Nextflow lint results

Generated: 2026-01-16T10:27:57.129371601Z
Nextflow version: 25.12.0-edge
Summary: 31 errors, 371 warnings

❌ Errors

Error: conf/modules/variant_calling/mutect2.config:106:21: Unexpected input: ':'

            withName: 'CALCULATECONTAMINATION' {
                    ^

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

Error: subworkflows/local/prepare_intervals/main.nf:67:34: Unexpected input: '='

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

Error: subworkflows/local/prepare_reference_and_intervals/main.nf:5:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/rnadnavar/subworkflows/local/prepare_intervals/main.nf'

include { PREPARE_INTERVALS                                    } from './../prepare_intervals/main'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: subworkflows/local/prepare_reference_and_intervals/main.nf:55:5: PREPARE_INTERVALS is not defined
```
    PREPARE_INTERVALS(fasta_fai, params.intervals, params.no_intervals)
    ^^^^^^^^^^^^^^^^^
```

Error: subworkflows/local/prepare_reference_and_intervals/main.nf:56:29: PREPARE_INTERVALS is not defined

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

Error: subworkflows/local/prepare_reference_and_intervals/main.nf:70:37: PREPARE_INTERVALS is not defined

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

Error: subworkflows/local/prepare_reference_and_intervals/main.nf:71:37: PREPARE_INTERVALS is not defined

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

Error: subworkflows/local/prepare_reference_and_intervals/main.nf:72:37: PREPARE_INTERVALS is not defined

    intervals_for_preprocessing   = PREPARE_INTERVALS.out.intervals_for_preprocessing
                                    ^^^^^^^^^^^^^^^^^

Error: subworkflows/local/prepare_reference_and_intervals/main.nf:73:37: PREPARE_INTERVALS is not defined

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

Error: subworkflows/local/prepare_reference_and_intervals/main.nf:74:37: PREPARE_INTERVALS is not defined

    intervals_bed_gz_tbi_combined = PREPARE_INTERVALS.out.intervals_bed_gz_tbi_combined
                                    ^^^^^^^^^^^^^^^^^

Error: subworkflows/local/samplesheet_to_channel/main.nf:26:14: Variables in a closure should be declared with def

            (meta, fastq_1, fastq_2, table, cram, crai, bam, bai, vcf, variantcaller, maf) = ch_items
             ^^^^

Error: subworkflows/local/samplesheet_to_channel/main.nf:26:20: Variables in a closure should be declared with def

            (meta, fastq_1, fastq_2, table, cram, crai, bam, bai, vcf, variantcaller, maf) = ch_items
                   ^^^^^^^

Error: subworkflows/local/samplesheet_to_channel/main.nf:26:29: Variables in a closure should be declared with def

            (meta, fastq_1, fastq_2, table, cram, crai, bam, bai, vcf, variantcaller, maf) = ch_items
                            ^^^^^^^

Error: subworkflows/local/samplesheet_to_channel/main.nf:26:38: Variables in a closure should be declared with def

            (meta, fastq_1, fastq_2, table, cram, crai, bam, bai, vcf, variantcaller, maf) = ch_items
                                     ^^^^^

Error: subworkflows/local/samplesheet_to_channel/main.nf:26:45: Variables in a closure should be declared with def

            (meta, fastq_1, fastq_2, table, cram, crai, bam, bai, vcf, variantcaller, maf) = ch_items
                                            ^^^^

Error: subworkflows/local/samplesheet_to_channel/main.nf:26:51: Variables in a closure should be declared with def

            (meta, fastq_1, fastq_2, table, cram, crai, bam, bai, vcf, variantcaller, maf) = ch_items
                                                  ^^^^

Error: subworkflows/local/samplesheet_to_channel/main.nf:26:57: Variables in a closure should be declared with def

            (meta, fastq_1, fastq_2, table, cram, crai, bam, bai, vcf, variantcaller, maf) = ch_items
                                                        ^^^

Error: subworkflows/local/samplesheet_to_channel/main.nf:26:62: Variables in a closure should be declared with def

            (meta, fastq_1, fastq_2, table, cram, crai, bam, bai, vcf, variantcaller, maf) = ch_items
                                                             ^^^

Error: subworkflows/local/samplesheet_to_channel/main.nf:26:67: Variables in a closure should be declared with def

            (meta, fastq_1, fastq_2, table, cram, crai, bam, bai, vcf, variantcaller, maf) = ch_items
                                                                  ^^^

Error: subworkflows/local/samplesheet_to_channel/main.nf:26:72: Variables in a closure should be declared with def

            (meta, fastq_1, fastq_2, table, cram, crai, bam, bai, vcf, variantcaller, maf) = ch_items
                                                                       ^^^^^^^^^^^^^

Error: subworkflows/local/samplesheet_to_channel/main.nf:26:87: Variables in a closure should be declared with def

            (meta, fastq_1, fastq_2, table, cram, crai, bam, bai, vcf, variantcaller, maf) = ch_items
                                                                                      ^^^

Error: tests/config/test_data.config:5:5: Unexpected input: 'includeConfig'

    includeConfig "https://raw.githubusercontent.com/nf-core/modules/master/tests/config/test_data.config"
    ^

Error: workflows/rnadnavar/main.nf:26:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/rnadnavar/subworkflows/local/prepare_intervals/main.nf'

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

Error: workflows/rnadnavar/main.nf:191:9: PREPARE_INTERVALS_FOR_REALIGNMENT is not defined

        PREPARE_INTERVALS_FOR_REALIGNMENT(fasta_fai, null, true)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/rnadnavar/main.nf:223:13: PREPARE_INTERVALS_FOR_REALIGNMENT is not defined

            PREPARE_INTERVALS_FOR_REALIGNMENT.out.intervals_bed,
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/rnadnavar/main.nf:224:13: PREPARE_INTERVALS_FOR_REALIGNMENT is not defined

            PREPARE_INTERVALS_FOR_REALIGNMENT.out.intervals_for_preprocessing,
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/rnadnavar/main.nf:225:13: PREPARE_INTERVALS_FOR_REALIGNMENT is not defined

            PREPARE_INTERVALS_FOR_REALIGNMENT.out.intervals_bed_gz_tbi,
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/rnadnavar/main.nf:226:13: PREPARE_INTERVALS_FOR_REALIGNMENT is not defined

            PREPARE_INTERVALS_FOR_REALIGNMENT.out.intervals_bed_combined,
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/rnadnavar/main.nf:227:13: PREPARE_INTERVALS_FOR_REALIGNMENT is not defined

            PREPARE_INTERVALS_FOR_REALIGNMENT.out.intervals_and_num_intervals,
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/rnadnavar/main.nf:228:13: PREPARE_INTERVALS_FOR_REALIGNMENT is not defined

            PREPARE_INTERVALS_FOR_REALIGNMENT.out.intervals_bed_gz_tbi_combined,
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

⚠️ Warnings

Warning: conf/modules/alignment/bam_align.config:48:46: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    ) { "mapped/${meta.id}/${it}" }
                                             ^^
```

Warning: conf/modules/alignment/bam_align.config:67:174: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: conf/modules/alignment/bam_align.config:172:209: Implicit closure parameter is deprecated, declare an explicit parameter instead

                saveAs: { (params.save_bam_mapped || (params.skip_tools && params.skip_tools.split(',').contains('markduplicates'))) && (meta.size * meta.numLanes == 1) ? "mapped/${meta.patient}/${meta.id}/${it}" : null }
                                                                                                                                                                                                                ^^

Warning: conf/modules/alignment/bam_align.config:184:209: Implicit closure parameter is deprecated, declare an explicit parameter instead

                saveAs: { (params.save_bam_mapped || (params.skip_tools && params.skip_tools.split(',').contains('markduplicates'))) && (meta.size * meta.numLanes == 1) ? "mapped/${meta.patient}/${meta.id}/${it}" : null }
                                                                                                                                                                                                                ^^

Warning: conf/modules/gatk4_preprocessing/markduplicates.config:64:145: 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/gatk4_preprocessing/prepare_recalibration.config:25:81: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: conf/modules/gatk4_preprocessing/recalibrate.config:25:82: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: conf/modules/gatk4_preprocessing/splitncigarreads.config:46:102: Implicit closure parameter is deprecated, declare an explicit parameter instead

                        saveAs: { params.save_bam_mapped ? "realignment/${meta.patient}/${meta.id}/${it}" : null },
                                                                                                     ^^

Warning: conf/modules/variant_calling/strelka.config:27:77: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: main.nf:60:5: Variable was declared but not used
```
    versions = Channel.empty()
    ^^^^^^^^
```
Warning: main.nf:60:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: modules/local/maf2bed/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/merge_maf/main.nf:22:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
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/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/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/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/learnreadorientationmodel/main.nf:23:48: 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/gffread/main.nf:26:103: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def extension   = args.contains("-T")       ? 'gtf' : ( ( ['-w', '-x', '-y' ].any { args.contains(it) } ) ? 'fasta' : 'gff3' )
                                                                                                      ^^

Warning: modules/nf-core/gffread/main.nf:30:61: Parameter was not used -- prefix with _ to suppress warning

    def args_sorted = args.replaceAll(/(.*)(-[wxy])(.*)/) { all, pre, param, post -> "$pre $post $param" }.trim()
                                                            ^^^

Warning: modules/nf-core/gffread/main.nf:49:103: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def extension   = args.contains("-T")       ? 'gtf' : ( ( ['-w', '-x', '-y' ].any { args.contains(it) } ) ? 'fasta' : 'gff3' )
                                                                                                      ^^

Warning: modules/nf-core/gunzip/main.nf:43:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/hisat2/extractsplicesites/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/star/align/main.nf:46:56: Implicit closure parameter is deprecated, declare an explicit parameter instead

    meta.single_end ? [reads].flatten().each{reads1 << it} : reads.eachWithIndex{ v, ix -> ( ix & 1 ? reads2 : reads1) << v }
                                                       ^^

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: modules/nf-core/vt/normalize/main.nf:53:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: subworkflows/local/annotation_cache_initialisation/main.nf:35:28: 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_align/main.nf:36:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
    reports   = Channel.empty()
                ^^^^^^^
```
Warning: subworkflows/local/bam_align/main.nf:37:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions  = Channel.empty()
                ^^^^^^^
```
Warning: subworkflows/local/bam_align/main.nf:40:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    bam_mapped_rna   = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/local/bam_align/main.nf:41:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    bam_mapped_dna   = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/local/bam_align/main.nf:42:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    bam_mapped       = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/local/bam_align/main.nf:43:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    cram_mapped      = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/local/bam_align/main.nf:54:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            bam:   it[0].data_type == "bam"
                   ^^
```
Warning: subworkflows/local/bam_align/main.nf:55:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            fastq: it[0].data_type == "fastq"
                   ^^
```

Warning: subworkflows/local/bam_align/main.nf:74:59: Parameter was not used -- prefix with _ to suppress warning

            reports = reports.mix(FASTQC.out.zip.collect{ meta, logs -> logs })
                                                          ^^^^

Warning: subworkflows/local/bam_align/main.nf:129:22: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                dna: it[0].status < 2
                     ^^
```
Warning: subworkflows/local/bam_align/main.nf:130:22: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                rna: it[0].status == 2
                     ^^
```

Warning: subworkflows/local/bam_align/main.nf:189:76: Implicit closure parameter is deprecated, declare an explicit parameter instead

        reports           = reports.mix(FASTQ_ALIGN_STAR.out.stats.collect{it[1]}.ifEmpty([]))
                                                                           ^^

Warning: subworkflows/local/bam_align/main.nf:190:80: Implicit closure parameter is deprecated, declare an explicit parameter instead

        reports           = reports.mix(FASTQ_ALIGN_STAR.out.log_final.collect{it[1]}.ifEmpty([]))
                                                                               ^^

Warning: subworkflows/local/bam_applybqsr/main.nf:19:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
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_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_gatk_preprocessing/main.nf:39:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
    reports   = Channel.empty()
                ^^^^^^^
```
Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:40:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions  = Channel.empty()
                ^^^^^^^
```
Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:41:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    cram_variant_calling = Channel.empty()
                           ^^^^^^^
```
Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:45:40: The use of Channel to access channel factories is deprecated -- use channel instead
```
        cram_markduplicates_no_spark = Channel.empty()
                                       ^^^^^^^
```

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:55:121: Parameter was not used -- prefix with _ to suppress warning

        cram_for_markduplicates = params.step == 'mapping' || realignment ? bam_mapped : input_sample.map{ meta, input, index -> [ meta, input ] }
                                                                                                                        ^^^^^

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:59:36: The use of Channel to access channel factories is deprecated -- use channel instead
```
        cram_skip_markduplicates = Channel.empty()
                                   ^^^^^^^
```
Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:68:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    bam:  it[0].data_type == "bam"
                          ^^
```
Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:69:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    cram: it[0].data_type == "cram"
                          ^^
```

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:73:73: Parameter was not used -- prefix with _ to suppress warning

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

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:76:44: The use of Channel to access channel factories is deprecated -- use channel instead

                cram_skip_markduplicates = Channel.empty().mix(input_markduplicates_convert.cram, BAM_TO_CRAM.out.cram)
                                           ^^^^^^^

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:82:70: Parameter was not used -- prefix with _ to suppress warning

            reports = reports.mix(CRAM_QC_NO_MD.out.reports.collect{ meta, report -> report })
                                                                     ^^^^

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:100:75: Parameter was not used -- prefix with _ to suppress warning

            reports = reports.mix(BAM_MARKDUPLICATES.out.reports.collect{ meta, report -> report })
                                                                          ^^^^

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:107:34: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_md_cram_for_restart = Channel.empty().mix(cram_markduplicates_no_spark)
                                 ^^^^^^^
```
Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:123:36: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_md_cram_for_restart   = Channel.empty().mix(input_sample)
                                   ^^^^^^^
```
Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:124:36: The use of Channel to access channel factories is deprecated -- use channel instead
```
        cram_skip_markduplicates = Channel.empty().mix(input_sample)
                                   ^^^^^^^
```
Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:134:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    bam:  it[0].data_type == "bam"
                          ^^
```
Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:135:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    cram: it[0].data_type == "cram"
                          ^^
```

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:138:83: Parameter was not used -- prefix with _ to suppress warning

                input_sncr_convert  = input_sncr_convert.bam.map{ meta, bam, bai, table -> [ meta, bam, bai ] }
                                                                                  ^^^^^

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:147:41: The use of Channel to access channel factories is deprecated -- use channel instead

                cram_skip_splitncigar = Channel.empty().mix(sncr_cram_from_bam, input_sncr_convert.cram)
                                        ^^^^^^^

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:157:37: The use of Channel to access channel factories is deprecated -- use channel instead
```
        cram_splitncigar_no_spark = Channel.empty()
                                    ^^^^^^^
```

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:161:55: Implicit closure parameter is deprecated, declare an explicit parameter instead

                                                dna:  it[0].status < 2
                                                      ^^

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:162:55: Implicit closure parameter is deprecated, declare an explicit parameter instead

                                                rna:  it[0].status >= 2
                                                      ^^

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:177:37: The use of Channel to access channel factories is deprecated -- use channel instead
```
            cram_skip_splitncigar = Channel.empty()
                                    ^^^^^^^
```

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:181:36: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_sncr_cram_for_restart = Channel.empty().mix(cram_splitncigar_no_spark).mix(cram_skip_splitncigar)
                                   ^^^^^^^

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:185:36: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_sncr_cram_for_restart = Channel.empty()
                                   ^^^^^^^
```
Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:197:22: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                bam: it[0].data_type == "bam"
                     ^^
```
Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:198:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                cram: it[0].data_type == "cram"
                      ^^
```

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:209:48: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_cram_for_bam_baserecalibrator = Channel.empty().mix(ch_cram_for_bam_baserecalibrator, input_prepare_recal_convert.cram)
                                               ^^^^^^^

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:220:48: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_cram_for_bam_baserecalibrator = Channel.empty().mix(ch_sncr_cram_for_restart, cram_skip_splitncigar )
                                               ^^^^^^^

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:228:38: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_table_bqsr_no_spark = Channel.empty()
                                     ^^^^^^^
```
Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:247:29: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_table_bqsr = Channel.empty().mix(
                            ^^^^^^^
```

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:250:58: Parameter was not used -- prefix with _ to suppress warning

            reports = reports.mix(ch_table_bqsr.collect{ meta, table -> table })
                                                         ^^^^

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:269:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                bam:  it[0].data_type == "bam"
                      ^^
```
Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:270:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                cram: it[0].data_type == "cram"
                      ^^
```

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:274:67: Parameter was not used -- prefix with _ to suppress warning

            input_only_table = input_recal_convert.bam.map{ meta, bam, bai, table -> [ meta, table ] }
                                                                  ^^^

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:274:72: Parameter was not used -- prefix with _ to suppress warning

            input_only_table = input_recal_convert.bam.map{ meta, bam, bai, table -> [ meta, table ] }
                                                                       ^^^

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:275:77: Parameter was not used -- prefix with _ to suppress warning

            input_only_bam   = input_recal_convert.bam.map{ meta, bam, bai, table -> [ meta, bam, bai ] }
                                                                            ^^^^^

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:281:30: The use of Channel to access channel factories is deprecated -- use channel instead
```
            cram_applybqsr = Channel.empty().mix(
                             ^^^^^^^
```
Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:289:45: The use of Channel to access channel factories is deprecated -- use channel instead
```
            cram_variant_calling_no_spark = Channel.empty()
                                            ^^^^^^^
```
Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:304:36: The use of Channel to access channel factories is deprecated -- use channel instead
```
            cram_variant_calling = Channel.empty().mix(
                                   ^^^^^^^
```

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:313:70: Parameter was not used -- prefix with _ to suppress warning

            reports = reports.mix(CRAM_QC_RECAL.out.reports.collect{ meta, report -> report })
                                                                     ^^^^

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:325:33: The use of Channel to access channel factories is deprecated -- use channel instead
```
            csv_recalibration = Channel.empty()
                                ^^^^^^^
```
Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:336:36: The use of Channel to access channel factories is deprecated -- use channel instead
```
            cram_variant_calling = Channel.empty().mix(
                                   ^^^^^^^
```

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:338:65: Parameter was not used -- prefix with _ to suppress warning

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

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:342:36: The use of Channel to access channel factories is deprecated -- use channel instead

            cram_variant_calling = Channel.empty().mix(ch_cram_for_bam_baserecalibrator)
                                   ^^^^^^^

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:351:19: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            bam:  it[0].data_type == "bam"
                  ^^
```
Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:352:19: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            cram: it[0].data_type == "cram"
                  ^^
```

Warning: subworkflows/local/bam_gatk_preprocessing/main.nf:361:32: The use of Channel to access channel factories is deprecated -- use channel instead

        cram_variant_calling = Channel.empty().mix(converted, input_variant_calling_convert.cram)
                               ^^^^^^^

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_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_splitncigarreads/main.nf:19:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling/main.nf:36:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
    reports   = Channel.empty()
                ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling/main.nf:37:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions  = Channel.empty()
                ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling/main.nf:40:43: The use of Channel to access channel factories is deprecated -- use channel instead
```
            cram_variant_calling_pair   = Channel.empty()
                                          ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling/main.nf:42:43: The use of Channel to access channel factories is deprecated -- use channel instead
```
            contamination_table_mutect2 = Channel.empty()
                                          ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling/main.nf:43:43: The use of Channel to access channel factories is deprecated -- use channel instead
```
            segmentation_table_mutect2  = Channel.empty()
                                          ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling/main.nf:44:43: The use of Channel to access channel factories is deprecated -- use channel instead
```
            artifact_priors_mutect2     = Channel.empty()
                                          ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling/main.nf:52:25: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                normal: it[0].status == 0
                        ^^
```

Warning: subworkflows/local/bam_variant_calling/main.nf:53:25: Implicit closure parameter is deprecated, declare an explicit parameter instead

                tumor:  it[0].status >= 1  // DNA and RNA should NOT have same sample id
                        ^^

Warning: subworkflows/local/bam_variant_calling/main.nf:76:13: Variable was declared but not used

            cram_variant_calling_tumor_only = cram_variant_calling_tumor_filtered.transpose().map{ it -> [it[1], it[2], it[3]] }
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Warning: subworkflows/local/bam_variant_calling/main.nf:133:43: The use of Channel to access channel factories is deprecated -- use channel instead

            vcf_to_normalise            = Channel.empty().mix(BAM_VARIANT_CALLING_SOMATIC.out.vcf_all)
                                          ^^^^^^^

Warning: subworkflows/local/bam_variant_calling/main.nf:134:43: The use of Channel to access channel factories is deprecated -- use channel instead

            contamination_table_mutect2 = Channel.empty().mix(BAM_VARIANT_CALLING_SOMATIC.out.contamination_table_mutect2)
                                          ^^^^^^^

Warning: subworkflows/local/bam_variant_calling/main.nf:135:43: The use of Channel to access channel factories is deprecated -- use channel instead

            segmentation_table_mutect2  = Channel.empty().mix(BAM_VARIANT_CALLING_SOMATIC.out.segmentation_table_mutect2)
                                          ^^^^^^^

Warning: subworkflows/local/bam_variant_calling/main.nf:136:43: The use of Channel to access channel factories is deprecated -- use channel instead

            artifact_priors_mutect2     = Channel.empty().mix(BAM_VARIANT_CALLING_SOMATIC.out.artifact_priors_mutect2)
                                          ^^^^^^^

Warning: subworkflows/local/bam_variant_calling/main.nf:148:84: Parameter was not used -- prefix with _ to suppress warning

        reports = reports.mix(VCF_QC_BCFTOOLS_VCFTOOLS.out.bcftools_stats.collect{ meta, stats -> stats })
                                                                                   ^^^^

Warning: subworkflows/local/bam_variant_calling/main.nf:149:90: Parameter was not used -- prefix with _ to suppress warning

        reports = reports.mix(VCF_QC_BCFTOOLS_VCFTOOLS.out.vcftools_tstv_counts.collect{ meta, counts -> counts })
                                                                                         ^^^^

Warning: subworkflows/local/bam_variant_calling/main.nf:150:88: Parameter was not used -- prefix with _ to suppress warning

        reports = reports.mix(VCF_QC_BCFTOOLS_VCFTOOLS.out.vcftools_tstv_qual.collect{ meta, qual -> qual })
                                                                                       ^^^^

Warning: subworkflows/local/bam_variant_calling/main.nf:151:93: Parameter was not used -- prefix with _ to suppress warning

        reports = reports.mix(VCF_QC_BCFTOOLS_VCFTOOLS.out.vcftools_filter_summary.collect{ meta, summary -> summary })
                                                                                            ^^^^

Warning: subworkflows/local/bam_variant_calling/main.nf:155:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
        cram_variant_calling_pair   = Channel.empty()
                                      ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling/main.nf:156:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
        vcf_to_normalise            = Channel.empty()
                                      ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling/main.nf:157:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
        contamination_table_mutect2 = Channel.empty()
                                      ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling/main.nf:158:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
        segmentation_table_mutect2  = Channel.empty()
                                      ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling/main.nf:159:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
        artifact_priors_mutect2     = Channel.empty()
                                      ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_pre_post_processing/main.nf:27:5: Parameter was not used -- prefix with _ to suppress warning
```
    dbsnp                           // channel: [optional]  germline_resource
    ^^^^^
```
Warning: subworkflows/local/bam_variant_calling_pre_post_processing/main.nf:28:5: Parameter was not used -- prefix with _ to suppress warning
```
    dbsnp_tbi                       // channel: [optional]  germline_resource_tbi
    ^^^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_pre_post_processing/main.nf:48:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
    reports   = Channel.empty()
                ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_pre_post_processing/main.nf:49:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions  = Channel.empty()
                ^^^^^^^
```

Warning: subworkflows/local/bam_variant_calling_pre_post_processing/main.nf:89:5: Variable was declared but not used

    cram_variant_calling_pair     = BAM_VARIANT_CALLING.out.cram_variant_calling_pair  // use same crams for force calling later
    ^^^^^^^^^^^^^^^^^^^^^^^^^

Warning: subworkflows/local/bam_variant_calling_pre_post_processing/main.nf:91:5: Variable was declared but not used

    contamination                 = BAM_VARIANT_CALLING.out.contamination_table
    ^^^^^^^^^^^^^

Warning: subworkflows/local/bam_variant_calling_pre_post_processing/main.nf:92:5: Variable was declared but not used

    segmentation                  = BAM_VARIANT_CALLING.out.segmentation_table
    ^^^^^^^^^^^^

Warning: subworkflows/local/bam_variant_calling_pre_post_processing/main.nf:93:5: Variable was declared but not used

    orientation                   = BAM_VARIANT_CALLING.out.artifact_priors
    ^^^^^^^^^^^

Warning: subworkflows/local/bam_variant_calling_somatic/main.nf:20:5: Parameter was not used -- prefix with _ to suppress warning

    intervals_bed_combined        // channel: [mandatory] intervals/target regions in one file unzipped
    ^^^^^^^^^^^^^^^^^^^^^^

Warning: subworkflows/local/bam_variant_calling_somatic/main.nf:29:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions          = Channel.empty()
                        ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic/main.nf:31:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf_manta         = Channel.empty()
                        ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic/main.nf:32:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf_strelka       = Channel.empty()
                        ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic/main.nf:33:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf_mutect2       = Channel.empty()
                        ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic/main.nf:34:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf_sage          = Channel.empty()
                        ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic/main.nf:84:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
        vcf_strelka = Channel.empty().mix(BAM_VARIANT_CALLING_SOMATIC_STRELKA.out.vcf)
                      ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic/main.nf:115:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
        contamination_table_mutect2 = Channel.empty()
                                      ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic/main.nf:116:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
        segmentation_table_mutect2  = Channel.empty()
                                      ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic/main.nf:117:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
        artifact_priors_mutect2     = Channel.empty()
                                      ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic/main.nf:122:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf_all = Channel.empty().mix(
              ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_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:37:11: 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_mutect2/main.nf:32:16: 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:35:80: The use of Channel to access channel factories is deprecated -- use channel instead

    germline_resource_pileup     = germline_resource_tbi ? germline_resource : Channel.empty()
                                                                               ^^^^^^^

Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:36:61: The use of Channel to access channel factories is deprecated -- use channel instead
```
    germline_resource_pileup_tbi = germline_resource_tbi ?: Channel.empty()
                                                            ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:67:23: 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:68:23: 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:74:23: 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: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_somatic_mutect2/main.nf:81:23: 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:82:23: 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:88:23: 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:89:23: 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:101:11: 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 ->
          ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:104:11: 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->
          ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:107:13: 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 ->
            ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:110:12: 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->
           ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:137:27: 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:138:27: 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:144:27: 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:145:27: 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:157:31: 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:158:31: 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:175:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_seg_to_filtermutectcalls = Channel.empty()
                                      ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:176:40: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_cont_to_filtermutectcalls = Channel.empty()
                                       ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:209:40: The use of Channel to access channel factories is deprecated -- use channel instead
```
        artifact_priors              = Channel.empty()
                                       ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:210:40: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_cont_to_filtermutectcalls = Channel.empty()
                                       ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:211:40: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_seg_to_filtermutectcalls  = Channel.empty()
                                       ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:212:40: The use of Channel to access channel factories is deprecated -- use channel instead
```
        pileup_table_normal          = Channel.empty()
                                       ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:213:40: The use of Channel to access channel factories is deprecated -- use channel instead
```
        pileup_table_tumor           = Channel.empty()
                                       ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_sage/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_sage/main.nf:26:50: The use of Channel to access channel factories is deprecated -- use channel instead
```
    if (!params.sage_ensembl_dir) sage_ensembl = Channel.value([])
                                                 ^^^^^^^
```

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

        UNTAR_SAGE_ENSEMBL(Channel.fromPath(params.sage_ensembl_dir).collect().map{ it -> [ [ id:it[0].baseName ], it ] })
                           ^^^^^^^

Warning: subworkflows/local/bam_variant_calling_somatic_sage/main.nf:32:28: The use of Channel to access channel factories is deprecated -- use channel instead

        UNZIP_SAGE_ENSEMBL(Channel.fromPath(params.sage_ensembl_dir).collect().map{ it -> [ [ id:it[0].baseName ], it ] })
                           ^^^^^^^

Warning: subworkflows/local/bam_variant_calling_somatic_sage/main.nf:36:24: The use of Channel to access channel factories is deprecated -- use channel instead

        sage_ensembl = Channel.fromPath(params.sage_ensembl_dir).collect().map{ it -> [ [ id:it[0].baseName ], it ] }
                       ^^^^^^^

Warning: subworkflows/local/bam_variant_calling_somatic_sage/main.nf:47:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.sage_highconfidence).collect().map{ it -> [ [ id:it[0].baseName ], it ] },
        ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_sage/main.nf:48:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.sage_actionablepanel).collect().map{ it -> [ [ id:it[0].baseName ], it ] },
        ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_sage/main.nf:49:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.sage_knownhotspots).collect().map{ it -> [ [ id:it[0].baseName ], it ] },
        ^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_sage/main.nf:57:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        intervals:    it[0].num_intervals > 1
                      ^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_sage/main.nf:58:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        no_intervals: it[0].num_intervals <= 1
                      ^^
```

Warning: subworkflows/local/bam_variant_calling_somatic_sage/main.nf:71:26: Parameter was not used -- prefix with _ to suppress warning

        .map{ meta, vcf, tbi -> [ meta - meta.subMap('normal_id', 'tumor_id','num_intervals') + [ variantcaller:'sage' ], vcf ] }
                         ^^^

Warning: subworkflows/local/bam_variant_calling_somatic_strelka/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_strelka/main.nf:28:93: Parameter was not used -- prefix with _ to suppress warning

        .map{ meta, normal_cram, normal_crai, tumor_cram, tumor_crai, manta_vcf, manta_tbi, intervals_gz_tbi, num_intervals -> [ meta + [ num_intervals:0 ], normal_cram, normal_crai, tumor_cram, tumor_crai, manta_vcf, manta_tbi, [], [] ] }
                                                                                            ^^^^^^^^^^^^^^^^

Warning: subworkflows/local/bam_variant_calling_somatic_strelka/main.nf:28:111: Parameter was not used -- prefix with _ to suppress warning

        .map{ meta, normal_cram, normal_crai, tumor_cram, tumor_crai, manta_vcf, manta_tbi, intervals_gz_tbi, num_intervals -> [ meta + [ num_intervals:0 ], normal_cram, normal_crai, tumor_cram, tumor_crai, manta_vcf, manta_tbi, [], [] ] }
                                                                                                              ^^^^^^^^^^^^^

Warning: subworkflows/local/bam_variant_calling_somatic_strelka/main.nf:37:5: Variable was declared but not used
```
    vcf_indels = STRELKA_SOMATIC.out.vcf_indels.branch{
    ^^^^^^^^^^
```
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:44:5: Variable was declared but not used
```
    vcf_snvs = STRELKA_SOMATIC.out.vcf_snvs.branch{
    ^^^^^^^^
```
Warning: subworkflows/local/bam_variant_calling_somatic_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_somatic_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/channel_baserecalibrator_create_csv/main.nf:8:9: Parameter was not used -- prefix with _ to suppress warning
```
        tools
        ^^^^^
```
Warning: subworkflows/local/cram_merge_index_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: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:23:42: Parameter was not used -- prefix with _ to suppress warning

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

Warning: subworkflows/local/fastq_align/main.nf:19:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/fastq_align/main.nf:20:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
    reports = Channel.empty()
              ^^^^^^^
```
Warning: subworkflows/local/fastq_align/main.nf:29:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
    bam = Channel.empty()
          ^^^^^^^
```
Warning: subworkflows/local/maf_filtering/main.nf:17:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions  = Channel.empty()
                ^^^^^^^
```
Warning: subworkflows/local/maf_filtering/main.nf:18:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
    maf       = Channel.empty()
                ^^^^^^^
```
Warning: subworkflows/local/maf_rna_filtering/main.nf:15:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:43:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:47:25: The use of Channel to access channel factories is deprecated -- use channel instead

        UNBGZIP_FASTA ( Channel.fromPath(params.fasta).collect().map{ fa -> [ [ id:fa.baseName[0] - ~/\.fa(sta)?$/ ], fa ] } )
                        ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:71:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
        bwa        = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:72:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
        bwamem2    = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:73:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
        hashtable  = Channel.empty()
                     ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:96:21: The use of Channel to access channel factories is deprecated -- use channel instead

                    Channel.fromPath(params.gtf).map{ it -> [[id:it[0].baseName], it] }
                    ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:101:26: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_gtf = Channel.fromPath(params.gtf).collect().map{gtf -> [[id:"gtf"], gtf]}
                         ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:106:21: The use of Channel to access channel factories is deprecated -- use channel instead

                    Channel.fromPath(params.gff).map{ it -> [[id:it[0].baseName], it] }
                    ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:111:26: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_gff = Channel.fromPath(params.gff).collect().map{gff -> [[id:"gff"], gff]}
                         ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:130:21: The use of Channel to access channel factories is deprecated -- use channel instead

                    Channel.fromPath(params.star_index).map{ it -> [[id:it[0].baseName], it] }
                    ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:135:33: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_star_index = Channel.fromPath(params.star_index).collect().map{star_index -> [[id:"star_index"], star_index]}
                                ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:148:35: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_splicesites  = Channel.fromPath(params.splicesites).collect().map{ it -> [ [ id:'null' ], it ]}
                                  ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:156:36: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_hisat2_index  = Channel.fromPath(params.hisat2_index).collect().map{it -> [ [ id:"hisat2_index" ], it ]}
                                   ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:171:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_star_index   = Channel.empty()
                          ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:172:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_gtf          = Channel.empty()
                          ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:173:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_hisat2_index = Channel.empty()
                          ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:174:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_splicesites  = Channel.value([])
                          ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:191:58: Parameter was not used -- prefix with _ to suppress warning

        dbsnp_tbi             = TABIX_DBSNP.out.tbi.map{ meta, tbi -> [tbi] }.collect()               // path: dbsnb.vcf.gz.tbi
                                                         ^^^^

Warning: subworkflows/local/prepare_genome/main.nf:194:61: Parameter was not used -- prefix with _ to suppress warning

        fasta_fai             = SAMTOOLS_FAIDX.out.fai.map{ meta, fai -> [fai] }                      // path: genome.fasta.fai
                                                            ^^^^

Warning: subworkflows/local/prepare_genome/main.nf:195:70: Parameter was not used -- prefix with _ to suppress warning

        germline_resource_tbi = TABIX_GERMLINE_RESOURCE.out.tbi.map{ meta, tbi -> [tbi] }.collect()   // path: germline_resource.vcf.gz.tbi
                                                                     ^^^^

Warning: subworkflows/local/prepare_genome/main.nf:196:63: Parameter was not used -- prefix with _ to suppress warning

        known_snps_tbi        = TABIX_KNOWN_SNPS.out.tbi.map{ meta, tbi -> [tbi] }.collect()          // path: {known_indels*}.vcf.gz.tbi
                                                              ^^^^

Warning: subworkflows/local/prepare_genome/main.nf:197:65: Parameter was not used -- prefix with _ to suppress warning

        known_indels_tbi      = TABIX_KNOWN_INDELS.out.tbi.map{ meta, tbi -> [tbi] }.collect()        // path: {known_indels*}.vcf.gz.tbi
                                                                ^^^^

Warning: subworkflows/local/prepare_genome/main.nf:198:56: Parameter was not used -- prefix with _ to suppress warning

        pon_tbi               = TABIX_PON.out.tbi.map{ meta, tbi -> [tbi] }.collect()                 // path: pon.vcf.gz.tbi
                                                       ^^^^

Warning: subworkflows/local/prepare_realignment/main.nf:24:9: Parameter was not used -- prefix with _ to suppress warning
```
        dict
        ^^^^
```
Warning: subworkflows/local/prepare_realignment/main.nf:31:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
        versions   = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/prepare_realignment/main.nf:32:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
        bam_mapped = Channel.empty()
                     ^^^^^^^
```

Warning: subworkflows/local/prepare_realignment/main.nf:39:52: Implicit closure parameter is deprecated, declare an explicit parameter instead

                                        norealign: it[0].status == 1
                                                   ^^

Warning: subworkflows/local/prepare_realignment/main.nf:40:52: Implicit closure parameter is deprecated, declare an explicit parameter instead

                                        realign:   it[0].status == 2 || it[0].status == 0
                                                   ^^

Warning: subworkflows/local/prepare_realignment/main.nf:40:73: Implicit closure parameter is deprecated, declare an explicit parameter instead

                                        realign:   it[0].status == 2 || it[0].status == 0
                                                                        ^^

Warning: subworkflows/local/prepare_realignment/main.nf:45:54: Implicit closure parameter is deprecated, declare an explicit parameter instead

                                        isconsensus: it[0].consensus == true
                                                     ^^

Warning: subworkflows/local/prepare_realignment/main.nf:46:54: Implicit closure parameter is deprecated, declare an explicit parameter instead

                                        noconsensus: it[0].consensus == false
                                                     ^^

Warning: subworkflows/local/prepare_realignment/main.nf:63:52: Implicit closure parameter is deprecated, declare an explicit parameter instead

                                        norealign: it[0].status == 1
                                                   ^^

Warning: subworkflows/local/prepare_realignment/main.nf:64:52: Implicit closure parameter is deprecated, declare an explicit parameter instead

                                        realign:   it[0].status == 2 || it[0].status == 0
                                                   ^^

Warning: subworkflows/local/prepare_realignment/main.nf:64:73: Implicit closure parameter is deprecated, declare an explicit parameter instead

                                        realign:   it[0].status == 2 || it[0].status == 0
                                                                        ^^

Warning: subworkflows/local/prepare_realignment/main.nf:67:52: Implicit closure parameter is deprecated, declare an explicit parameter instead

                                        norealign: it[0].status == 1
                                                   ^^

Warning: subworkflows/local/prepare_realignment/main.nf:68:52: Implicit closure parameter is deprecated, declare an explicit parameter instead

                                        realign:   it[0].status == 2 || it[0].status == 0
                                                   ^^

Warning: subworkflows/local/prepare_realignment/main.nf:68:73: Implicit closure parameter is deprecated, declare an explicit parameter instead

                                        realign:   it[0].status == 2 || it[0].status == 0
                                                                        ^^

Warning: subworkflows/local/prepare_realignment/main.nf:138:44: Parameter was not used -- prefix with _ to suppress warning

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

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:11:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:14:54: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:14:116: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:15:54: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:15:116: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:16:54: The use of Channel to access channel factories is deprecated -- use channel instead

    fasta              = params.fasta              ? Channel.fromPath(params.fasta).collect()                    : Channel.empty()
                                                     ^^^^^^^

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:16:116: The use of Channel to access channel factories is deprecated -- use channel instead

    fasta              = params.fasta              ? Channel.fromPath(params.fasta).collect()                    : Channel.empty()
                                                                                                                   ^^^^^^^

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:17:54: The use of Channel to access channel factories is deprecated -- use channel instead

    germline_resource  = params.germline_resource  ? Channel.fromPath(params.germline_resource).collect()        : Channel.value([]) //Mutec2 does not require a germline resource, so set to optional input
                                                     ^^^^^^^

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:17:116: The use of Channel to access channel factories is deprecated -- use channel instead

    germline_resource  = params.germline_resource  ? Channel.fromPath(params.germline_resource).collect()        : Channel.value([]) //Mutec2 does not require a germline resource, so set to optional input
                                                                                                                   ^^^^^^^

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:18:54: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:18:116: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:19:54: The use of Channel to access channel factories is deprecated -- use channel instead

    pon                = params.pon                ? Channel.fromPath(params.pon).collect()                      : Channel.value([]) //PON is optional for Mutect2 (but highly recommended)
                                                     ^^^^^^^

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:19:116: The use of Channel to access channel factories is deprecated -- use channel instead

    pon                = params.pon                ? Channel.fromPath(params.pon).collect()                      : Channel.value([]) //PON is optional for Mutect2 (but highly recommended)
                                                                                                                   ^^^^^^^

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:20:5: Variable was declared but not used

    whitelist          = params.whitelist          ? Channel.fromPath(params.whitelist).collect()                : Channel.value([]) // whitelist optional for filtering
    ^^^^^^^^^

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:20:54: The use of Channel to access channel factories is deprecated -- use channel instead

    whitelist          = params.whitelist          ? Channel.fromPath(params.whitelist).collect()                : Channel.value([]) // whitelist optional for filtering
                                                     ^^^^^^^

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:20:116: The use of Channel to access channel factories is deprecated -- use channel instead

    whitelist          = params.whitelist          ? Channel.fromPath(params.whitelist).collect()                : Channel.value([]) // whitelist optional for filtering
                                                                                                                   ^^^^^^^

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:34:99: The use of Channel to access channel factories is deprecated -- use channel instead

    bwa                    = params.fasta                   ? params.bwa                        ? Channel.fromPath(params.bwa).collect()                           : PREPARE_GENOME.out.bwa                   : []
                                                                                                  ^^^^^^^

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:35:99: The use of Channel to access channel factories is deprecated -- use channel instead

    bwamem2                = params.fasta                   ? params.bwamem2                    ? Channel.fromPath(params.bwamem2).collect()                       : PREPARE_GENOME.out.bwamem2               : []
                                                                                                  ^^^^^^^

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:36:99: The use of Channel to access channel factories is deprecated -- use channel instead

    dragmap                = params.fasta                   ? params.dragmap                    ? Channel.fromPath(params.dragmap).collect()                       : PREPARE_GENOME.out.hashtable             : []
                                                                                                  ^^^^^^^

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:37:99: The use of Channel to access channel factories is deprecated -- use channel instead

    hisat2_index           = params.fasta                   ? params.hisat2_index               ? Channel.fromPath(params.hisat2_index).map{ it -> [ [id:'ht_idx'], it ] }.collect()                          : PREPARE_GENOME.out.hisat2_index : []
                                                                                                  ^^^^^^^

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:38:99: The use of Channel to access channel factories is deprecated -- use channel instead

    splicesites            = params.fasta                   ? params.splicesites                ? Channel.fromPath(params.splicesites).collect()                   : PREPARE_GENOME.out.splicesites           : []
                                                                                                  ^^^^^^^

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:39:63: The use of Channel to access channel factories is deprecated -- use channel instead

    dict                   = params.dict                    ? Channel.fromPath(params.dict).map{ it -> [ [id:'dict'], it ] }.collect()                             : PREPARE_GENOME.out.dict
                                                              ^^^^^^^

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:40:99: The use of Channel to access channel factories is deprecated -- use channel instead

    fasta_fai              = params.fasta                   ? params.fasta_fai                  ? Channel.fromPath(params.fasta_fai).collect()                     : PREPARE_GENOME.out.fasta_fai             : []
                                                                                                  ^^^^^^^

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:41:99: The use of Channel to access channel factories is deprecated -- use channel instead

    dbsnp_tbi              = params.dbsnp                   ? params.dbsnp_tbi                  ? Channel.fromPath(params.dbsnp_tbi).collect()                     : PREPARE_GENOME.out.dbsnp_tbi             : Channel.value([])
                                                                                                  ^^^^^^^

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:41:209: The use of Channel to access channel factories is deprecated -- use channel instead

    dbsnp_tbi              = params.dbsnp                   ? params.dbsnp_tbi                  ? Channel.fromPath(params.dbsnp_tbi).collect()                     : PREPARE_GENOME.out.dbsnp_tbi             : Channel.value([])
                                                                                                                                                                                                                ^^^^^^^

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:42:99: The use of Channel to access channel factories is deprecated -- use channel instead

    germline_resource_tbi  = params.germline_resource       ? params.germline_resource_tbi      ? Channel.fromPath(params.germline_resource_tbi).collect()         : PREPARE_GENOME.out.germline_resource_tbi : []
                                                                                                  ^^^^^^^

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:43:99: The use of Channel to access channel factories is deprecated -- use channel instead

    known_indels_tbi       = params.known_indels            ? params.known_indels_tbi           ? Channel.fromPath(params.known_indels_tbi).collect()              : PREPARE_GENOME.out.known_indels_tbi      : Channel.value([])
                                                                                                  ^^^^^^^

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:43:209: The use of Channel to access channel factories is deprecated -- use channel instead

    known_indels_tbi       = params.known_indels            ? params.known_indels_tbi           ? Channel.fromPath(params.known_indels_tbi).collect()              : PREPARE_GENOME.out.known_indels_tbi      : Channel.value([])
                                                                                                                                                                                                                ^^^^^^^

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:44:99: The use of Channel to access channel factories is deprecated -- use channel instead

    known_snps_tbi         = params.known_snps              ? params.known_snps_tbi             ? Channel.fromPath(params.known_snps_tbi).collect()                : PREPARE_GENOME.out.known_snps_tbi        : Channel.value([])
                                                                                                  ^^^^^^^

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:44:209: The use of Channel to access channel factories is deprecated -- use channel instead

    known_snps_tbi         = params.known_snps              ? params.known_snps_tbi             ? Channel.fromPath(params.known_snps_tbi).collect()                : PREPARE_GENOME.out.known_snps_tbi        : Channel.value([])
                                                                                                                                                                                                                ^^^^^^^

Warning: subworkflows/local/prepare_reference_and_intervals/main.nf:45:99: The use of Channel to access channel factories is deprecated -- use channel instead

    pon_tbi                = params.pon                     ? params.pon_tbi                    ? Channel.fromPath(params.pon_tbi).collect()                       : PREPARE_GENOME.out.pon_tbi               : []
                                                                                                  ^^^^^^^

Warning: subworkflows/local/samplesheet_to_channel/main.nf:24:16: Parameter was not used -- prefix with _ to suppress warning
```
        .map { patient_sample, num_lanes, ch_items ->
               ^^^^^^^^^^^^^^
```

Warning: subworkflows/local/samplesheet_to_channel/main.nf:164:30: Implicit closure parameter is deprecated, declare an explicit parameter instead

        input_sample.filter{ it[0].status == 1 | it[0].status == 2 }.ifEmpty{ // In this case, the sample-sheet contains no tumor-samples
                             ^^

Warning: subworkflows/local/samplesheet_to_channel/main.nf:164:50: Implicit closure parameter is deprecated, declare an explicit parameter instead

        input_sample.filter{ it[0].status == 1 | it[0].status == 2 }.ifEmpty{ // In this case, the sample-sheet contains no tumor-samples
                                                 ^^

Warning: subworkflows/local/samplesheet_to_channel/main.nf:176:30: Implicit closure parameter is deprecated, declare an explicit parameter instead

        input_sample.filter{ it[0].status == 0 }.ifEmpty{ // In this case, the sample-sheet contains no normal/germline-samples
                             ^^

Warning: subworkflows/local/samplesheet_to_channel/main.nf:245:68: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: subworkflows/local/utils_nfcore_rnadnavar_pipeline/main.nf:40:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_rnadnavar_pipeline/main.nf:99:9: Variable was declared but not used
```
    def checkPathParamList = [
        ^^^^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_rnadnavar_pipeline/main.nf:129:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ? Channel.empty()
          ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_rnadnavar_pipeline/main.nf:131:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ? Channel.fromList(samplesheetToList(input, "${projectDir}/assets/schema_input.json"))
              ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_rnadnavar_pipeline/main.nf:132:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
            : Channel.fromList(samplesheetToList(params.input_restart, "${projectDir}/assets/schema_input.json"))
              ^^^^^^^
```
Warning: subworkflows/local/vcf_annotate/main.nf:18:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    reports  = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/vcf_annotate/main.nf:19:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf_ann  = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/vcf_annotate/main.nf:20:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    tab_ann  = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/vcf_annotate/main.nf:21:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    json_ann = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/vcf_annotate/main.nf:22:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```

Warning: subworkflows/local/vcf_annotate/main.nf:29:63: The use of Channel to access channel factories is deprecated -- use channel instead

            vep_cache_version  = params.vep_cache_version  ?: Channel.empty()
                                                              ^^^^^^^

Warning: subworkflows/local/vcf_annotate/main.nf:30:63: The use of Channel to access channel factories is deprecated -- use channel instead

            vep_genome         = params.vep_genome         ?: Channel.empty()
                                                              ^^^^^^^

Warning: subworkflows/local/vcf_annotate/main.nf:31:63: The use of Channel to access channel factories is deprecated -- use channel instead

            vep_species        = params.vep_species        ?: Channel.empty()
                                                              ^^^^^^^

Warning: subworkflows/local/vcf_consensus/main.nf:23:31: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions                = Channel.empty()
                              ^^^^^^^
```
Warning: subworkflows/local/vcf_consensus/main.nf:25:31: The use of Channel to access channel factories is deprecated -- use channel instead
```
    maf_from_consensus_dna  = Channel.empty()
                              ^^^^^^^
```
Warning: subworkflows/local/vcf_consensus/main.nf:26:31: The use of Channel to access channel factories is deprecated -- use channel instead
```
    mafs_from_varcal_dna    = Channel.empty()
                              ^^^^^^^
```
Warning: subworkflows/local/vcf_consensus/main.nf:27:31: The use of Channel to access channel factories is deprecated -- use channel instead
```
    consensus_maf           = Channel.empty()
                              ^^^^^^^
```

Warning: subworkflows/local/vcf_consensus/main.nf:38:38: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: subworkflows/local/vcf_consensus/main.nf:39:38: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: subworkflows/local/vcf_consensus/main.nf:45:69: Implicit closure parameter is deprecated, declare an explicit parameter instead

            tools_list = params.tools.split(',').toList().findAll { it in ['sage', 'strelka', 'mutect2'] }.unique()
                                                                    ^^

Warning: subworkflows/local/vcf_consensus/main.nf:68:38: Implicit closure parameter is deprecated, declare an explicit parameter instead

                                dna: it[0].status <= 1
                                     ^^

Warning: subworkflows/local/vcf_consensus/main.nf:69:38: Implicit closure parameter is deprecated, declare an explicit parameter instead

                                rna: it[0].status == 2
                                     ^^

Warning: subworkflows/local/vcf_consensus/main.nf:73:38: Implicit closure parameter is deprecated, declare an explicit parameter instead

                                dna: it[0].status <= 1
                                     ^^

Warning: subworkflows/local/vcf_consensus/main.nf:74:38: Implicit closure parameter is deprecated, declare an explicit parameter instead

                                rna: it[0].status == 2
                                     ^^

Warning: subworkflows/local/vcf_consensus/main.nf:145:13: Variable was declared but not used

            mafs_to_rescue = mafs_dna_crossed_with_rna_rescue.mix(mafs_rna_crossed_with_dna_rescue)
            ^^^^^^^^^^^^^^

Warning: subworkflows/local/vcf_consensus/main.nf:149:38: Implicit closure parameter is deprecated, declare an explicit parameter instead

                                dna: it[0].status <= 1
                                     ^^

Warning: subworkflows/local/vcf_consensus/main.nf:150:38: Implicit closure parameter is deprecated, declare an explicit parameter instead

                                rna: it[0].status == 2
                                     ^^

Warning: subworkflows/local/vcf_consensus/main.nf:154:13: Variable was declared but not used

            run_rescue_out = RUN_CONSENSUS_RESCUE.out.maf.branch{
            ^^^^^^^^^^^^^^

Warning: subworkflows/local/vcf_consensus/main.nf:155:31: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                intervals:    it[0].num_intervals > 1
                              ^^
```

Warning: subworkflows/local/vcf_consensus/main.nf:156:31: Implicit closure parameter is deprecated, declare an explicit parameter instead

                no_intervals: it[0].num_intervals <= 1
                              ^^

Warning: subworkflows/local/vcf_consensus/main.nf:179:38: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: subworkflows/local/vcf_consensus/main.nf:180:38: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: subworkflows/local/vcf_normalize/main.nf:22:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    version          = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/local/vcf_normalize/main.nf:32:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
        vcf_decomposed  = Channel.empty()
                          ^^^^^^^
```
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/nf-core/bam_sort_stats_samtools/main.nf:16:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/nf-core/bam_stats_samtools/main.nf:15:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_align_hisat2/main.nf:14:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_align_star/main.nf:20:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf:19:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: workflows/rnadnavar/main.nf:54:5: Parameter was not used -- prefix with _ to suppress warning
```
    ch_samplesheet // channel: samplesheet read in from --input
    ^^^^^^^^^^^^^^
```
Warning: workflows/rnadnavar/main.nf:58:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_files = Channel.empty()
                       ^^^^^^^
```
Warning: workflows/rnadnavar/main.nf:59:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    multiqc_report = Channel.empty()
                     ^^^^^^^
```
Warning: workflows/rnadnavar/main.nf:60:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
    reports = Channel.empty()
              ^^^^^^^
```
Warning: workflows/rnadnavar/main.nf:62:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```

Warning: workflows/rnadnavar/main.nf:66:57: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_from_samplesheet = params.build_only_index ? Channel.empty() : Channel.fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
                                                        ^^^^^^^

Warning: workflows/rnadnavar/main.nf:66:75: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_from_samplesheet = params.build_only_index ? Channel.empty() : Channel.fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
                                                                          ^^^^^^^

Warning: workflows/rnadnavar/main.nf:69:57: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_from_samplesheet = params.build_only_index ? Channel.empty() : Channel.fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
                                                        ^^^^^^^

Warning: workflows/rnadnavar/main.nf:69:75: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_from_samplesheet = params.build_only_index ? Channel.empty() : Channel.fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
                                                                          ^^^^^^^

Warning: workflows/rnadnavar/main.nf:78:5: Variable was declared but not used

    multiqc_config = Channel.fromPath("${projectDir}/assets/multiqc_config.yml", checkIfExists: true)
    ^^^^^^^^^^^^^^

Warning: workflows/rnadnavar/main.nf:78:22: The use of Channel to access channel factories is deprecated -- use channel instead

    multiqc_config = Channel.fromPath("${projectDir}/assets/multiqc_config.yml", checkIfExists: true)
                     ^^^^^^^

Warning: workflows/rnadnavar/main.nf:79:5: Variable was declared but not used

    multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
    ^^^^^^^^^^^^^^^^^^^^^

Warning: workflows/rnadnavar/main.nf:79:53: The use of Channel to access channel factories is deprecated -- use channel instead

    multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
                                                    ^^^^^^^

Warning: workflows/rnadnavar/main.nf:79:116: The use of Channel to access channel factories is deprecated -- use channel instead

    multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
                                                                                                                   ^^^^^^^

Warning: workflows/rnadnavar/main.nf:80:5: Variable was declared but not used

    multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
    ^^^^^^^^^^^^

Warning: workflows/rnadnavar/main.nf:80:42: The use of Channel to access channel factories is deprecated -- use channel instead

    multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
                                         ^^^^^^^

Warning: workflows/rnadnavar/main.nf:80:103: The use of Channel to access channel factories is deprecated -- use channel instead

    multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
                                                                                                      ^^^^^^^

Warning: workflows/rnadnavar/main.nf:85:27: 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: workflows/rnadnavar/main.nf:87:67: Parameter was not used -- prefix with _ to suppress warning

        vep_cache = ENSEMBLVEP_DOWNLOAD.out.cache.collect().map { meta, cache -> [cache] }
                                                                  ^^^^

Warning: workflows/rnadnavar/main.nf:91:25: The use of Channel to access channel factories is deprecated -- use channel instead

        UNZIP_VEP_CACHE(Channel.fromPath(params.vep_cache).collect().map { it -> [[id: it[0].baseName], it] })
                        ^^^^^^^

Warning: workflows/rnadnavar/main.nf:92:64: Implicit closure parameter is deprecated, declare an explicit parameter instead

        vep_cache = UNZIP_VEP_CACHE.out.unzipped_archive.map { it[1] }
                                                               ^^

Warning: workflows/rnadnavar/main.nf:131:5: Variable was declared but not used

    known_sites_snps = PREPARE_REFERENCE_AND_INTERVALS.out.known_sites_snps
    ^^^^^^^^^^^^^^^^

Warning: workflows/rnadnavar/main.nf:132:5: Variable was declared but not used

    known_sites_snps_tbi = PREPARE_REFERENCE_AND_INTERVALS.out.known_sites_snps_tbi
    ^^^^^^^^^^^^^^^^^^^^

Warning: workflows/rnadnavar/main.nf:209:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.empty(),
            ^^^^^^^
```
Warning: workflows/rnadnavar/main.nf:211:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.empty(),
            ^^^^^^^
```
Warning: workflows/rnadnavar/main.nf:241:34: The use of Channel to access channel factories is deprecated -- use channel instead
```
        realigned_filtered_maf = Channel.empty()
                                 ^^^^^^^
```
Warning: workflows/rnadnavar/main.nf:247:18: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            dna: it[0].status < 2
                 ^^
```
Warning: workflows/rnadnavar/main.nf:248:18: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            rna: it[0].status >= 2
                 ^^
```
Warning: workflows/rnadnavar/main.nf:251:18: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            dna: it[0].status < 2
                 ^^
```
Warning: workflows/rnadnavar/main.nf:252:18: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            rna: it[0].status >= 2
                 ^^
```
Warning: workflows/rnadnavar/main.nf:262:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
    version_yaml = Channel.empty()
                   ^^^^^^^
```

Warning: workflows/rnadnavar/main.nf:269:29: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_multiqc_config = Channel.fromPath("${projectDir}/assets/multiqc_config.yml", checkIfExists: true)
                            ^^^^^^^

Warning: workflows/rnadnavar/main.nf:270:60: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
                                                           ^^^^^^^

Warning: workflows/rnadnavar/main.nf:270:123: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
                                                                                                                          ^^^^^^^

Warning: workflows/rnadnavar/main.nf:271:49: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
                                                ^^^^^^^

Warning: workflows/rnadnavar/main.nf:271:110: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
                                                                                                             ^^^^^^^

Warning: workflows/rnadnavar/main.nf:273:31: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
                              ^^^^^^^

Warning: workflows/rnadnavar/main.nf:275:34: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
                                 ^^^^^^^

Warning: workflows/rnadnavar/main.nf:310:72: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

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