:76:23: Parameter was not used -- prefix with _ to suppress warning
```
            fasta.map{meta, it -> [ it ]},
                      ^^^^
```
Warning: subworkflows/local/bam_joint_calling_germline_sentieon/main.nf:77:21: Parameter was not used -- prefix with _ to suppress warning
```
            fai.map{meta, it -> [ it ]})
                    ^^^^
```
Warning: subworkflows/local/bam_joint_calling_germline_sentieon/main.nf:84:23: Parameter was not used -- prefix with _ to suppress warning
```
            fasta.map{meta, it -> [ it ]},
                      ^^^^
```
Warning: subworkflows/local/bam_joint_calling_germline_sentieon/main.nf:85:21: Parameter was not used -- prefix with _ to suppress warning
```
            fai.map{meta, it -> [ it ]})
                    ^^^^
```

Warning: subworkflows/local/bam_joint_calling_germline_sentieon/main.nf:115:87: Parameter was not used -- prefix with _ to suppress warning

        vqsr_vcf_for_join = SENTIEON_APPLYVARCAL_INDEL.out.vcf.ifEmpty([[:], []]).map{meta, vcf -> [[id: 'joint_variant_calling'] , vcf]}
                                                                                      ^^^^

Warning: subworkflows/local/bam_joint_calling_germline_sentieon/main.nf:116:87: Parameter was not used -- prefix with _ to suppress warning

        vqsr_tbi_for_join = SENTIEON_APPLYVARCAL_INDEL.out.tbi.ifEmpty([[:], []]).map{meta, tbi -> [[id: 'joint_variant_calling'] , tbi]}
                                                                                      ^^^^

Warning: subworkflows/local/bam_joint_calling_germline_sentieon/main.nf:123:13: Parameter was not used -- prefix with _ to suppress warning
```
            meta, joint_vcf, recal_vcf ->
            ^^^^
```
Warning: subworkflows/local/bam_joint_calling_germline_sentieon/main.nf:131:13: Parameter was not used -- prefix with _ to suppress warning
```
            meta, joint_tbi, recal_tbi ->
            ^^^^
```
Warning: subworkflows/local/bam_markduplicates/main.nf:18:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_markduplicates/main.nf:19:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    reports  = Channel.empty()
               ^^^^^^^
```

Warning: subworkflows/local/bam_markduplicates/main.nf:22:42: Parameter was not used -- prefix with _ to suppress warning

    GATK4_MARKDUPLICATES(bam, fasta.map{ meta, fasta -> [ fasta ] }, fasta_fai.map{ meta, fasta_fai -> [ fasta_fai ] })
                                         ^^^^

Warning: subworkflows/local/bam_markduplicates/main.nf:22:85: Parameter was not used -- prefix with _ to suppress warning

    GATK4_MARKDUPLICATES(bam, fasta.map{ meta, fasta -> [ fasta ] }, fasta_fai.map{ meta, fasta_fai -> [ fasta_fai ] })
                                                                                    ^^^^

Warning: subworkflows/local/bam_markduplicates_spark/main.nf:21:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_markduplicates_spark/main.nf:22:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
    reports = Channel.empty()
              ^^^^^^^
```

Warning: subworkflows/local/bam_markduplicates_spark/main.nf:25:47: Parameter was not used -- prefix with _ to suppress warning

    GATK4SPARK_MARKDUPLICATES(bam, fasta.map{ meta, fasta -> [ fasta ] }, fasta_fai.map{ meta, fasta_fai -> [ fasta_fai ] }, dict.map{ meta, dict -> [ dict ] })
                                              ^^^^

Warning: subworkflows/local/bam_markduplicates_spark/main.nf:25:90: Parameter was not used -- prefix with _ to suppress warning

    GATK4SPARK_MARKDUPLICATES(bam, fasta.map{ meta, fasta -> [ fasta ] }, fasta_fai.map{ meta, fasta_fai -> [ fasta_fai ] }, dict.map{ meta, dict -> [ dict ] })
                                                                                         ^^^^

Warning: subworkflows/local/bam_markduplicates_spark/main.nf:25:136: Parameter was not used -- prefix with _ to suppress warning

    GATK4SPARK_MARKDUPLICATES(bam, fasta.map{ meta, fasta -> [ fasta ] }, fasta_fai.map{ meta, fasta_fai -> [ fasta_fai ] }, dict.map{ meta, dict -> [ dict ] })
                                                                                                                                       ^^^^

Warning: subworkflows/local/bam_markduplicates_spark/main.nf:37:53: Parameter was not used -- prefix with _ to suppress warning

    GATK4_ESTIMATELIBRARYCOMPLEXITY(bam, fasta.map{ meta, fasta -> [ fasta ] }, fasta_fai.map{ meta, fasta_fai -> [ fasta_fai ] }, dict.map{ meta, dict -> [ dict ] })
                                                    ^^^^

Warning: subworkflows/local/bam_markduplicates_spark/main.nf:37:96: Parameter was not used -- prefix with _ to suppress warning

    GATK4_ESTIMATELIBRARYCOMPLEXITY(bam, fasta.map{ meta, fasta -> [ fasta ] }, fasta_fai.map{ meta, fasta_fai -> [ fasta_fai ] }, dict.map{ meta, dict -> [ dict ] })
                                                                                               ^^^^

Warning: subworkflows/local/bam_markduplicates_spark/main.nf:37:142: Parameter was not used -- prefix with _ to suppress warning

    GATK4_ESTIMATELIBRARYCOMPLEXITY(bam, fasta.map{ meta, fasta -> [ fasta ] }, fasta_fai.map{ meta, fasta_fai -> [ fasta_fai ] }, dict.map{ meta, dict -> [ dict ] })
                                                                                                                                             ^^^^

Warning: subworkflows/local/bam_merge_index_samtools/main.nf:15:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_sentieon_dedup/main.nf:16:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_sentieon_dedup/main.nf:17:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    reports  = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_cnvkit/main.nf:21:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_deepvariant/main.nf:21:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_deepvariant/main.nf:33:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals:    it[0].num_intervals > 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_deepvariant/main.nf:34:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_deepvariant/main.nf:40:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals:    it[0].num_intervals > 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_deepvariant/main.nf:41:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_deepvariant/main.nf:54:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals:    it[0].num_intervals > 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_deepvariant/main.nf:55:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_deepvariant/main.nf:59:12: The use of Channel to access channel factories is deprecated -- use channel instead
```
    gvcf = Channel.empty().mix(MERGE_DEEPVARIANT_GVCF.out.vcf, gvcf_out.no_intervals)
           ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_deepvariant/main.nf:64:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf = Channel.empty().mix(MERGE_DEEPVARIANT_VCF.out.vcf, vcf_out.no_intervals)
          ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_deepvariant/main.nf:68:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
    tbi = Channel.empty().mix(MERGE_DEEPVARIANT_VCF.out.tbi, tbi_out.no_intervals)
          ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_freebayes/main.nf:23:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_freebayes/main.nf:37:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals:    it[0].num_intervals > 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_freebayes/main.nf:38:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:26:5: Parameter was not used -- prefix with _ to suppress warning
```
    bam                               // channel: [mandatory] meta, bam
    ^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:55:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:58:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    gvcf_sentieon_dnascope   = Channel.empty()
                               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:59:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    gvcf_sentieon_haplotyper = Channel.empty()
                               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:61:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    out_indexcov             = Channel.empty()
                               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:62:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf_deepvariant          = Channel.empty()
                               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:63:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf_freebayes            = Channel.empty()
                               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:64:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf_haplotypecaller      = Channel.empty()
                               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:65:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf_manta                = Channel.empty()
                               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:66:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf_mpileup              = Channel.empty()
                               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:67:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf_sentieon_dnascope    = Channel.empty()
                               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:68:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf_sentieon_haplotyper  = Channel.empty()
                               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:69:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf_strelka              = Channel.empty()
                               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:70:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf_tiddit               = Channel.empty()
                               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:71:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    tbi_deepvariant          = Channel.empty()
                               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:72:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    tbi_freebayes            = Channel.empty()
                               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:73:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    tbi_haplotypecaller      = Channel.empty()
                               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:74:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    tbi_manta                = Channel.empty()
                               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:75:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    tbi_mpileup              = Channel.empty()
                               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:76:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    tbi_sentieon_dnascope    = Channel.empty()
                               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:77:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    tbi_sentieon_haplotyper  = Channel.empty()
                               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:78:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    tbi_strelka              = Channel.empty()
                               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:79:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    tbi_tiddit               = Channel.empty()
                               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:98:35: Parameter was not used -- prefix with _ to suppress warning
```
            cram.map{ meta, cram, crai -> [ meta, [], cram ] },
                                  ^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:181:32: Parameter was not used -- prefix with _ to suppress warning
```
                    fasta.map{ meta, fasta -> [ fasta ] },
                               ^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:182:36: Parameter was not used -- prefix with _ to suppress warning
```
                    fasta_fai.map{ meta, fasta_fai -> [ fasta_fai ] },
                                   ^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:183:31: Parameter was not used -- prefix with _ to suppress warning
```
                    dict.map{ meta, dict -> [ dict ] },
                              ^^^^
```

Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:243:9: Variable was declared but not used

        gvcf_tbi_sentieon_dnascope = BAM_VARIANT_CALLING_SENTIEON_DNASCOPE.out.gvcf_tbi
        ^^^^^^^^^^^^^^^^^^^^^^^^^^

Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:303:9: Variable was declared but not used

        gvcf_tbi_sentieon_haplotyper = BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER.out.gvcf_tbi
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:332:32: Parameter was not used -- prefix with _ to suppress warning
```
                    fasta.map{ meta, it -> [ it ] },
                               ^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:333:36: Parameter was not used -- prefix with _ to suppress warning
```
                    fasta_fai.map{ meta, it -> [ it ] },
                                   ^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:334:31: Parameter was not used -- prefix with _ to suppress warning
```
                    dict.map{ meta, dict -> [ dict ] },
                              ^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:354:24: Parameter was not used -- prefix with _ to suppress warning
```
            fasta.map{ meta, fasta -> [ fasta ] },
                       ^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:355:28: Parameter was not used -- prefix with _ to suppress warning
```
            fasta_fai.map{ meta, fasta_fai -> [ fasta_fai ] },
                           ^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:378:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf_all = Channel.empty().mix(
              ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_all/main.nf:390:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
    tbi_all = Channel.empty().mix(
              ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_manta/main.nf:18:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_manta/main.nf:30:5: Variable was declared but not used
```
    small_indels_vcf     = MANTA_GERMLINE.out.candidate_small_indels_vcf
    ^^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_germline_manta/main.nf:31:5: Variable was declared but not used
```
    sv_vcf               = MANTA_GERMLINE.out.candidate_sv_vcf
    ^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_haplotypecaller/main.nf:22:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_haplotypecaller/main.nf:24:21: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf           = Channel.empty()
                    ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_haplotypecaller/main.nf:25:21: The use of Channel to access channel factories is deprecated -- use channel instead
```
    realigned_bam = Channel.empty()
                    ^^^^^^^
```

Warning: subworkflows/local/bam_variant_calling_haplotypecaller/main.nf:45:32: Parameter was not used -- prefix with _ to suppress warning

        .map{ meta, gvcf, tbi, cram, crai, intervals, dragstr_model -> [ meta, gvcf, tbi, intervals ] }
                               ^^^^

Warning: subworkflows/local/bam_variant_calling_haplotypecaller/main.nf:45:38: Parameter was not used -- prefix with _ to suppress warning

        .map{ meta, gvcf, tbi, cram, crai, intervals, dragstr_model -> [ meta, gvcf, tbi, intervals ] }
                                     ^^^^

Warning: subworkflows/local/bam_variant_calling_haplotypecaller/main.nf:45:55: Parameter was not used -- prefix with _ to suppress warning

        .map{ meta, gvcf, tbi, cram, crai, intervals, dragstr_model -> [ meta, gvcf, tbi, intervals ] }
                                                      ^^^^^^^^^^^^^

Warning: subworkflows/local/bam_variant_calling_haplotypecaller/main.nf:53:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            intervals:    it[0].num_intervals > 1
                          ^^
```
Warning: subworkflows/local/bam_variant_calling_haplotypecaller/main.nf:54:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            no_intervals: it[0].num_intervals <= 1
                          ^^
```
Warning: subworkflows/local/bam_variant_calling_haplotypecaller/main.nf:62:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            intervals:    it[0].num_intervals > 1
                          ^^
```
Warning: subworkflows/local/bam_variant_calling_haplotypecaller/main.nf:63:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            no_intervals: it[0].num_intervals <= 1
                          ^^
```
Warning: subworkflows/local/bam_variant_calling_haplotypecaller/main.nf:71:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            intervals:    it[0].num_intervals > 1
                          ^^
```
Warning: subworkflows/local/bam_variant_calling_haplotypecaller/main.nf:72:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            no_intervals: it[0].num_intervals <= 1
                          ^^
```
Warning: subworkflows/local/bam_variant_calling_haplotypecaller/main.nf:78:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
    haplotypecaller_vcf = Channel.empty().mix(
                          ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_haplotypecaller/main.nf:82:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
    haplotypecaller_tbi = Channel.empty().mix(
                          ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_indexcov/main.nf:18:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```

Warning: subworkflows/local/bam_variant_calling_indexcov/main.nf:30:65: Implicit closure parameter is deprecated, declare an explicit parameter instead

    indexcov_input_ch = reindex_ch.output.map{[[id:"indexcov"], it[1], it[2]]}.groupTuple()
                                                                ^^

Warning: subworkflows/local/bam_variant_calling_indexcov/main.nf:30:72: Implicit closure parameter is deprecated, declare an explicit parameter instead

    indexcov_input_ch = reindex_ch.output.map{[[id:"indexcov"], it[1], it[2]]}.groupTuple()
                                                                       ^^

Warning: subworkflows/local/bam_variant_calling_mpileup/main.nf:20:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_mpileup/main.nf:36:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals: it[0].num_intervals > 1
                   ^^
```
Warning: subworkflows/local/bam_variant_calling_mpileup/main.nf:37:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_mpileup/main.nf:42:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals: it[0].num_intervals > 1
                   ^^
```
Warning: subworkflows/local/bam_variant_calling_mpileup/main.nf:43:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_mpileup/main.nf:48:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals: it[0].num_intervals > 1
                   ^^
```
Warning: subworkflows/local/bam_variant_calling_mpileup/main.nf:49:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:19:5: Parameter was not used -- prefix with _ to suppress warning
```
    dbsnp_vqsr                        // channel: [optional]
    ^^^^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:27:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:29:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    gvcf               = Channel.empty()
                         ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:30:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf                = Channel.empty()
                         ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:31:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    genotype_intervals = Channel.empty()
                         ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:60:30: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        emit_mode_items.any{ it.equals('gvcf') })
                             ^^
```

Warning: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:66:36: Parameter was not used -- prefix with _ to suppress warning

            .map{ meta, gvcf, tbi, cram, crai, intervals -> [ meta, gvcf, tbi, intervals ] }
                                   ^^^^

Warning: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:66:42: Parameter was not used -- prefix with _ to suppress warning

            .map{ meta, gvcf, tbi, cram, crai, intervals -> [ meta, gvcf, tbi, intervals ] }
                                         ^^^^

Warning: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:74:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            intervals:    it[0].num_intervals > 1
                          ^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:75:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            no_intervals: it[0].num_intervals <= 1
                          ^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:82:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            intervals:    it[0].num_intervals > 1
                          ^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:83:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            no_intervals: it[0].num_intervals <= 1
                          ^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:90:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            intervals:    it[0].num_intervals > 1
                          ^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:91:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            no_intervals: it[0].num_intervals <= 1
                          ^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:98:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            intervals:    it[0].num_intervals > 1
                          ^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:99:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            no_intervals: it[0].num_intervals <= 1
                          ^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:114:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
    dnascope_vcf = Channel.empty().mix(
                   ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:118:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    haplotyper_tbi = Channel.empty().mix(
                     ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:137:12: The use of Channel to access channel factories is deprecated -- use channel instead
```
    gvcf = Channel.empty().mix(
           ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:141:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    gvcf_tbi = Channel.empty().mix(
               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:19:5: Parameter was not used -- prefix with _ to suppress warning
```
    dbsnp_vqsr                     // channel: [optional]
    ^^^^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:25:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:27:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    gvcf               = Channel.empty()
                         ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:28:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf                = Channel.empty()
                         ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:29:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    genotype_intervals = Channel.empty()
                         ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:56:30: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        emit_mode_items.any{ it.equals('gvcf') })
                             ^^
```

Warning: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:62:36: Parameter was not used -- prefix with _ to suppress warning

            .map{ meta, gvcf, tbi, cram, crai, intervals -> [ meta, gvcf, tbi, intervals ] }
                                   ^^^^

Warning: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:62:42: Parameter was not used -- prefix with _ to suppress warning

            .map{ meta, gvcf, tbi, cram, crai, intervals -> [ meta, gvcf, tbi, intervals ] }
                                         ^^^^

Warning: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:70:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            intervals:    it[0].num_intervals > 1
                          ^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:71:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            no_intervals: it[0].num_intervals <= 1
                          ^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:78:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            intervals:    it[0].num_intervals > 1
                          ^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:79:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            no_intervals: it[0].num_intervals <= 1
                          ^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:86:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            intervals:    it[0].num_intervals > 1
                          ^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:87:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            no_intervals: it[0].num_intervals <= 1
                          ^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:94:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            intervals:    it[0].num_intervals > 1
                          ^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:95:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            no_intervals: it[0].num_intervals <= 1
                          ^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:110:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    haplotyper_vcf = Channel.empty().mix(
                     ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:114:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    haplotyper_tbi = Channel.empty().mix(
                     ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:133:12: The use of Channel to access channel factories is deprecated -- use channel instead
```
    gvcf = Channel.empty().mix(
           ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:137:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    gvcf_tbi = Channel.empty().mix(
               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_single_strelka/main.nf:20:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_single_strelka/main.nf:32:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals:    it[0].num_intervals > 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_single_strelka/main.nf:33:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_single_strelka/main.nf:39:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals:    it[0].num_intervals > 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_single_strelka/main.nf:40:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_single_strelka/main.nf:46:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals:    it[0].num_intervals > 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_single_strelka/main.nf:47:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_single_strelka/main.nf:59:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf = Channel.empty().mix(MERGE_STRELKA.out.vcf, vcf_out.no_intervals)
          ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_single_strelka/main.nf:63:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
    tbi = Channel.empty().mix(MERGE_STRELKA.out.tbi, tbi_out.no_intervals)
          ^^^^^^^
```

Warning: subworkflows/local/bam_variant_calling_single_tiddit/main.nf:24:62: Parameter was not used -- prefix with _ to suppress warning

    vcf = TABIX_BGZIP_TIDDIT_SV.out.gz_index.map { meta, gz, tbi -> [meta + [variantcaller: 'tiddit'], gz] }
                                                             ^^^

Warning: subworkflows/local/bam_variant_calling_single_tiddit/main.nf:25:58: Parameter was not used -- prefix with _ to suppress warning

    tbi = TABIX_BGZIP_TIDDIT_SV.out.gz_index.map { meta, gz, tbi -> [meta + [variantcaller: 'tiddit'], tbi] }
                                                         ^^

Warning: subworkflows/local/bam_variant_calling_somatic_ascat/main.nf:22:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf:26:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf:34:59: Implicit closure parameter is deprecated, declare an explicit parameter instead

        def tumor_file = cnv instanceof List ? cnv.find { it.toString().endsWith("gz_CNVs") } : cnv //only find if its a list, else it returns only the filename without the path
                                                          ^^

Warning: subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf:43:63: Implicit closure parameter is deprecated, declare an explicit parameter instead

        def tumor_file = ratio instanceof List ? ratio.find { it.toString().endsWith("gz_ratio.txt") } : ratio //same here as cnv
                                                              ^^

Warning: subworkflows/local/bam_variant_calling_somatic_manta/main.nf:17:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_manta/main.nf:31:5: Variable was declared but not used
```
    candidate_sv_vcf = MANTA_SOMATIC.out.candidate_sv_vcf
    ^^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_manta/main.nf:39:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf = Channel.empty().mix(diploid_sv_vcf, somatic_sv_vcf).map{ meta, vcf -> [ meta + [ variantcaller:'manta' ], vcf ] }
          ^^^^^^^
```

Warning: subworkflows/local/bam_variant_calling_somatic_manta/main.nf:40:11: The use of Channel to access channel factories is deprecated -- use channel instead

    tbi = Channel.empty().mix(diploid_sv_vcf_tbi, somatic_sv_vcf_tbi).map{ meta, tbi -> [ meta + [ variantcaller:'manta' ], tbi ] }
          ^^^^^^^

Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:31:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:35:59: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    germline_resource_pileup = germline_resource.filter { it != [] }
                                                          ^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:36:67: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    germline_resource_pileup_tbi = germline_resource_tbi.filter { it != [] }
                                                                  ^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:72:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals: it[0].num_intervals > 1
                   ^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:73:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:78:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals: it[0].num_intervals > 1
                   ^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:79:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:84:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals: it[0].num_intervals > 1
                   ^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:85:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:90:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals: it[0].num_intervals > 1
                   ^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:91:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:103:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf = Channel.empty()
          ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:108:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
    tbi = Channel.empty()
          ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:113:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
    stats = Channel.empty()
            ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:118:12: The use of Channel to access channel factories is deprecated -- use channel instead
```
    f1r2 = Channel.empty()
           ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:145:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals: it[0].num_intervals > 1
                   ^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:146:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:151:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals: it[0].num_intervals > 1
                   ^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:152:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```

Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:165:26: The use of Channel to access channel factories is deprecated -- use channel instead

    pileup_table_tumor = Channel.empty().mix(GATHERPILEUPSUMMARIES_TUMOR.out.table, pileup_table_tumor_branch.no_intervals).map { meta, table -> [meta - meta.subMap('normal_id', 'tumor_id', 'num_intervals') + [id: meta.patient], meta.id, table] }
                         ^^^^^^^

Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:166:27: The use of Channel to access channel factories is deprecated -- use channel instead

    pileup_table_normal = Channel.empty().mix(GATHERPILEUPSUMMARIES_NORMAL.out.table, pileup_table_normal_branch.no_intervals).map { meta, table -> [meta - meta.subMap('normal_id', 'tumor_id', 'num_intervals') + [id: meta.patient], meta.id, table] }
                          ^^^^^^^

Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:186:38: The use of Channel to access channel factories is deprecated -- use channel instead
```
    calculatecontamination_out_seg = Channel.empty()
                                     ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:187:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
    calculatecontamination_out_cont = Channel.empty()
                                      ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:223:19: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .unique { it[0] }
                  ^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:228:19: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .unique { it[0] }
                  ^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_strelka/main.nf:20:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_strelka/main.nf:32:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals:    it[0].num_intervals > 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_strelka/main.nf:33:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_strelka/main.nf:39:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals:    it[0].num_intervals > 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_strelka/main.nf:40:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_strelka/main.nf:53:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals:    it[0].num_intervals > 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_strelka/main.nf:54:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_strelka/main.nf:60:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals:    it[0].num_intervals > 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_strelka/main.nf:61:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```

Warning: subworkflows/local/bam_variant_calling_somatic_strelka/main.nf:65:11: The use of Channel to access channel factories is deprecated -- use channel instead

    vcf = Channel.empty().mix(MERGE_STRELKA_INDELS.out.vcf, MERGE_STRELKA_SNVS.out.vcf, vcf_indels.no_intervals, vcf_snvs.no_intervals)
          ^^^^^^^

Warning: subworkflows/local/bam_variant_calling_somatic_strelka/main.nf:69:11: The use of Channel to access channel factories is deprecated -- use channel instead

    tbi = Channel.empty().mix(MERGE_STRELKA_INDELS.out.tbi, MERGE_STRELKA_SNVS.out.tbi, tbi_indels.no_intervals, tbi_snvs.no_intervals)
          ^^^^^^^

Warning: subworkflows/local/bam_variant_calling_somatic_tiddit/main.nf:20:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_tnscope/main.nf:22:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_tnscope/main.nf:45:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals:    it[0].num_intervals > 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_tnscope/main.nf:46:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_tnscope/main.nf:51:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals:    it[0].num_intervals > 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_tnscope/main.nf:52:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_tnscope/main.nf:63:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf   = Channel.empty()
            ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_tnscope/main.nf:67:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
    index = Channel.empty()
            ^^^^^^^
```

Warning: subworkflows/local/bam_variant_calling_tumor_only_all/main.nf:34:5: Parameter was not used -- prefix with _ to suppress warning

    intervals_bed_gz_tbi          // channel: [mandatory] [ interval.bed.gz, interval.bed.gz.tbi, num_intervals ] or [ [], [], 0 ] if no intervals
    ^^^^^^^^^^^^^^^^^^^^

Warning: subworkflows/local/bam_variant_calling_tumor_only_all/main.nf:48:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_all/main.nf:51:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    out_msisensor2 = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_all/main.nf:52:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf_freebayes  = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_all/main.nf:53:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf_lofreq     = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_all/main.nf:54:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf_manta      = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_all/main.nf:55:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf_mpileup    = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_all/main.nf:56:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf_mutect2    = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_all/main.nf:57:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf_tiddit     = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_all/main.nf:58:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf_tnscope    = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_all/main.nf:61:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    tbi_freebayes  = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_all/main.nf:62:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    tbi_lofreq     = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_all/main.nf:63:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    tbi_manta      = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_all/main.nf:64:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    tbi_mpileup    = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_all/main.nf:65:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    tbi_mutect2    = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_all/main.nf:66:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    tbi_tiddit     = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_all/main.nf:67:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    tbi_tnscope    = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_all/main.nf:221:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf_all = Channel.empty()
              ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_all/main.nf:232:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
    tbi_all = Channel.empty()
              ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_controlfreec/main.nf:26:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_lofreq/main.nf:13:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_lofreq/main.nf:25:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals:    it[0].num_intervals > 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_lofreq/main.nf:26:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_lofreq/main.nf:32:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals:    it[0].num_intervals > 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_lofreq/main.nf:33:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```

Warning: subworkflows/local/bam_variant_calling_tumor_only_lofreq/main.nf:43:11: The use of Channel to access channel factories is deprecated -- use channel instead

    vcf = Channel.empty().mix(MERGE_LOFREQ.out.vcf, vcf_branch.no_intervals).map{ meta, vcf -> [ meta - meta.subMap('num_intervals') + [ variantcaller:'lofreq' ], vcf ] }
          ^^^^^^^

Warning: subworkflows/local/bam_variant_calling_tumor_only_lofreq/main.nf:44:11: The use of Channel to access channel factories is deprecated -- use channel instead

    tbi = Channel.empty().mix(MERGE_LOFREQ.out.tbi, tbi_branch.no_intervals).map{ meta, tbi -> [ meta - meta.subMap('num_intervals') + [ variantcaller:'lofreq' ], tbi ] }
          ^^^^^^^

Warning: subworkflows/local/bam_variant_calling_tumor_only_manta/main.nf:18:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_manta/main.nf:30:5: Variable was declared but not used
```
    small_indels_vcf = MANTA_TUMORONLY.out.candidate_small_indels_vcf
    ^^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_manta/main.nf:31:5: Variable was declared but not used
```
    candidate_sv_vcf = MANTA_TUMORONLY.out.candidate_sv_vcf
    ^^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf:30:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf:34:59: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    germline_resource_pileup = germline_resource.filter { it != [] }
                                                          ^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf:35:67: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    germline_resource_pileup_tbi = germline_resource_tbi.filter { it != [] }
                                                                  ^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf:62:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals: it[0].num_intervals > 1
                   ^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf:63:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf:68:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals: it[0].num_intervals > 1
                   ^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf:69:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf:74:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals: it[0].num_intervals > 1
                   ^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf:75:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf:80:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals: it[0].num_intervals > 1
                   ^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf:81:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```

Warning: subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf:94:11: The use of Channel to access channel factories is deprecated -- use channel instead

    vcf = Channel.empty().mix(MERGE_MUTECT2.out.vcf, vcf_branch.no_intervals).map { meta, vcf -> [meta - meta.subMap('num_intervals'), vcf] }
          ^^^^^^^

Warning: subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf:95:11: The use of Channel to access channel factories is deprecated -- use channel instead

    tbi = Channel.empty().mix(MERGE_MUTECT2.out.tbi, tbi_branch.no_intervals).map { meta, tbi -> [meta - meta.subMap('num_intervals'), tbi] }
          ^^^^^^^

Warning: subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf:96:13: The use of Channel to access channel factories is deprecated -- use channel instead

    stats = Channel.empty().mix(MERGEMUTECTSTATS.out.stats, stats_branch.no_intervals).map { meta, stats -> [meta - meta.subMap('num_intervals'), stats] }
            ^^^^^^^

Warning: subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf:97:12: The use of Channel to access channel factories is deprecated -- use channel instead

    f1r2 = Channel.empty().mix(f1r2_to_merge, f1r2_branch.no_intervals).map { meta, f1r2 -> [meta - meta.subMap('num_intervals'), f1r2] }
           ^^^^^^^

Warning: subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf:109:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals: it[0].num_intervals > 1
                   ^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf:110:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```

Warning: subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf:119:20: The use of Channel to access channel factories is deprecated -- use channel instead

    pileup_table = Channel.empty().mix(GATHERPILEUPSUMMARIES.out.table, pileup_table_branch.no_intervals).map { meta, table -> [meta - meta.subMap('num_intervals') + [id: meta.sample], table] }
                   ^^^^^^^

Warning: subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf:125:38: The use of Channel to access channel factories is deprecated -- use channel instead
```
    calculatecontamination_out_seg = Channel.empty()
                                     ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf:126:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
    calculatecontamination_out_cont = Channel.empty()
                                      ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf:160:19: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .unique { it[0] }
                  ^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf:165:19: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .unique { it[0] }
                  ^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_tnscope/main.nf:22:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_tnscope/main.nf:45:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals:    it[0].num_intervals > 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_tnscope/main.nf:46:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_tnscope/main.nf:51:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals:    it[0].num_intervals > 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_tnscope/main.nf:52:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_tnscope/main.nf:63:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf   = Channel.empty()
            ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_tumor_only_tnscope/main.nf:67:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
    index = Channel.empty()
            ^^^^^^^
```
Warning: subworkflows/local/cram_qc_mosdepth_samtools/main.nf:17:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/cram_qc_mosdepth_samtools/main.nf:18:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
    reports = Channel.empty()
              ^^^^^^^
```

Warning: subworkflows/local/cram_qc_mosdepth_samtools/main.nf:23:43: Parameter was not used -- prefix with _ to suppress warning

    MOSDEPTH(cram.combine(intervals.map { meta, bed -> [bed ?: []] }), fasta)
                                          ^^^^

Warning: subworkflows/local/cram_sampleqc/main.nf:14:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/cram_sampleqc/main.nf:15:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
    reports = Channel.empty()
              ^^^^^^^
```
Warning: subworkflows/local/post_variantcalling/main.nf:36:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/post_variantcalling/main.nf:37:12: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcfs = Channel.empty()
           ^^^^^^^
```
Warning: subworkflows/local/post_variantcalling/main.nf:38:12: The use of Channel to access channel factories is deprecated -- use channel instead
```
    tbis = Channel.empty()
           ^^^^^^^
```
Warning: subworkflows/local/post_variantcalling/main.nf:84:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
        all_vcfs = Channel.empty().mix(germline_vcfs, tumor_only_vcfs, somatic_vcfs)
                   ^^^^^^^
```

Warning: subworkflows/local/post_variantcalling/main.nf:85:48: Parameter was not used -- prefix with _ to suppress warning

                                .branch{ meta, vcf ->
                                               ^^^

Warning: subworkflows/local/post_variantcalling/main.nf:90:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
        all_tbis = Channel.empty().mix(germline_tbis, tumor_only_tbis, somatic_tbis)
                   ^^^^^^^
```

Warning: subworkflows/local/post_variantcalling/main.nf:91:48: Parameter was not used -- prefix with _ to suppress warning

                                .branch{ meta, tbi ->
                                               ^^^

Warning: subworkflows/local/post_variantcalling/main.nf:97:42: Parameter was not used -- prefix with _ to suppress warning

        all_vcfs.other.subscribe { meta, vcf ->
                                         ^^^

Warning: subworkflows/local/prepare_genome/main.nf:57:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:60:24: The use of Channel to access channel factories is deprecated -- use channel instead

    fasta = fasta_in ? Channel.fromPath(fasta_in).map { fasta -> [[id: fasta.baseName], fasta] }.collect() : Channel.empty()
                       ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:60:110: The use of Channel to access channel factories is deprecated -- use channel instead

    fasta = fasta_in ? Channel.fromPath(fasta_in).map { fasta -> [[id: fasta.baseName], fasta] }.collect() : Channel.empty()
                                                                                                             ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:70:31: The use of Channel to access channel factories is deprecated -- use channel instead

            index_alignment = Channel.fromPath(bwa_in).map { index -> [[id: 'bwa'], index] }.collect()
                              ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:78:31: The use of Channel to access channel factories is deprecated -- use channel instead

            index_alignment = Channel.fromPath(bwamem2_in).map { index -> [[id: 'bwamem2'], index] }.collect()
                              ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:86:31: The use of Channel to access channel factories is deprecated -- use channel instead

            index_alignment = Channel.fromPath(dragmap_in).map { index -> [[id: 'dragmap'], index] }.collect()
                              ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:90:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
        index_alignment = Channel.empty()
                          ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:99:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
        dict = Channel.fromPath(dict_in).map { it -> [[id: 'dict'], it] }.collect()
               ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:102:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
        dict = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:111:21: The use of Channel to access channel factories is deprecated -- use channel instead
```
        fasta_fai = Channel.fromPath(fasta_fai_in).map { it -> [[id: 'fai'], it] }.collect()
                    ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:114:21: The use of Channel to access channel factories is deprecated -- use channel instead
```
        fasta_fai = Channel.empty()
                    ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:118:21: The use of Channel to access channel factories is deprecated -- use channel instead
```
    bbsplit_index = Channel.empty()
                    ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:127:33: The use of Channel to access channel factories is deprecated -- use channel instead

                bbsplit_index = Channel.value(file(bbsplit_index_in, checkIfExists: true))
                                ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:132:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.from(file(bbsplit_fasta_list_in, checkIfExists: true))
            ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:137:29: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                .collect { [it] }
                            ^^
```

Warning: subworkflows/local/prepare_genome/main.nf:150:54: The use of Channel to access channel factories is deprecated -- use channel instead

    bcftools_annotations = bcftools_annotations_in ? Channel.fromPath(bcftools_annotations_in).collect() : Channel.value([])
                                                     ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:150:108: The use of Channel to access channel factories is deprecated -- use channel instead

    bcftools_annotations = bcftools_annotations_in ? Channel.fromPath(bcftools_annotations_in).collect() : Channel.value([])
                                                                                                           ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:151:62: The use of Channel to access channel factories is deprecated -- use channel instead

    bcftools_annotations_tbi = bcftools_annotations_tbi_in ? Channel.fromPath(bcftools_annotations_tbi_in).collect() : Channel.value([])
                                                             ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:151:120: The use of Channel to access channel factories is deprecated -- use channel instead

    bcftools_annotations_tbi = bcftools_annotations_tbi_in ? Channel.fromPath(bcftools_annotations_tbi_in).collect() : Channel.value([])
                                                                                                                       ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:159:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    dbsnp = dbsnp_in ? Channel.fromPath(dbsnp_in).collect() : Channel.value([])
                       ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:159:63: The use of Channel to access channel factories is deprecated -- use channel instead

    dbsnp = dbsnp_in ? Channel.fromPath(dbsnp_in).collect() : Channel.value([])
                                                              ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:160:32: The use of Channel to access channel factories is deprecated -- use channel instead

    dbsnp_tbi = dbsnp_tbi_in ? Channel.fromPath(dbsnp_tbi_in).collect() : Channel.value([])
                               ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:160:75: The use of Channel to access channel factories is deprecated -- use channel instead

    dbsnp_tbi = dbsnp_tbi_in ? Channel.fromPath(dbsnp_tbi_in).collect() : Channel.value([])
                                                                          ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:168:48: The use of Channel to access channel factories is deprecated -- use channel instead

    germline_resource = germline_resource_in ? Channel.fromPath(germline_resource_in).collect() : Channel.value([])
                                               ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:168:99: The use of Channel to access channel factories is deprecated -- use channel instead

    germline_resource = germline_resource_in ? Channel.fromPath(germline_resource_in).collect() : Channel.value([])
                                                                                                  ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:169:56: The use of Channel to access channel factories is deprecated -- use channel instead

    germline_resource_tbi = germline_resource_tbi_in ? Channel.fromPath(germline_resource_tbi_in).collect() : Channel.value([])
                                                       ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:169:111: The use of Channel to access channel factories is deprecated -- use channel instead

    germline_resource_tbi = germline_resource_tbi_in ? Channel.fromPath(germline_resource_tbi_in).collect() : Channel.value([])
                                                                                                              ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:177:38: The use of Channel to access channel factories is deprecated -- use channel instead

    known_indels = known_indels_in ? Channel.fromPath(known_indels_in).collect() : Channel.value([])
                                     ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:177:84: The use of Channel to access channel factories is deprecated -- use channel instead

    known_indels = known_indels_in ? Channel.fromPath(known_indels_in).collect() : Channel.value([])
                                                                                   ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:178:46: The use of Channel to access channel factories is deprecated -- use channel instead

    known_indels_tbi = known_indels_tbi_in ? Channel.fromPath(known_indels_tbi_in).collect() : Channel.value([])
                                             ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:178:96: The use of Channel to access channel factories is deprecated -- use channel instead

    known_indels_tbi = known_indels_tbi_in ? Channel.fromPath(known_indels_tbi_in).collect() : Channel.value([])
                                                                                               ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:186:34: The use of Channel to access channel factories is deprecated -- use channel instead

    known_snps = known_snps_in ? Channel.fromPath(known_snps_in).collect() : Channel.value([])
                                 ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:186:78: The use of Channel to access channel factories is deprecated -- use channel instead

    known_snps = known_snps_in ? Channel.fromPath(known_snps_in).collect() : Channel.value([])
                                                                             ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:187:42: The use of Channel to access channel factories is deprecated -- use channel instead

    known_snps_tbi = known_snps_tbi_in ? Channel.fromPath(known_snps_tbi_in).collect() : Channel.value([])
                                         ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:187:90: The use of Channel to access channel factories is deprecated -- use channel instead

    known_snps_tbi = known_snps_tbi_in ? Channel.fromPath(known_snps_tbi_in).collect() : Channel.value([])
                                                                                         ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:195:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
    pon = pon_in ? Channel.fromPath(pon_in).collect() : Channel.value([])
                   ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:195:57: The use of Channel to access channel factories is deprecated -- use channel instead

    pon = pon_in ? Channel.fromPath(pon_in).collect() : Channel.value([])
                                                        ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:196:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    pon_tbi = pon_tbi_in ? Channel.fromPath(pon_tbi_in).collect() : Channel.value([])
                           ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:196:69: The use of Channel to access channel factories is deprecated -- use channel instead

    pon_tbi = pon_tbi_in ? Channel.fromPath(pon_tbi_in).collect() : Channel.value([])
                                                                    ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:213:33: The use of Channel to access channel factories is deprecated -- use channel instead

        UNTAR_MSISENSOR2_MODELS(Channel.fromPath(file(msisensor2_models_in)).map { archive -> [[id: archive.baseName], archive] })
                                ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:218:29: The use of Channel to access channel factories is deprecated -- use channel instead

        msisensor2_models = Channel.fromPath(msisensor2_models_in).map { model -> [[id:model.baseName], model] }.collect()
                            ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:221:29: The use of Channel to access channel factories is deprecated -- use channel instead
```
        msisensor2_models = Channel.value([])
                            ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:225:29: The use of Channel to access channel factories is deprecated -- use channel instead
```
        msisensorpro_scan = Channel.fromPath(msisensorpro_scan_in)
                            ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:233:29: The use of Channel to access channel factories is deprecated -- use channel instead
```
        msisensorpro_scan = Channel.value([])
                            ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:238:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ascat_alleles = Channel.empty()
                        ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:241:23: The use of Channel to access channel factories is deprecated -- use channel instead

        UNZIP_ALLELES(Channel.fromPath(file(ascat_alleles_in)).map { archive -> [[id: archive.baseName], archive] })
                      ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:246:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ascat_alleles = Channel.fromPath(ascat_alleles_in).collect()
                        ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:250:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ascat_loci = Channel.empty()
                     ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:253:20: The use of Channel to access channel factories is deprecated -- use channel instead

        UNZIP_LOCI(Channel.fromPath(file(ascat_loci_in)).map { archive -> [[id: archive.baseName], archive] })
                   ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:258:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ascat_loci = Channel.fromPath(ascat_loci_in).collect()
                     ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:262:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ascat_loci_gc = Channel.value([])
                        ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:265:18: The use of Channel to access channel factories is deprecated -- use channel instead

        UNZIP_GC(Channel.fromPath(file(ascat_loci_gc_in)).map { archive -> [[id: archive.baseName], archive] })
                 ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:270:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ascat_loci_gc = Channel.fromPath(ascat_loci_gc_in).collect()
                        ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:274:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ascat_loci_rt = Channel.value([])
                        ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:277:18: The use of Channel to access channel factories is deprecated -- use channel instead

        UNZIP_RT(Channel.fromPath(file(ascat_loci_rt_in)).map { archive -> [[id: archive.baseName], archive] })
                 ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:282:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ascat_loci_rt = Channel.fromPath(ascat_loci_rt_in).collect()
                        ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:286:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
        chr_dir = Channel.value([])
                  ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:289:23: The use of Channel to access channel factories is deprecated -- use channel instead

        UNTAR_CHR_DIR(Channel.fromPath(file(chr_dir_in)).map { archive -> [[id: archive.baseName], archive] })
                      ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:294:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
        chr_dir = Channel.fromPath(chr_dir_in).collect()
                  ^^^^^^^
```
Warning: subworkflows/local/prepare_reference_cnvkit/main.nf:10:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/prepare_snpsift_databases/main.nf:16:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        has_vardb: it.vardb != null
                   ^^
```

Warning: subworkflows/local/prepare_snpsift_databases/main.nf:23:45: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_branched.needs_vardb.map { [[id: it.vcf.baseName], it.vcf, it.tbi, it.fields ? it.fields.replace(';', ',') : ''] }
                                            ^^

Warning: subworkflows/local/prepare_snpsift_databases/main.nf:23:63: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_branched.needs_vardb.map { [[id: it.vcf.baseName], it.vcf, it.tbi, it.fields ? it.fields.replace(';', ',') : ''] }
                                                              ^^

Warning: subworkflows/local/prepare_snpsift_databases/main.nf:23:71: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_branched.needs_vardb.map { [[id: it.vcf.baseName], it.vcf, it.tbi, it.fields ? it.fields.replace(';', ',') : ''] }
                                                                      ^^

Warning: subworkflows/local/prepare_snpsift_databases/main.nf:23:79: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_branched.needs_vardb.map { [[id: it.vcf.baseName], it.vcf, it.tbi, it.fields ? it.fields.replace(';', ',') : ''] }
                                                                              ^^

Warning: subworkflows/local/prepare_snpsift_databases/main.nf:23:91: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_branched.needs_vardb.map { [[id: it.vcf.baseName], it.vcf, it.tbi, it.fields ? it.fields.replace(';', ',') : ''] }
                                                                                          ^^

Warning: subworkflows/local/prepare_snpsift_databases/main.nf:29:46: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .join(ch_branched.needs_vardb.map { [it.vcf.baseName, it] })
                                             ^^
```
Warning: subworkflows/local/prepare_snpsift_databases/main.nf:29:63: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .join(ch_branched.needs_vardb.map { [it.vcf.baseName, it] })
                                                              ^^
```
Warning: subworkflows/local/prepare_snpsift_databases/main.nf:34:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [it.vcf, it.tbi, it.vardb, it.fields ? it.fields.replace(';', ',') : '', it.prefix ?: ''] }
                ^^
```

Warning: subworkflows/local/prepare_snpsift_databases/main.nf:34:25: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .map { [it.vcf, it.tbi, it.vardb, it.fields ? it.fields.replace(';', ',') : '', it.prefix ?: ''] }
                        ^^

Warning: subworkflows/local/prepare_snpsift_databases/main.nf:34:33: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .map { [it.vcf, it.tbi, it.vardb, it.fields ? it.fields.replace(';', ',') : '', it.prefix ?: ''] }
                                ^^

Warning: subworkflows/local/prepare_snpsift_databases/main.nf:34:43: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .map { [it.vcf, it.tbi, it.vardb, it.fields ? it.fields.replace(';', ',') : '', it.prefix ?: ''] }
                                          ^^

Warning: subworkflows/local/prepare_snpsift_databases/main.nf:34:55: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .map { [it.vcf, it.tbi, it.vardb, it.fields ? it.fields.replace(';', ',') : '', it.prefix ?: ''] }
                                                      ^^

Warning: subworkflows/local/prepare_snpsift_databases/main.nf:34:89: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .map { [it.vcf, it.tbi, it.vardb, it.fields ? it.fields.replace(';', ',') : '', it.prefix ?: ''] }
                                                                                        ^^

Warning: subworkflows/local/prepare_snpsift_databases/main.nf:42:32: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                list.collect { it[0] },  // db_vcf
                               ^^
```
Warning: subworkflows/local/prepare_snpsift_databases/main.nf:43:32: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                list.collect { it[1] },  // db_vcf_tbi
                               ^^
```
Warning: subworkflows/local/prepare_snpsift_databases/main.nf:44:32: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                list.collect { it[2] },  // db_vardb
                               ^^
```
Warning: subworkflows/local/prepare_snpsift_databases/main.nf:45:32: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                list.collect { it[3] },  // db_fields
                               ^^
```
Warning: subworkflows/local/prepare_snpsift_databases/main.nf:46:32: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                list.collect { it[4] }   // db_prefixes
                               ^^
```
Warning: subworkflows/local/samplesheet_to_channel/main.nf:13:5: Parameter was not used -- prefix with _ to suppress warning
```
    bcftools_columns              // Path: bcftools columns
    ^^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/samplesheet_to_channel/main.nf:53:49: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            def status0_count = samples.count { it.status == 0 }
                                                ^^
```
Warning: subworkflows/local/samplesheet_to_channel/main.nf:54:49: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            def status1_count = samples.count { it.status == 1 }
                                                ^^
```
Warning: subworkflows/local/samplesheet_to_channel/main.nf:70:16: Parameter was not used -- prefix with _ to suppress warning
```
        .map { combination_key, combination_list ->
               ^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/samplesheet_to_channel/main.nf:90:41: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            [patient, samples.collect { it.sample }]
                                        ^^
```
Warning: subworkflows/local/samplesheet_to_channel/main.nf:245:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .filter { it[0].status == 1 }
                      ^^
```
Warning: subworkflows/local/samplesheet_to_channel/main.nf:263:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .filter { it[0].status == 0 }
                      ^^
```
Warning: subworkflows/local/samplesheet_to_channel/main.nf:437:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            if (it[0].sex == 'NA') {
                ^^
```
Warning: subworkflows/local/samplesheet_to_channel/main.nf:446:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            if (it[0].status == 1 && !it[0].containsKey('contamination')) {
                ^^
```
Warning: subworkflows/local/samplesheet_to_channel/main.nf:446:39: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            if (it[0].status == 1 && !it[0].containsKey('contamination')) {
                                      ^^
```
Warning: subworkflows/local/vcf_consensus/main.nf:15:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/vcf_consensus/main.nf:18:24: Parameter was not used -- prefix with _ to suppress warning
```
        .branch{ meta, vcf, tbi ->
                       ^^^
```
Warning: subworkflows/local/vcf_consensus/main.nf:18:29: Parameter was not used -- prefix with _ to suppress warning
```
        .branch{ meta, vcf, tbi ->
                            ^^^
```

Warning: subworkflows/local/vcf_consensus/main.nf:54:70: Implicit closure parameter is deprecated, declare an explicit parameter instead

                            def sorted_vcfs = sorted_pairs.collect { it[0] }
                                                                     ^^

Warning: subworkflows/local/vcf_consensus/main.nf:55:66: Implicit closure parameter is deprecated, declare an explicit parameter instead

                            def callers = sorted_pairs.collect { it[1] }
                                                                 ^^

Warning: subworkflows/local/vcf_consensus/main.nf:65:19: Parameter was not used -- prefix with _ to suppress warning
```
        .filter { meta, dir ->
                  ^^^^
```
Warning: subworkflows/local/vcf_qc_bcftools_vcftools/main.nf:13:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/vcf_variant_filtering_gatk/main.nf:17:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/nf-core/bam_ngscheckmate/main.nf:13:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: workflows/sarek/main.nf:141:18: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            bam: it[0].data_type == "bam"
                 ^^
```
Warning: workflows/sarek/main.nf:142:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            fastq_gz: it[0].data_type == "fastq_gz"
                      ^^
```

Warning: workflows/sarek/main.nf:143:34: Implicit closure parameter is deprecated, declare an explicit parameter instead

            one_fastq_gz_spring: it[0].data_type == "one_fastq_gz_spring"
                                 ^^

Warning: workflows/sarek/main.nf:144:34: Implicit closure parameter is deprecated, declare an explicit parameter instead

            two_fastq_gz_spring: it[0].data_type == "two_fastq_gz_spring"
                                 ^^

Warning: workflows/sarek/main.nf:291:77: Parameter was not used -- prefix with _ to suppress warning

            cram_variant_calling_status_tmp = cram_variant_calling.branch { meta, file, index ->
                                                                            ^^^^

Warning: workflows/sarek/main.nf:291:89: Parameter was not used -- prefix with _ to suppress warning

            cram_variant_calling_status_tmp = cram_variant_calling.branch { meta, file, index ->
                                                                                        ^^^^^

Warning: workflows/sarek/main.nf:311:75: Parameter was not used -- prefix with _ to suppress warning

        cram_variant_calling_status = cram_variant_calling.branch { meta, file, index ->
                                                                          ^^^^

Warning: workflows/sarek/main.nf:311:81: Parameter was not used -- prefix with _ to suppress warning

        cram_variant_calling_status = cram_variant_calling.branch { meta, file, index ->
                                                                                ^^^^^

Warning: workflows/sarek/main.nf:317:73: Parameter was not used -- prefix with _ to suppress warning

        bam_variant_calling_status = bam_variant_calling.branch { meta, file, index ->
                                                                        ^^^^

Warning: workflows/sarek/main.nf:317:79: Parameter was not used -- prefix with _ to suppress warning

        bam_variant_calling_status = bam_variant_calling.branch { meta, file, index ->
                                                                              ^^^^^

Warning: workflows/sarek/main.nf:703:76: Implicit closure parameter is deprecated, declare an explicit parameter instead

            def InputStream gzipStream = new java.util.zip.GZIPInputStream(it)
                                                                           ^^

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