Nextflow lint results

Generated: 2026-01-27T00:17:45.425967157Z
Nextflow version: 25.12.0-edge
Summary: 7 errors, 115 warnings

❌ Errors

Error: conf/modules.config:282:17: Unexpected input: ':'

        withName: '.*:SOMATIC_SV:TABIX_SV_VCF' {
                ^

Error: nextflow.config:350:34: manifest is not defined

\033[0;35m  nf-core/pacsomatic ${manifest.version}\033[0m
                                 ^^^^^^^^

Error: nextflow.config:353:26: manifest is not defined

        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                         ^^^^^^^^

Error: nextflow.config:353:69: manifest is not defined

        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                                                                    ^^^^^^^^

Error: nextflow.config:353:186: manifest is not defined

        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                                                                                                                                                                                         ^^^^^^^^

Error: nextflow.config:362:22: validation is not defined

        beforeText = validation.help.beforeText
                     ^^^^^^^^^^

Error: nextflow.config:363:21: validation is not defined

        afterText = validation.help.afterText
                    ^^^^^^^^^^

⚠️ Warnings

Warning: modules/local/annotatr_dmr/main.nf:22:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/annotatr_dmr/main.nf:23:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/dss_dmr/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/dss_dmr/main.nf:22:9: Variable was declared but not used

    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^

Warning: modules/local/purple/main.nf:32:9: Variable was declared but not used

    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^

Warning: modules/local/purple/main.nf:87:9: Variable was declared but not used

    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^

Warning: modules/nf-core/bcftools/concat/main.nf:32:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def input = vcfs.sort{it.toString()}.join(" ")
                          ^^
```
Warning: modules/nf-core/bcftools/index/main.nf:23:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/nf-core/bcftools/index/main.nf:40:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```

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

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

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

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

Warning: modules/nf-core/clair3/main.nf:72:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/gunzip/main.nf:43:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/pbmm2/align/main.nf:41:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/pbtk/pbmerge/main.nf:38:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/severus/main.nf:59:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: nextflow.config:353:129: Implicit closure parameter is deprecated, declare an explicit parameter instead

        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                                                                                                                                ^^

Warning: subworkflows/local/cnv_calling/main.nf:19:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/germline_calling_phasing/main.nf:17:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/germline_calling_phasing/main.nf:53:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_phased_bam_bai = Channel.empty()
                        ^^^^^^^
```
Warning: subworkflows/local/germline_calling_phasing/main.nf:54:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_phased_vcf_tbi = Channel.empty()
                        ^^^^^^^
```

Warning: subworkflows/local/germline_calling_phasing/main.nf:73:25: Parameter was not used -- prefix with _ to suppress warning

            .multiMap { meta_id, meta, vcf, tbi, meta2, bam, bai ->
                        ^^^^^^^

Warning: subworkflows/local/methylation_analysis/main.nf:19:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/methylation_analysis/main.nf:49:18: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_dmr_tsv = Channel.empty()
                 ^^^^^^^
```
Warning: subworkflows/local/methylation_analysis/main.nf:50:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_dmr_annotated = Channel.empty()
                       ^^^^^^^
```

Warning: subworkflows/local/methylation_analysis/main.nf:56:20: Parameter was not used -- prefix with _ to suppress warning

            .map { patient_normal_id, pair_meta, tumor_bed, normal_meta, normal_bed ->
                   ^^^^^^^^^^^^^^^^^

Warning: subworkflows/local/methylation_analysis/main.nf:56:61: Parameter was not used -- prefix with _ to suppress warning

            .map { patient_normal_id, pair_meta, tumor_bed, normal_meta, normal_bed ->
                                                            ^^^^^^^^^^^

Warning: subworkflows/local/prepare_genome.nf:17:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:22:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_genome_fasta = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:23:21: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_genome_fai = Channel.empty()
                    ^^^^^^^
```
Warning: subworkflows/local/signature_analysis/main.nf:21:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/signature_analysis/main.nf:26:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_chord_mutation = Channel.empty()
                        ^^^^^^^
```
Warning: subworkflows/local/signature_analysis/main.nf:27:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_chord_prediction = Channel.empty()
                          ^^^^^^^
```
Warning: subworkflows/local/signature_analysis/main.nf:84:31: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_mutational_signature = Channel.empty()
                              ^^^^^^^
```
Warning: subworkflows/local/somatic_snv_indel/main.nf:24:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/somatic_snv_indel/main.nf:44:18: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_vep_vcf = Channel.empty()
                 ^^^^^^^
```
Warning: subworkflows/local/somatic_snv_indel/main.nf:45:18: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_vep_tab = Channel.empty()
                 ^^^^^^^
```
Warning: subworkflows/local/somatic_snv_indel/main.nf:56:35: The use of Channel to access channel factories is deprecated -- use channel instead
```
                ch_vep_download = Channel.value(
                                  ^^^^^^^
```

Warning: subworkflows/local/somatic_snv_indel/main.nf:64:28: Parameter was not used -- prefix with _ to suppress warning

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

Warning: subworkflows/local/somatic_snv_indel/main.nf:89:34: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_germline_phased_bam_bai = Channel.empty()
                                 ^^^^^^^
```
Warning: subworkflows/local/somatic_snv_indel/main.nf:91:34: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_germline_phased_vcf     = Channel.empty()
                                 ^^^^^^^
```
Warning: subworkflows/local/somatic_snv_indel/main.nf:92:34: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_somatic_phased_vcf      = Channel.empty()
                                 ^^^^^^^
```

Warning: subworkflows/local/somatic_snv_indel/main.nf:119:25: Parameter was not used -- prefix with _ to suppress warning

            .multiMap { meta_id, meta, vcf, tbi, meta2, bam, bai, meta3, somatic_vcf, somatic_tbi ->
                        ^^^^^^^

Warning: subworkflows/local/somatic_snv_indel/main.nf:119:34: Parameter was not used -- prefix with _ to suppress warning

            .multiMap { meta_id, meta, vcf, tbi, meta2, bam, bai, meta3, somatic_vcf, somatic_tbi ->
                                 ^^^^

Warning: subworkflows/local/somatic_snv_indel/main.nf:119:50: Parameter was not used -- prefix with _ to suppress warning

            .multiMap { meta_id, meta, vcf, tbi, meta2, bam, bai, meta3, somatic_vcf, somatic_tbi ->
                                                 ^^^^^

Warning: subworkflows/local/somatic_sv/main.nf:24:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/somatic_sv/main.nf:64:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_annotsv_tsv = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/svpack_annotate/main.nf:22:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/tumor_clonality/main.nf:26:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/tumor_clonality/main.nf:38:59: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def missing_params = required_params.findAll { !params[it] }
                                                          ^^
```
Warning: subworkflows/local/tumor_clonality/main.nf:66:5: Variable was declared but not used
```
    ch_amber_dir = AMBER.out.amber_dir
    ^^^^^^^^^^^^
```
Warning: subworkflows/local/tumor_clonality/main.nf:91:5: Variable was declared but not used
```
    ch_cobalt_dir = COBALT.out.cobalt_dir
    ^^^^^^^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_pacsomatic_pipeline/main.nf:32:5: Parameter was not used -- prefix with _ to suppress warning
```
    monochrome_logs   // boolean: Do not use coloured log outputs
    ^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_pacsomatic_pipeline/main.nf:35:5: Parameter was not used -- prefix with _ to suppress warning
```
    input             //  string: Path to input samplesheet
    ^^^^^
```
Warning: subworkflows/local/utils_nfcore_pacsomatic_pipeline/main.nf:39:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_pacsomatic_pipeline/main.nf:84:5: The use of Channel to access channel factories is deprecated -- use channel instead
```
    Channel
    ^^^^^^^
```
Warning: subworkflows/local/utils_pacsomatic_pipeline/main.nf:95:32: Parameter was not used -- prefix with _ to suppress warning
```
            } catch (Exception e) {
                               ^
```
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/utils_nfcore_pipeline/main.nf:101:98: The use of Channel to access channel factories is deprecated -- use channel instead

    return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML()))
                                                                                                 ^^^^^^^

Warning: workflows/pacsomatic.nf:50:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: workflows/pacsomatic.nf:51:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_files = Channel.empty()
                       ^^^^^^^
```
Warning: workflows/pacsomatic.nf:52:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_report = Channel.empty()
                        ^^^^^^^
```
Warning: workflows/pacsomatic.nf:59:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ? Channel.value([[:], file(params.severus_trf_bed, checkIfExists: true)])
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:60:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        : Channel.value([[:], []])
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:63:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ? Channel.value([[:], file(params.svpack_ctrl_vcf, checkIfExists: true)])
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:64:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        : Channel.value([[:], []])
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:67:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ? Channel.value([[:], file(params.svpack_ref_gff, checkIfExists: true)])
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:68:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        : Channel.value([[:], []])
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:71:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ? Channel.value([[:], file(params.annotsv_cache, checkIfExists: true)])
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:72:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        : Channel.empty()
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:76:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ? Channel.value([[:], file(params.cnv_target_bed, checkIfExists: true)])
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:77:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        : Channel.value([[:], []])
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:80:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ? Channel.value([[:], file(params.cnv_reference, checkIfExists: true)])
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:81:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        : Channel.value([[:], []])
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:84:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ? Channel.value(file(params.cnv_germline_vcf, checkIfExists: true))
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:85:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        : Channel.value([[]])
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:89:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ? Channel.value(file(params.target_regions_bed, checkIfExists: true))
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:90:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        : Channel.value([])
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:93:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ? Channel.value(file(params.heterozygous_sites, checkIfExists: true))
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:94:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        : Channel.value([])
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:97:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ? Channel.value(file(params.diploid_regions, checkIfExists: true))
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:98:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        : Channel.value([])
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:101:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ? Channel.value(file(params.target_region_normalisation, checkIfExists: true))
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:102:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        : Channel.value([])
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:105:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ? Channel.value(file(params.gc_profile, checkIfExists: true))
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:106:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        : Channel.value([])
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:110:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ? Channel.value(file(params.known_hotspots_somatic, checkIfExists: true))
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:111:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        : Channel.value([])
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:114:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ? Channel.value(file(params.known_hotspots_germline, checkIfExists: true))
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:115:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        : Channel.value([])
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:118:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ? Channel.value(file(params.driver_gene_panel, checkIfExists: true))
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:119:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        : Channel.value([])
          ^^^^^^^
```

Warning: workflows/pacsomatic.nf:122:11: The use of Channel to access channel factories is deprecated -- use channel instead

        ? Channel.value(file(params.ensembl_data_dir, checkIfExists: true, type: 'dir'))
          ^^^^^^^

Warning: workflows/pacsomatic.nf:123:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        : Channel.value([])
          ^^^^^^^
```
Warning: workflows/pacsomatic.nf:194:33: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_mosdepth_multiqc_files = Channel.empty()
                                ^^^^^^^
```
Warning: workflows/pacsomatic.nf:212:35: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            ch_genome_fasta.map { it[1] },
                                  ^^
```
Warning: workflows/pacsomatic.nf:213:33: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            ch_genome_fai.map { it[1] },
                                ^^
```
Warning: workflows/pacsomatic.nf:281:5: Variable was declared but not used
```
    ch_vcf_normals = ch_vcf_normals_tmp
    ^^^^^^^^^^^^^^
```
Warning: workflows/pacsomatic.nf:282:16: Parameter was not used -- prefix with _ to suppress warning
```
        .map { patient, meta, vcf, tbi ->
               ^^^^^^^
```
Warning: workflows/pacsomatic.nf:287:16: Parameter was not used -- prefix with _ to suppress warning
```
        .map { patient, meta, vcf, tbi ->
               ^^^^^^^
```
Warning: workflows/pacsomatic.nf:294:29: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_somatic_snv_vcf_gz = Channel.empty()
                            ^^^^^^^
```
Warning: workflows/pacsomatic.nf:295:29: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_somatic_phased_bam = Channel.empty()
                            ^^^^^^^
```
Warning: workflows/pacsomatic.nf:317:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_somatic_sv_vcf = Channel.empty()
                        ^^^^^^^
```
Warning: workflows/pacsomatic.nf:418:36: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_multiqc_config        = Channel.fromPath(
                                   ^^^^^^^
```
Warning: workflows/pacsomatic.nf:421:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.fromPath(params.multiqc_config, checkIfExists: true) :
            ^^^^^^^
```
Warning: workflows/pacsomatic.nf:422:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.empty()
            ^^^^^^^
```
Warning: workflows/pacsomatic.nf:424:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
            ^^^^^^^
```
Warning: workflows/pacsomatic.nf:425:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.empty()
            ^^^^^^^
```

Warning: workflows/pacsomatic.nf:429:31: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/pacsomatic.nf:435:49: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_methods_description                = Channel.value(
                                                ^^^^^^^

Warning: workflows/pacsomatic.nf:447:74: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_multiqc_files = ch_multiqc_files.mix(ch_ordered_stats.collect{it[1]}.ifEmpty([]))
                                                                         ^^

Warning: workflows/pacsomatic.nf:448:77: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_multiqc_files = ch_multiqc_files.mix(ch_ordered_flagstat.collect{it[1]}.ifEmpty([]))
                                                                            ^^

Warning: workflows/pacsomatic.nf:449:77: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_multiqc_files = ch_multiqc_files.mix(ch_ordered_idxstats.collect{it[1]}.ifEmpty([]))
                                                                            ^^

Warning: workflows/pacsomatic.nf:450:83: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_multiqc_files = ch_multiqc_files.mix(ch_mosdepth_multiqc_files.collect{it[1]}.ifEmpty([]))
                                                                                  ^^

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