Nextflow lint results

Generated: 2026-03-18T00:25:01.559352922Z
Nextflow version: 26.02.0-edge
Summary: 177 warnings

⚠️ Warnings

Warning: conf/modules.config:496:36: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        return args_list.findAll { it }.join(' ').trim()
                                   ^^
```

Warning: main.nf:59:9: The use of Channel to access channel factories is deprecated -- use channel instead

        Channel.empty() // FIXED: Added missing multiqc_report parameter
        ^^^^^^^

Warning: modules/local/fix_header_sv/cutesv/main.nf:19:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/fix_header_sv/jasmine/main.nf:19:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/rtg/mendelian/main.nf:23:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/rtg/mendelian_violations/main.nf:23:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/sniffles/trio/main.nf:18:40: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def snf_input = snf_files.collect{ it.toString() }.join(' ')
                                       ^^
```
Warning: modules/local/straglr/main.nf:39:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/svanna/main.nf:28:71: Implicit closure parameter is deprecated, declare an explicit parameter instead

        hpo_args = hpo_terms.split(';').collect { "--phenotype-term ${it}" }.join(' ')
                                                                      ^^

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/merge/main.nf:28:58: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

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

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

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

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

Warning: modules/nf-core/cat/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/clair3/main.nf:72:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/deepvariant/vcfstatsreport/main.nf:25:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/glnexus/main.nf:27:33: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def input = gvcfs.collect { it.toString() }
                                ^^
```
Warning: modules/nf-core/gunzip/main.nf:43:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/jasminesv/main.nf:37:39: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def unzip_inputs = vcfs.collect { it.name.endsWith(".vcf.gz") ? "    bgzip -d --threads ${task.cpus} ${args4} ${it}" : "" }.join("\n")
                                      ^^

Warning: modules/nf-core/jasminesv/main.nf:37:117: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def unzip_inputs = vcfs.collect { it.name.endsWith(".vcf.gz") ? "    bgzip -d --threads ${task.cpus} ${args4} ${it}" : "" }.join("\n")
                                                                                                                    ^^

Warning: modules/nf-core/minimap2/align/main.nf:67:9: Variable was declared but not used

    def target = reference ?: (bam_input ? error("BAM input requires reference") : reads)
        ^^^^^^

Warning: modules/nf-core/modkit/pileup/main.nf:58:9: Variable was declared but not used
```
    def args   = task.ext.args ?: ''
        ^^^^
```
Warning: subworkflows/local/align/main.nf:17:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/local/align/main.nf:42:40: Parameter was not used -- prefix with _ to suppress warning

            .map { meta_sample, reads, meta_ref, index ->
                                       ^^^^^^^^

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

            ch_align_input.map { meta_sample, reads, meta_index, index ->
                                                     ^^^^^^^^^^

Warning: subworkflows/local/align/main.nf:54:66: Parameter was not used -- prefix with _ to suppress warning

            ch_align_input.map { meta_sample, reads, meta_index, index ->
                                                                 ^^^^^

Warning: subworkflows/local/align/main.nf:57:34: Parameter was not used -- prefix with _ to suppress warning

            ch_align_input.map { meta_sample, reads, meta_index, index ->
                                 ^^^^^^^^^^^

Warning: subworkflows/local/align/main.nf:57:47: Parameter was not used -- prefix with _ to suppress warning

            ch_align_input.map { meta_sample, reads, meta_index, index ->
                                              ^^^^^

Warning: subworkflows/local/annotate_sniffles/main.nf:17:44: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_candidate_genes = candidate_genes ? Channel.fromPath(candidate_genes).map{[[id:"candidate_genes"], it]}.collect() : Channel.value([[id:"empty"], []])
                                           ^^^^^^^

Warning: subworkflows/local/annotate_sniffles/main.nf:17:107: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_candidate_genes = candidate_genes ? Channel.fromPath(candidate_genes).map{[[id:"candidate_genes"], it]}.collect() : Channel.value([[id:"empty"], []])
                                                                                                          ^^

Warning: subworkflows/local/annotate_sniffles/main.nf:17:124: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_candidate_genes = candidate_genes ? Channel.fromPath(candidate_genes).map{[[id:"candidate_genes"], it]}.collect() : Channel.value([[id:"empty"], []])
                                                                                                                           ^^^^^^^

Warning: subworkflows/local/annotate_sniffles/main.nf:18:50: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_false_positive_snv = false_positive_snv ? Channel.fromPath(false_positive_snv).map{[[id:"false_positive"], it]}.collect() : Channel.value([[id:"empty"], []])
                                                 ^^^^^^^

Warning: subworkflows/local/annotate_sniffles/main.nf:18:115: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_false_positive_snv = false_positive_snv ? Channel.fromPath(false_positive_snv).map{[[id:"false_positive"], it]}.collect() : Channel.value([[id:"empty"], []])
                                                                                                                  ^^

Warning: subworkflows/local/annotate_sniffles/main.nf:18:132: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_false_positive_snv = false_positive_snv ? Channel.fromPath(false_positive_snv).map{[[id:"false_positive"], it]}.collect() : Channel.value([[id:"empty"], []])
                                                                                                                                   ^^^^^^^

Warning: subworkflows/local/annotate_sniffles/main.nf:19:46: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_gene_transcripts = gene_transcripts ? Channel.fromPath(gene_transcripts).map{[[id:"transcripts"], it]}.collect() : Channel.value([[id:"empty"], []])
                                             ^^^^^^^

Warning: subworkflows/local/annotate_sniffles/main.nf:19:106: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_gene_transcripts = gene_transcripts ? Channel.fromPath(gene_transcripts).map{[[id:"transcripts"], it]}.collect() : Channel.value([[id:"empty"], []])
                                                                                                         ^^

Warning: subworkflows/local/annotate_sniffles/main.nf:19:123: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_gene_transcripts = gene_transcripts ? Channel.fromPath(gene_transcripts).map{[[id:"transcripts"], it]}.collect() : Channel.value([[id:"empty"], []])
                                                                                                                          ^^^^^^^

Warning: subworkflows/local/annotate_sniffles/main.nf:29:16: Parameter was not used -- prefix with _ to suppress warning
```
        .map { id, meta, sv_vcf, hpo ->
               ^^
```
Warning: subworkflows/local/annotate_sniffles/main.nf:41:16: Parameter was not used -- prefix with _ to suppress warning
```
        .map { id, meta, sv_vcf, snv_vcf ->
               ^^
```
Warning: subworkflows/local/annotate_snv/main.nf:15:22: Parameter was not used -- prefix with _ to suppress warning
```
        .map { meta, vcf -> [meta, snpeff_db] }.first()
                     ^^^
```

Warning: subworkflows/local/annotate_snv/main.nf:23:50: Parameter was not used -- prefix with _ to suppress warning

        .combine(SNPEFF_DOWNLOAD.out.cache.map { meta, cache -> cache })
                                                 ^^^^

Warning: subworkflows/local/annotate_snv/main.nf:28:44: Parameter was not used -- prefix with _ to suppress warning

        ch_vcf_with_cache.map { meta, vcf, meta2, cache -> [meta, vcf] },
                                           ^^^^^

Warning: subworkflows/local/annotate_snv/main.nf:28:51: Parameter was not used -- prefix with _ to suppress warning

        ch_vcf_with_cache.map { meta, vcf, meta2, cache -> [meta, vcf] },
                                                  ^^^^^

Warning: subworkflows/local/annotate_snv/main.nf:30:33: Parameter was not used -- prefix with _ to suppress warning

        ch_vcf_with_cache.map { meta, vcf, meta2, cache -> [meta2, cache] }
                                ^^^^

Warning: subworkflows/local/annotate_snv/main.nf:30:39: Parameter was not used -- prefix with _ to suppress warning

        ch_vcf_with_cache.map { meta, vcf, meta2, cache -> [meta2, cache] }
                                      ^^^

Warning: subworkflows/local/annotate_svim/main.nf:17:44: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_candidate_genes = candidate_genes ? Channel.fromPath(candidate_genes).map{[[id:"candidate_genes"], it]}.collect() : Channel.value([[id:"empty"], []])
                                           ^^^^^^^

Warning: subworkflows/local/annotate_svim/main.nf:17:107: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_candidate_genes = candidate_genes ? Channel.fromPath(candidate_genes).map{[[id:"candidate_genes"], it]}.collect() : Channel.value([[id:"empty"], []])
                                                                                                          ^^

Warning: subworkflows/local/annotate_svim/main.nf:17:124: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_candidate_genes = candidate_genes ? Channel.fromPath(candidate_genes).map{[[id:"candidate_genes"], it]}.collect() : Channel.value([[id:"empty"], []])
                                                                                                                           ^^^^^^^

Warning: subworkflows/local/annotate_svim/main.nf:18:50: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_false_positive_snv = false_positive_snv ? Channel.fromPath(false_positive_snv).map{[[id:"false_positive"], it]}.collect() : Channel.value([[id:"empty"], []])
                                                 ^^^^^^^

Warning: subworkflows/local/annotate_svim/main.nf:18:115: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_false_positive_snv = false_positive_snv ? Channel.fromPath(false_positive_snv).map{[[id:"false_positive"], it]}.collect() : Channel.value([[id:"empty"], []])
                                                                                                                  ^^

Warning: subworkflows/local/annotate_svim/main.nf:18:132: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_false_positive_snv = false_positive_snv ? Channel.fromPath(false_positive_snv).map{[[id:"false_positive"], it]}.collect() : Channel.value([[id:"empty"], []])
                                                                                                                                   ^^^^^^^

Warning: subworkflows/local/annotate_svim/main.nf:19:46: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_gene_transcripts = gene_transcripts ? Channel.fromPath(gene_transcripts).map{[[id:"transcripts"], it]}.collect() : Channel.value([[id:"empty"], []])
                                             ^^^^^^^

Warning: subworkflows/local/annotate_svim/main.nf:19:106: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_gene_transcripts = gene_transcripts ? Channel.fromPath(gene_transcripts).map{[[id:"transcripts"], it]}.collect() : Channel.value([[id:"empty"], []])
                                                                                                         ^^

Warning: subworkflows/local/annotate_svim/main.nf:19:123: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_gene_transcripts = gene_transcripts ? Channel.fromPath(gene_transcripts).map{[[id:"transcripts"], it]}.collect() : Channel.value([[id:"empty"], []])
                                                                                                                          ^^^^^^^

Warning: subworkflows/local/annotate_svim/main.nf:29:16: Parameter was not used -- prefix with _ to suppress warning
```
        .map { id, meta, sv_vcf, hpo ->
               ^^
```
Warning: subworkflows/local/annotate_svim/main.nf:41:16: Parameter was not used -- prefix with _ to suppress warning
```
        .map { id, meta, sv_vcf, snv_vcf ->
               ^^
```
Warning: subworkflows/local/annotate_unified/main.nf:15:22: Parameter was not used -- prefix with _ to suppress warning
```
        .map { meta, vcf -> [meta, snpeff_db] }.first()
                     ^^^
```

Warning: subworkflows/local/annotate_unified/main.nf:23:58: Parameter was not used -- prefix with _ to suppress warning

        .combine(SNPEFF_DOWNLOAD_UNIFIED.out.cache.map { meta, cache -> cache })
                                                         ^^^^

Warning: subworkflows/local/annotate_unified/main.nf:28:44: Parameter was not used -- prefix with _ to suppress warning

        ch_vcf_with_cache.map { meta, vcf, meta2, cache -> [meta, vcf] },
                                           ^^^^^

Warning: subworkflows/local/annotate_unified/main.nf:28:51: Parameter was not used -- prefix with _ to suppress warning

        ch_vcf_with_cache.map { meta, vcf, meta2, cache -> [meta, vcf] },
                                                  ^^^^^

Warning: subworkflows/local/annotate_unified/main.nf:30:33: Parameter was not used -- prefix with _ to suppress warning

        ch_vcf_with_cache.map { meta, vcf, meta2, cache -> [meta2, cache] }
                                ^^^^

Warning: subworkflows/local/annotate_unified/main.nf:30:39: Parameter was not used -- prefix with _ to suppress warning

        ch_vcf_with_cache.map { meta, vcf, meta2, cache -> [meta2, cache] }
                                      ^^^

Warning: subworkflows/local/annotsv_db/main.nf:14:37: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .map { [[id:"annotsv"], it] }
                                    ^^
```

Warning: subworkflows/local/annotsv_db/main.nf:18:40: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_annotsv_annotations_input = Channel.fromPath(annotsv_annotations).map{[[id:"annotsv_annotations"], it]}.collect()
                                       ^^^^^^^

Warning: subworkflows/local/annotsv_db/main.nf:18:111: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_annotsv_annotations_input = Channel.fromPath(annotsv_annotations).map{[[id:"annotsv_annotations"], it]}.collect()
                                                                                                              ^^

Warning: subworkflows/local/annotsv_db/main.nf:25:38: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_annotsv_annotations = Channel.fromPath(annotsv_annotations).map{[[id:"annotsv_annotations"], it]}.collect()
                                     ^^^^^^^

Warning: subworkflows/local/annotsv_db/main.nf:25:109: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_annotsv_annotations = Channel.fromPath(annotsv_annotations).map{[[id:"annotsv_annotations"], it]}.collect()
                                                                                                            ^^

Warning: subworkflows/local/bam2fastq/main.nf:15:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/call_hificnv/main.nf:12:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/call_snv/main.nf:19:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/call_snv/main.nf:21:14: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_vcf = Channel.empty()
             ^^^^^^^
```
Warning: subworkflows/local/call_snv/main.nf:22:14: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_tbi = Channel.empty()
             ^^^^^^^
```
Warning: subworkflows/local/call_snv/main.nf:23:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_gvcf = Channel.empty()
              ^^^^^^^
```
Warning: subworkflows/local/call_snv/main.nf:24:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_gtbi = Channel.empty()
              ^^^^^^^
```
Warning: subworkflows/local/call_snv/main.nf:25:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_vcf_deepvariant = Channel.empty()
                         ^^^^^^^
```
Warning: subworkflows/local/call_snv/main.nf:26:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_tbi_deepvariant = Channel.empty()
                         ^^^^^^^
```
Warning: subworkflows/local/call_snv/main.nf:27:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    html_report = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/call_snv/main.nf:76:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.value([]),   // empty channel for samples
            ^^^^^^^
```
Warning: subworkflows/local/call_snv/main.nf:77:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.value([]),   // empty channel for regions
            ^^^^^^^
```
Warning: subworkflows/local/call_snv/main.nf:78:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.value([])    // empty channel for filters
            ^^^^^^^
```
Warning: subworkflows/local/call_snv/main.nf:109:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
                Channel.value([]),
                ^^^^^^^
```
Warning: subworkflows/local/call_snv/main.nf:110:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
                Channel.value([]),
                ^^^^^^^
```
Warning: subworkflows/local/call_snv/main.nf:111:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
                Channel.value([])
                ^^^^^^^
```

Warning: subworkflows/local/call_snv/main.nf:129:27: The use of Channel to access channel factories is deprecated -- use channel instead

            html_report = Channel.empty()  // FIXED: Added parentheses
                          ^^^^^^^

Warning: subworkflows/local/call_str/main.nf:14:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/call_sv/main.nf:82:19: Parameter was not used -- prefix with _ to suppress warning
```
        .filter { meta, vcf, tbi -> vcf != null }
                  ^^^^
```
Warning: subworkflows/local/call_sv/main.nf:82:30: Parameter was not used -- prefix with _ to suppress warning
```
        .filter { meta, vcf, tbi -> vcf != null }
                             ^^^
```
Warning: subworkflows/local/call_sv/main.nf:85:19: Parameter was not used -- prefix with _ to suppress warning
```
        .filter { meta, vcf, tbi -> vcf != null }
                  ^^^^
```
Warning: subworkflows/local/call_sv/main.nf:85:30: Parameter was not used -- prefix with _ to suppress warning
```
        .filter { meta, vcf, tbi -> vcf != null }
                             ^^^
```
Warning: subworkflows/local/filter_sv/main.nf:20:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
ch_versions = Channel.empty()
              ^^^^^^^
```
Warning: subworkflows/local/filter_sv/main.nf:21:31: The use of Channel to access channel factories is deprecated -- use channel instead
```
target_bed_ch = target_bed ?: Channel.value([])
                              ^^^^^^^
```
Warning: subworkflows/local/filter_sv/main.nf:26:5: The use of Channel to access channel factories is deprecated -- use channel instead
```
    Channel.value([]),
    ^^^^^^^
```
Warning: subworkflows/local/filter_sv/main.nf:28:5: The use of Channel to access channel factories is deprecated -- use channel instead
```
    Channel.value([])
    ^^^^^^^
```

Warning: subworkflows/local/filter_sv/main.nf:48:20: Parameter was not used -- prefix with _ to suppress warning

            .map { clean_meta, vcf, tbi, original_meta, summary, bed ->
                   ^^^^^^^^^^

Warning: subworkflows/local/filter_sv/main.nf:53:54: Parameter was not used -- prefix with _ to suppress warning

            ch_sv_mosdepth_bed.map { meta, vcf, tbi, summary, bed -> tuple(meta, vcf, tbi) },
                                                     ^^^^^^^

Warning: subworkflows/local/filter_sv/main.nf:53:63: Parameter was not used -- prefix with _ to suppress warning

            ch_sv_mosdepth_bed.map { meta, vcf, tbi, summary, bed -> tuple(meta, vcf, tbi) },
                                                              ^^^

Warning: subworkflows/local/filter_sv/main.nf:54:44: Parameter was not used -- prefix with _ to suppress warning

            ch_sv_mosdepth_bed.map { meta, vcf, tbi, summary, bed -> tuple(meta, summary) },
                                           ^^^

Warning: subworkflows/local/filter_sv/main.nf:54:49: Parameter was not used -- prefix with _ to suppress warning

            ch_sv_mosdepth_bed.map { meta, vcf, tbi, summary, bed -> tuple(meta, summary) },
                                                ^^^

Warning: subworkflows/local/filter_sv/main.nf:54:63: Parameter was not used -- prefix with _ to suppress warning

            ch_sv_mosdepth_bed.map { meta, vcf, tbi, summary, bed -> tuple(meta, summary) },
                                                              ^^^

Warning: subworkflows/local/filter_sv/main.nf:55:44: Parameter was not used -- prefix with _ to suppress warning

            ch_sv_mosdepth_bed.map { meta, vcf, tbi, summary, bed -> tuple(meta, bed) },
                                           ^^^

Warning: subworkflows/local/filter_sv/main.nf:55:49: Parameter was not used -- prefix with _ to suppress warning

            ch_sv_mosdepth_bed.map { meta, vcf, tbi, summary, bed -> tuple(meta, bed) },
                                                ^^^

Warning: subworkflows/local/filter_sv/main.nf:55:54: Parameter was not used -- prefix with _ to suppress warning

            ch_sv_mosdepth_bed.map { meta, vcf, tbi, summary, bed -> tuple(meta, bed) },
                                                     ^^^^^^^

Warning: subworkflows/local/haplotag_bam/main.nf:13:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/joint_genotype_snv/main.nf:13:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/joint_genotype_snv/main.nf:17:16: Parameter was not used -- prefix with _ to suppress warning
```
        .map { meta, data -> [data.id, data.family_id] }
               ^^^^
```
Warning: subworkflows/local/joint_genotype_snv/main.nf:18:19: Parameter was not used -- prefix with _ to suppress warning
```
        .filter { sample_id, family_id ->
                  ^^^^^^^^^
```
Warning: subworkflows/local/joint_genotype_snv/main.nf:26:16: Parameter was not used -- prefix with _ to suppress warning
```
        .map { sample_id, gvcf, family_id -> [family_id, gvcf] }
               ^^^^^^^^^
```

Warning: subworkflows/local/joint_genotype_snv/main.nf:28:19: Parameter was not used -- prefix with _ to suppress warning

        .filter { family_id, gvcfs -> gvcfs.size() == 3 }  // Only trios
                  ^^^^^^^^^

Warning: subworkflows/local/longphase_variants/main.nf:13:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/merge_sv/main.nf:16:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/merge_sv/main.nf:23:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_chr_norm ?: Channel.value([])
                       ^^^^^^^
```

Warning: subworkflows/local/merge_sv/main.nf:32:76: Parameter was not used -- prefix with _ to suppress warning

    jasmine_vcf = FIX_HEADER_JASMINE.out.vcf_with_samples.map { meta, vcf, samples -> [meta, vcf] }
                                                                           ^^^^^^^

Warning: subworkflows/local/merge_sv/main.nf:39:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.value([]),  // regions - use Channel.value([]) instead of []
        ^^^^^^^
```
Warning: subworkflows/local/merge_sv/main.nf:40:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.value([]),  // targets
        ^^^^^^^
```
Warning: subworkflows/local/merge_sv/main.nf:41:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.value([])   // samples
        ^^^^^^^
```

Warning: subworkflows/local/merge_sv/main.nf:49:69: Parameter was not used -- prefix with _ to suppress warning

                FIX_HEADER_JASMINE.out.vcf_with_samples.map { meta, vcf, samples -> [meta, samples] },
                                                                    ^^^

Warning: subworkflows/local/methyl/main.nf:16:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/mosdepth/main.nf:15:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/rtg_compare_snv/main.nf:13:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/rtg_compare_sv/main.nf:14:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/local/sniffles_trio/main.nf:16:31: Parameter was not used -- prefix with _ to suppress warning

            samplesheet.map { meta, data -> [data.id, data.family_id] },
                              ^^^^

Warning: subworkflows/local/sniffles_trio/main.nf:19:19: Parameter was not used -- prefix with _ to suppress warning
```
        .filter { sample_id, snf, family_id ->
                  ^^^^^^^^^
```

Warning: subworkflows/local/sniffles_trio/main.nf:19:30: Parameter was not used -- prefix with _ to suppress warning

        .filter { sample_id, snf, family_id ->
                             ^^^

Warning: subworkflows/local/sniffles_trio/main.nf:22:16: Parameter was not used -- prefix with _ to suppress warning

        .map { sample_id, snf, family_id -> [family_id, snf] }  // Key by family_id
               ^^^^^^^^^

Warning: subworkflows/local/sniffles_trio/main.nf:24:19: Parameter was not used -- prefix with _ to suppress warning

        .filter { family_id, snf_files_list -> snf_files_list.size() == 3 }
                  ^^^^^^^^^

Warning: subworkflows/local/unify_vcf/main.nf:16:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_longraredisease_pipeline/main.nf:32:5: Parameter was not used -- prefix with _ to suppress warning
```
    monochrome_logs   // boolean: Do not use coloured log outputs (FIXED: removed underscore)
    ^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_longraredisease_pipeline/main.nf:35:5: Parameter was not used -- prefix with _ to suppress warning
```
    input             //  string: Path to input samplesheet (FIXED: removed underscore)
    ^^^^^
```
Warning: subworkflows/local/utils_nfcore_longraredisease_pipeline/main.nf:42:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_longraredisease_pipeline/main.nf:166:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_samplesheet = Channel.fromList(samplesheet_data)
                     ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_longraredisease_pipeline/main.nf:364:21: The use of Channel to access channel factories is deprecated -- use channel instead
```
    def baseTools = Channel.from(['nextflow', 'nf_core', 'bioconda', 'biocontainers', 'multiqc'])
                    ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_longraredisease_pipeline/main.nf:393:33: Parameter was not used -- prefix with _ to suppress warning
```
        paramsMap.each { param, paramStatus ->
                                ^^^^^^^^^^^
```

Warning: subworkflows/local/utils_nfcore_longraredisease_pipeline/main.nf:423:61: Parameter was not used -- prefix with _ to suppress warning

    def dependentWorkflows = workflowDependencies.findAll { workflow, dependencies ->
                                                            ^^^^^^^^

Warning: subworkflows/local/utils_nfcore_longraredisease_pipeline/main.nf:427:41: Parameter was not used -- prefix with _ to suppress warning

    dependentWorkflows.each { workflow, dependencies ->
                                        ^^^^^^^^^^^^

Warning: subworkflows/local/utils_nfcore_longraredisease_pipeline/main.nf:443:61: Parameter was not used -- prefix with _ to suppress warning

        def requiringWorkflows = fileDependencies.findAll { workflow, files ->
                                                            ^^^^^^^^

Warning: subworkflows/local/utils_nfcore_longraredisease_pipeline/main.nf:447:45: Parameter was not used -- prefix with _ to suppress warning

        requiringWorkflows.each { workflow, files ->
                                            ^^^^^

Warning: subworkflows/local/utils_nfcore_longraredisease_pipeline/main.nf:460:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
    return param ? Channel.fromPath(param, checkIfExists: true)
                   ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_longraredisease_pipeline/main.nf:467:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
    return param ? Channel.fromList(samplesheetToList(param, schema)) : defaultValue
                   ^^^^^^^
```
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: workflows/longraredisease.nf:102:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_samplesheet = Channel.fromList(samplesheet_data)
                     ^^^^^^^
```
Warning: workflows/longraredisease.nf:128:16: Parameter was not used -- prefix with _ to suppress warning
```
        .map { meta, data ->
               ^^^^
```
Warning: workflows/longraredisease.nf:148:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: workflows/longraredisease.nf:150:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_fasta = Channel
               ^^^^^^^
```
Warning: workflows/longraredisease.nf:175:20: Parameter was not used -- prefix with _ to suppress warning
```
            .map { meta, data -> data.family_id }
                   ^^^^
```

Warning: workflows/longraredisease.nf:180:20: Parameter was not used -- prefix with _ to suppress warning

            .map { meta, sdf -> sdf }  // Extract just the SDF path
                   ^^^^

Warning: workflows/longraredisease.nf:190:18: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_trf = Channel
                 ^^^^^^^
```
Warning: workflows/longraredisease.nf:199:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
                ch_trf = Channel.empty()
                         ^^^^^^^
```

Warning: workflows/longraredisease.nf:226:21: Implicit closure parameter is deprecated, declare an explicit parameter instead

                    it.name.endsWith('.fastq.gz') || it.name.endsWith('.fq.gz')
                    ^^

Warning: workflows/longraredisease.nf:226:54: Implicit closure parameter is deprecated, declare an explicit parameter instead

                    it.name.endsWith('.fastq.gz') || it.name.endsWith('.fq.gz')
                                                     ^^

Warning: workflows/longraredisease.nf:299:68: Implicit closure parameter is deprecated, declare an explicit parameter instead

                    def bam_files = bam_path.listFiles().findAll { it.name.endsWith('.bam') }
                                                                   ^^

Warning: workflows/longraredisease.nf:366:65: Parameter was not used -- prefix with _ to suppress warning

        ch_final_sorted_bam = ch_aligned_input.map { meta, bam, bai -> [meta, bam] }
                                                                ^^^

Warning: workflows/longraredisease.nf:367:60: Parameter was not used -- prefix with _ to suppress warning

        ch_final_sorted_bai = ch_aligned_input.map { meta, bam, bai -> [meta, bai] }
                                                           ^^^

Warning: workflows/longraredisease.nf:566:31: Parameter was not used -- prefix with _ to suppress warning

                    .filter { meta, vcf, tbi -> vcf != null }
                              ^^^^

Warning: workflows/longraredisease.nf:566:42: Parameter was not used -- prefix with _ to suppress warning

                    .filter { meta, vcf, tbi -> vcf != null }
                                         ^^^

Warning: workflows/longraredisease.nf:576:82: Parameter was not used -- prefix with _ to suppress warning

            ch_sv_vcf_final = FILTER_SV_SNIFFLES.out.ch_vcf_tbi.map { meta, vcf, tbi -> [meta, vcf] }
                                                                                 ^^^

Warning: workflows/longraredisease.nf:584:27: Parameter was not used -- prefix with _ to suppress warning

                .filter { meta, vcf, tbi -> vcf != null }
                          ^^^^

Warning: workflows/longraredisease.nf:584:38: Parameter was not used -- prefix with _ to suppress warning

                .filter { meta, vcf, tbi -> vcf != null }
                                     ^^^

Warning: workflows/longraredisease.nf:595:74: Parameter was not used -- prefix with _ to suppress warning

            ch_svim_vcf = FILTER_SV_SVIM.out.ch_vcf_tbi.map { meta, vcf, tbi -> [meta, vcf] }
                                                                         ^^^

Warning: workflows/longraredisease.nf:601:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_sv_vcf_final = Channel.empty()
                          ^^^^^^^
```
Warning: workflows/longraredisease.nf:655:19: Parameter was not used -- prefix with _ to suppress warning
```
        .filter { meta, data ->
                  ^^^^
```
Warning: workflows/longraredisease.nf:670:16: Parameter was not used -- prefix with _ to suppress warning
```
        .map { sample_id, meta, vcf, hpo_terms ->
               ^^^^^^^^^
```

Warning: workflows/longraredisease.nf:677:43: Parameter was not used -- prefix with _ to suppress warning

            ch_sv_svanna.map { meta, vcf, hpo_terms -> [meta, vcf] },
                                          ^^^^^^^^^

Warning: workflows/longraredisease.nf:679:32: Parameter was not used -- prefix with _ to suppress warning

            ch_sv_svanna.map { meta, vcf, hpo_terms -> hpo_terms }
                               ^^^^

Warning: workflows/longraredisease.nf:679:38: Parameter was not used -- prefix with _ to suppress warning

            ch_sv_svanna.map { meta, vcf, hpo_terms -> hpo_terms }
                                     ^^^

Warning: workflows/longraredisease.nf:764:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_str_vcf = Channel.empty()
                         ^^^^^^^
```
Warning: workflows/longraredisease.nf:803:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_cnv_vcf = Channel.empty()
                         ^^^^^^^
```
Warning: workflows/longraredisease.nf:852:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_cnv_vcf = Channel.empty()
                         ^^^^^^^
```

Warning: workflows/longraredisease.nf:868:27: Parameter was not used -- prefix with _ to suppress warning

                .filter { meta, vcf, tbi -> vcf != null }
                          ^^^^

Warning: workflows/longraredisease.nf:868:38: Parameter was not used -- prefix with _ to suppress warning

                .filter { meta, vcf, tbi -> vcf != null }
                                     ^^^

Warning: workflows/longraredisease.nf:879:78: Parameter was not used -- prefix with _ to suppress warning

            ch_cutesv_vcf = FILTER_SV_CUTESV.out.ch_vcf_tbi.map { meta, vcf, tbi -> [meta, vcf] }
                                                                             ^^^

Warning: workflows/longraredisease.nf:943:37: Parameter was not used -- prefix with _ to suppress warning

        ch_combined.map { meta, sv, cnv, str -> [meta, sv] },
                                    ^^^

Warning: workflows/longraredisease.nf:943:42: Parameter was not used -- prefix with _ to suppress warning

        ch_combined.map { meta, sv, cnv, str -> [meta, sv] },
                                         ^^^

Warning: workflows/longraredisease.nf:944:33: Parameter was not used -- prefix with _ to suppress warning

        ch_combined.map { meta, sv, cnv, str -> [meta, cnv ?: []] },
                                ^^

Warning: workflows/longraredisease.nf:944:42: Parameter was not used -- prefix with _ to suppress warning

        ch_combined.map { meta, sv, cnv, str -> [meta, cnv ?: []] },
                                         ^^^

Warning: workflows/longraredisease.nf:945:33: Parameter was not used -- prefix with _ to suppress warning

        ch_combined.map { meta, sv, cnv, str -> [meta, str ?: []] },
                                ^^

Warning: workflows/longraredisease.nf:945:37: Parameter was not used -- prefix with _ to suppress warning

        ch_combined.map { meta, sv, cnv, str -> [meta, str ?: []] },
                                    ^^^

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