Nextflow lint results

Generated: 2026-03-07T00:18:57.703877690Z
Nextflow version: 26.02.0-edge
Summary: 21 errors, 61 warnings

❌ Errors

Error: modules/local/hicpro/dnase_mapping_stats.nf:2:10: sample is not defined
```
    tag "$sample = $bam"
         ^^^^^^^
```

Error: modules/nf-core/bwa/index/main.nf:14:27: bwa is not defined

    tuple val(meta), path(bwa) , emit: index
                          ^^^

Error: subworkflows/local/compartments.nf:26:28: cool is already declared

            cool.map{meta, cool, res -> [meta, cool] },
                           ^^^^

Error: subworkflows/local/hicpro.nf:18:5: meta was assigned but not declared
```
    meta = row[0].clone()
    ^^^^
```
Error: subworkflows/local/hicpro.nf:19:5: meta is not defined
```
    meta.remove('chunk')
    ^^^^
```
Error: subworkflows/local/hicpro.nf:20:13: meta is not defined
```
    return [meta, row[1]]
            ^^^^
```
Error: subworkflows/local/utils_nfcore_hic_pipeline/main.nf:314:9: meta was assigned but not declared
```
        meta = row[0].clone()
        ^^^^
```
Error: subworkflows/local/utils_nfcore_hic_pipeline/main.nf:315:9: meta is not defined
```
        meta.chunk = i
        ^^^^
```
Error: subworkflows/local/utils_nfcore_hic_pipeline/main.nf:316:9: meta is not defined
```
        meta.part = row[1].size()
        ^^^^
```
Error: subworkflows/local/utils_nfcore_hic_pipeline/main.nf:317:17: meta is not defined
```
        map += [meta, file]
                ^^^^
```

Error: workflows/hic.nf:26:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_map_res = Channel.from( params.bin_size ).splitCsv().flatten().toInteger()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/hic.nf:28:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
if (params.res_zoomify){
^
```
Error: workflows/hic.nf:33:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
if (params.res_tads && !params.skip_tads){
^
```
Error: workflows/hic.nf:43:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
if (params.res_dist_decay && !params.skip_dist_decay){
^
```
Error: workflows/hic.nf:53:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
if (params.res_compartments && !params.skip_compartments){
^
```
Error: workflows/hic.nf:63:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
ch_map_res = ch_map_res.unique()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```

Error: workflows/hic.nf:106:13: ch_map_res is not defined

            ch_map_res
            ^^^^^^^^^^

Error: workflows/hic.nf:130:9: ch_map_res is not defined
```
        ch_map_res
        ^^^^^^^^^^
```

Error: workflows/hic.nf:139:22: ch_ddecay_res is not defined

            .combine(ch_ddecay_res)
                     ^^^^^^^^^^^^^

Error: workflows/hic.nf:155:22: ch_comp_res is not defined

            .combine(ch_comp_res)
                     ^^^^^^^^^^^

Error: workflows/hic.nf:173:22: ch_tads_res is not defined

            .combine(ch_tads_res)
                     ^^^^^^^^^^^

⚠️ Warnings

Warning: main.nf:50:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: modules/local/hicexplorer/hicPlotDistVsCounts.nf:22:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/split_cooler_dump.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/bowtie2/align/main.nf:93:9: Variable was declared but not used

    def reference = fasta && extension=="cram"  ? "--reference ${fasta}" : ""
        ^^^^^^^^^

Warning: modules/nf-core/bwa/mem/main.nf:56:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/bwa/mem/main.nf:59:9: Variable was declared but not used

    def samtools_command = sort_bam ? 'sort' : 'view'
        ^^^^^^^^^^^^^^^^

Warning: modules/nf-core/custom/getchromsizes/main.nf:23:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/samtools/flagstat/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: subworkflows/local/compartments.nf:12:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/compartments.nf:26:34: Parameter was not used -- prefix with _ to suppress warning
```
            cool.map{meta, cool, res -> [meta, cool] },
                                 ^^^
```
Warning: subworkflows/local/compartments.nf:27:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.value([])
            ^^^^^^^
```
Warning: subworkflows/local/cooler.nf:31:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/cooler.nf:57:22: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_cool.map{[it[0], it[1], ""]}
                     ^^
```
Warning: subworkflows/local/cooler.nf:57:29: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_cool.map{[it[0], it[1], ""]}
                            ^^
```

Warning: subworkflows/local/cooler.nf:65:26: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_res_zoomify = Channel.from(params.res_zoomify).splitCsv().flatten().unique().toInteger()
                         ^^^^^^^

Warning: subworkflows/local/cooler.nf:70:18: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter{ it[2] == it[3] }
                 ^^
```
Warning: subworkflows/local/cooler.nf:70:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter{ it[2] == it[3] }
                          ^^
```
Warning: subworkflows/local/cooler.nf:84:38: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        COOLER_BALANCE.out.cool.map{[it[0], it[1], ""]}
                                     ^^
```
Warning: subworkflows/local/cooler.nf:84:45: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        COOLER_BALANCE.out.cool.map{[it[0], it[1], ""]}
                                            ^^
```
Warning: subworkflows/local/hicpro.nf:35:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/hicpro.nf:140:30: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_hicpro_raw_maps = Channel.empty()
                             ^^^^^^^
```
Warning: subworkflows/local/hicpro.nf:141:31: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_hicpro_iced_maps = Channel.empty()
                              ^^^^^^^
```
Warning: subworkflows/local/hicpro_mapping.nf:23:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/pairtools.nf:36:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/pairtools.nf:42:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.value([])
        ^^^^^^^
```
Warning: subworkflows/local/pairtools.nf:71:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            single: it[0].part <=1
                    ^^
```
Warning: subworkflows/local/pairtools.nf:72:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            multiple: it[0].part > 1
                      ^^
```
Warning: subworkflows/local/prepare_genome.nf:18:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:24:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_fasta = Channel.fromPath( fasta )
               ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:39:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_index = Channel.fromPath( bwt2_index , checkIfExists: true)
                       ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:56:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_index = Channel.fromPath( bwa_index , checkIfExists: true)
                       ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:72:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_chromsize = Channel.fromPath( params.chromosome_size , checkIfExists: true)
                       ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:82:31: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_restriction_site = Channel.value(restriction_site)
                              ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:84:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_ligation_site = Channel.value(ligation_site)
                           ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:86:31: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_restriction_site = Channel.value(params.restriction_site)
                              ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:87:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_ligation_site = Channel.value(params.ligation_site)
                           ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:89:31: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_restriction_site = Channel.empty()
                              ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:90:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_ligation_site = Channel.empty()
                           ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:107:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath( params.restriction_fragments, checkIfExists: true )
        ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:111:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_resfrag = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/tads.nf:10:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/tads.nf:11:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_tads = Channel.empty()
              ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_hic_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_hic_pipeline/main.nf:35:5: Parameter was not used -- prefix with _ to suppress warning
```
    input             //  string: Path to input samplesheet
    ^^^^^
```
Warning: workflows/hic.nf:26:14: The use of Channel to access channel factories is deprecated -- use channel instead
```
ch_map_res = Channel.from( params.bin_size ).splitCsv().flatten().toInteger()
             ^^^^^^^
```

Warning: workflows/hic.nf:29:19: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_zoom_res = Channel.from( params.res_zoomify ).splitCsv().flatten().toInteger()
                  ^^^^^^^

Warning: workflows/hic.nf:34:19: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_tads_res = Channel.from( "${params.res_tads}" ).splitCsv().flatten().toInteger()
                  ^^^^^^^

Warning: workflows/hic.nf:37:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_tads_res=Channel.empty()
                ^^^^^^^
```

Warning: workflows/hic.nf:44:21: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_ddecay_res = Channel.from( "${params.res_dist_decay}" ).splitCsv().flatten().toInteger()
                    ^^^^^^^

Warning: workflows/hic.nf:47:21: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_ddecay_res = Channel.empty()
                    ^^^^^^^
```

Warning: workflows/hic.nf:54:19: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_comp_res = Channel.from( "${params.res_compartments}" ).splitCsv().flatten().toInteger()
                  ^^^^^^^

Warning: workflows/hic.nf:57:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_comp_res = Channel.empty()
                  ^^^^^^^
```
Warning: workflows/hic.nf:79:5: Parameter was not used -- prefix with _ to suppress warning
```
    ch_restriction_site
    ^^^^^^^^^^^^^^^^^^^
```

Warning: workflows/hic.nf:92:68: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]})
                                                                   ^^

Warning: workflows/hic.nf:140:22: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .filter{ it[0].resolution == it[2] }
                     ^^
```
Warning: workflows/hic.nf:140:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .filter{ it[0].resolution == it[2] }
                                         ^^
```
Warning: workflows/hic.nf:156:22: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .filter{ it[0].resolution == it[2] }
                     ^^
```
Warning: workflows/hic.nf:156:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .filter{ it[0].resolution == it[2] }
                                         ^^
```
Warning: workflows/hic.nf:174:22: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .filter{ it[0].resolution == it[2] }
                     ^^
```
Warning: workflows/hic.nf:174:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .filter{ it[0].resolution == it[2] }
                                         ^^
```
Warning: workflows/hic.nf:187:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    def topic_versions = Channel.topic("versions")
                         ^^^^^^^
```

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