Nextflow lint results

Generated: 2026-03-20T00:23:40.837196161Z
Nextflow version: 26.03.0-edge
Summary: 56 errors, 61 warnings

❌ Errors

Error: modules/local/cagefightr/enhancer_calling/main.nf:18:5: The script: or exec: label is required when other sections are present
```
    """
    ^
```
Error: modules/local/cager/processing/main.nf:21:5: The script: or exec: label is required when other sections are present
```
    """
    ^
```
Error: modules/local/cager/readin/main.nf:18:5: The script: or exec: label is required when other sections are present
```
    """
    ^
```
Error: modules/local/cager/report/main.nf:20:5: The script: or exec: label is required when other sections are present
```
    """
    ^
```
Error: modules/local/cager/tag_qc/main.nf:21:5: The script: or exec: label is required when other sections are present
```
    """
    ^
```
Error: modules/local/cager/tagcluster_qc/main.nf:21:5: The script: or exec: label is required when other sections are present
```
    """
    ^
```
Error: modules/local/forge_bsgenome/main.nf:14:5: The script: or exec: label is required when other sections are present
```
    """
    ^
```
Error: modules/local/gtf2txdb/main.nf:12:5: The script: or exec: label is required when other sections are present
```
    """
    ^
```
Error: modules/local/relativisation/main.nf:15:5: The script: or exec: label is required when other sections are present
```
    """
    ^
```

Error: modules/local/write_sample_list/main.nf:16:48: PWD is not defined

        line="${meta.id},${meta.single_end},[${PWD}/${params.outdir}/bigwig/${bw_or_bam[0]} ${PWD}/${params.outdir}/bigwig/${bw_or_bam[1]}],${meta.id}"
                                               ^^^

Error: modules/local/write_sample_list/main.nf:16:95: PWD is not defined

        line="${meta.id},${meta.single_end},[${PWD}/${params.outdir}/bigwig/${bw_or_bam[0]} ${PWD}/${params.outdir}/bigwig/${bw_or_bam[1]}],${meta.id}"
                                                                                              ^^^

Error: modules/local/write_sample_list/main.nf:21:47: PWD is not defined

        line="${meta.id},${meta.single_end},${PWD}/${params.outdir}/samtools_sort/${bw_or_bam[0]},${meta.id}"
                                              ^^^

Error: subworkflows/local/cager/main.nf:93:5: id was assigned but not declared
```
    id = row.id
    ^^
```
Error: subworkflows/local/cager/main.nf:94:5: single_end was assigned but not declared
```
    single_end = row.single_end
    ^^^^^^^^^^
```
Error: subworkflows/local/cager/main.nf:95:5: str1_bw was assigned but not declared
```
    str1_bw = row.path.split(" ")[0].minus('[')
    ^^^^^^^
```
Error: subworkflows/local/cager/main.nf:96:5: new_name was assigned but not declared
```
    new_name = row.new_name
    ^^^^^^^^
```

Error: subworkflows/local/cager/main.nf:97:9: str1_bw is not defined

    if (str1_bw.split("\\.")[-1].minus(']') != "bam") {
        ^^^^^^^

Error: subworkflows/local/cager/main.nf:98:9: str2_bw was assigned but not declared
```
        str2_bw = row.path.split(" ")[1].minus(']')
        ^^^^^^^
```

Error: subworkflows/local/cager/main.nf:99:17: id is not defined

        return [id, single_end, str1_bw, str2_bw, new_name]
                ^^

Error: subworkflows/local/cager/main.nf:99:21: single_end is not defined

        return [id, single_end, str1_bw, str2_bw, new_name]
                    ^^^^^^^^^^

Error: subworkflows/local/cager/main.nf:99:33: str1_bw is not defined

        return [id, single_end, str1_bw, str2_bw, new_name]
                                ^^^^^^^

Error: subworkflows/local/cager/main.nf:99:42: str2_bw is not defined

        return [id, single_end, str1_bw, str2_bw, new_name]
                                         ^^^^^^^

Error: subworkflows/local/cager/main.nf:99:51: new_name is not defined

        return [id, single_end, str1_bw, str2_bw, new_name]
                                                  ^^^^^^^^

Error: subworkflows/local/cager/main.nf:101:13: id is not defined

    return [id, single_end, str1_bw, new_name]
            ^^

Error: subworkflows/local/cager/main.nf:101:17: single_end is not defined

    return [id, single_end, str1_bw, new_name]
                ^^^^^^^^^^

Error: subworkflows/local/cager/main.nf:101:29: str1_bw is not defined

    return [id, single_end, str1_bw, new_name]
                            ^^^^^^^

Error: subworkflows/local/cager/main.nf:101:38: new_name is not defined

    return [id, single_end, str1_bw, new_name]
                                     ^^^^^^^^

Error: subworkflows/local/deduplication/main.nf:21:9: Incorrect number of call arguments, expected 3 but received 1
```
        SORT_FOR_FIXMATE (
        ^
```
Error: subworkflows/local/deduplication/main.nf:29:9: Incorrect number of call arguments, expected 3 but received 1
```
        SORT_AFTER_FIXMATE(ch_bam_to_sort)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```

Error: subworkflows/local/input_from_folder/main.nf:30:17: Variables in a closure should be declared with def

                num_fields_of_interest = "$params.sample_name_fields".toInteger()
                ^^^^^^^^^^^^^^^^^^^^^^

Error: subworkflows/local/input_from_folder/main.nf:31:17: Variables in a closure should be declared with def

                split_field_num = old_meta.split('_').size()
                ^^^^^^^^^^^^^^^

Error: subworkflows/local/input_from_folder/main.nf:33:21: Variables in a closure should be declared with def
```
                    sample_name = old_meta
                    ^^^^^^^^^^^
```

Error: subworkflows/local/input_from_folder/main.nf:34:21: Variables in a closure should be declared with def

                    lane_n_fastq = tuple(fastq.name, fastq)
                    ^^^^^^^^^^^^

Error: subworkflows/local/input_from_folder/main.nf:36:21: Variables in a closure should be declared with def

                    num_fields_to_cut = split_field_num - num_fields_of_interest
                    ^^^^^^^^^^^^^^^^^

Error: subworkflows/local/input_from_folder/main.nf:46:19: lane_n_fastq is already declared

            meta, lane_n_fastq ->
                  ^^^^^^^^^^^^

Error: subworkflows/local/input_from_folder/main.nf:48:17: Variables in a closure should be declared with def
```
                fastq = lane_n_fastq*.getAt(1).flatten()
                ^^^^^
```
Error: subworkflows/local/mapped_inputs/main.nf:19:5: files_in was assigned but not declared
```
    files_in = row.path
    ^^^^^^^^
```
Error: subworkflows/local/mapped_inputs/main.nf:20:5: files was assigned but not declared
```
    files = files_in.split(' ')
    ^^^^^
```
Error: subworkflows/local/mapped_inputs/main.nf:20:13: files_in is not defined
```
    files = files_in.split(' ')
            ^^^^^^^^
```
Error: subworkflows/local/mapped_inputs/main.nf:21:9: files is not defined
```
    if (files.size() == 2){
        ^^^^^
```
Error: subworkflows/local/mapped_inputs/main.nf:22:9: bigwig_1 was assigned but not declared
```
        bigwig_1 = file(files[0].minus('['))
        ^^^^^^^^
```

Error: subworkflows/local/mapped_inputs/main.nf:22:25: files is not defined

        bigwig_1 = file(files[0].minus('['))
                        ^^^^^

Error: subworkflows/local/mapped_inputs/main.nf:23:9: bigwig_2 was assigned but not declared
```
        bigwig_2 = file(files[1].minus(']'))
        ^^^^^^^^
```

Error: subworkflows/local/mapped_inputs/main.nf:23:25: files is not defined

        bigwig_2 = file(files[1].minus(']'))
                        ^^^^^

Error: subworkflows/local/mapped_inputs/main.nf:24:17: bigwig_1 is not defined
```
        return [bigwig_1, bigwig_2]
                ^^^^^^^^
```

Error: subworkflows/local/mapped_inputs/main.nf:24:27: bigwig_2 is not defined

        return [bigwig_1, bigwig_2]
                          ^^^^^^^^

Error: subworkflows/local/mapped_inputs/main.nf:25:16: files is not defined
```
    } else if (files.size() == 1){
               ^^^^^
```
Error: subworkflows/local/mapped_inputs/main.nf:26:9: bam was assigned but not declared
```
        bam = file(files[0].minus('[').minus(']'))
        ^^^
```

Error: subworkflows/local/mapped_inputs/main.nf:26:20: files is not defined

        bam = file(files[0].minus('[').minus(']'))
                   ^^^^^

Error: subworkflows/local/mapped_inputs/main.nf:27:17: bam is not defined
```
        return [bam]
                ^^^
```

Error: subworkflows/local/star/main.nf:55:51: wigs is already declared

            wigs_for_conversion = wigs.map{ meta, wigs ->
                                                  ^^^^

Error: subworkflows/local/star/main.nf:57:17: Variables in a closure should be declared with def

                wigs_to_use = [wigs[0], wigs[1]]
                ^^^^^^^^^^^

Error: subworkflows/local/star/main.nf:61:51: wigs is already declared

            wigs_for_conversion = wigs.map{ meta, wigs ->
                                                  ^^^^

Error: workflows/customcage.nf:98:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
def multiqc_report = []
^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/customcage.nf:188:17: Variables in a closure should be declared with def
```
                file1 = paths[0]
                ^^^^^
```
Error: workflows/customcage.nf:189:17: Variables in a closure should be declared with def
```
                file2 = paths[1]
                ^^^^^
```

⚠️ Warnings

Warning: modules/local/cagefightr/enhancer_calling/main.nf:29:25: The use of projectDir in a process is discouraged -- input files should be provided as process inputs
```
        --project_dir ${projectDir}
                        ^^^^^^^^^^
```
Warning: modules/local/cager/processing/main.nf:46:25: The use of projectDir in a process is discouraged -- input files should be provided as process inputs
```
        --project_dir ${projectDir} \
                        ^^^^^^^^^^
```
Warning: modules/local/cager/readin/main.nf:30:25: The use of projectDir in a process is discouraged -- input files should be provided as process inputs
```
        --project_dir ${projectDir} \
                        ^^^^^^^^^^
```
Warning: modules/local/cager/tag_qc/main.nf:35:25: The use of projectDir in a process is discouraged -- input files should be provided as process inputs
```
        --project_dir ${projectDir}
                        ^^^^^^^^^^
```
Warning: modules/local/cager/tagcluster_qc/main.nf:39:25: The use of projectDir in a process is discouraged -- input files should be provided as process inputs
```
        --project_dir ${projectDir} \
                        ^^^^^^^^^^
```
Warning: modules/local/samtools/dedup/main.nf:33:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/samtools/view_mapq/main.nf:37:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/ucsc/wigtobigwig/main.nf:47:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```

Warning: subworkflows/local/bowtie2/main.nf:18:52: Parameter was not used -- prefix with _ to suppress warning

        sample_meta = ch_reads_to_align.map{ meta, fastq ->
                                                   ^^^^^

Warning: subworkflows/local/bowtie2/main.nf:26:74: Parameter was not used -- prefix with _ to suppress warning

            ch_index = sample_meta.combine(BOWTIE2_BUILD.out.index.map { genome_name, index -> index } )
                                                                         ^^^^^^^^^^^

Warning: subworkflows/local/bowtie2/main.nf:28:59: Parameter was not used -- prefix with _ to suppress warning

            ch_index = sample_meta.combine(ch_index.map { genome_name, index -> index })
                                                          ^^^^^^^^^^^

Warning: subworkflows/local/bowtie2/main.nf:32:59: Parameter was not used -- prefix with _ to suppress warning

            ch_fasta = sample_meta.combine(ch_fasta.map { genome_name, fasta -> fasta } )
                                                          ^^^^^^^^^^^

Warning: subworkflows/local/bowtie2/main.nf:44:79: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_multiqc_files = ch_multiqc_files.mix(BOWTIE2_ALIGN.out.log.collect{it[1]})
                                                                              ^^

Warning: subworkflows/local/cager/main.nf:26:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_data_type = Channel.of("bam")
                           ^^^^^^^
```
Warning: subworkflows/local/cager/main.nf:28:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_data_type = Channel.of(params.datatype)
                           ^^^^^^^
```
Warning: subworkflows/local/cager/main.nf:33:43: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .map { create_mapping_channel(it) }
                                          ^^
```
Warning: subworkflows/local/cager/main.nf:74:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_template = Channel.fromPath(params.markdown_path)
                      ^^^^^^^
```
Warning: subworkflows/local/mapped_inputs/main.nf:12:38: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { create_sample_channel(it) }
                                     ^^
```
Warning: subworkflows/local/parameter_checks/main.nf:23:29: The use of Channel to access channel factories is deprecated -- use channel instead
```
            input_handler = Channel.fromPath(params.input, checkIfExists: true)
                            ^^^^^^^
```
Warning: subworkflows/local/parameter_checks/main.nf:29:45: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                .map { create_fastq_channel(it) }
                                            ^^
```

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

        sample_meta = ch_fastq.map{ meta, fastq ->
                                          ^^^^^

Warning: subworkflows/local/parameter_checks/main.nf:47:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_genome_name = Channel.of(params.genome_name)
                         ^^^^^^^
```
Warning: subworkflows/local/parameter_checks/main.nf:53:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_pre_idx = Channel.fromPath(params.index, checkIfExists: true)
                         ^^^^^^^
```
Warning: subworkflows/local/parameter_checks/main.nf:56:29: The use of Channel to access channel factories is deprecated -- use channel instead
```
                ch_pre_fa = Channel.fromPath(params.genome, checkIfExists: true)
                            ^^^^^^^
```
Warning: subworkflows/local/parameter_checks/main.nf:59:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
                ch_fasta = Channel.empty()
                           ^^^^^^^
```
Warning: subworkflows/local/parameter_checks/main.nf:62:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_pre_fa = Channel.fromPath(params.genome, checkIfExists: true)
                        ^^^^^^^
```
Warning: subworkflows/local/parameter_checks/main.nf:64:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_index = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/local/prepare_cager_metadata/main.nf:41:9: Variable was declared but not used
```
        ch_txdb = GTF2TXDB(ch_gtf)
        ^^^^^^^
```

Warning: subworkflows/local/prepare_mapping_metadata/main.nf:17:43: Parameter was not used -- prefix with _ to suppress warning

            chrom_size_fa = ch_fasta.map{ meta, fasta ->
                                          ^^^^

Warning: subworkflows/local/prepare_mapping_metadata/main.nf:30:30: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_chrom_sizes = Channel.of([
                             ^^^^^^^
```

Warning: subworkflows/local/preprocessing/main.nf:40:72: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: subworkflows/local/preprocessing/main.nf:41:76: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_multiqc_files = ch_multiqc_files.mix(TRIMGALORE.out.log.collect{it[1]}.ifEmpty([]))
                                                                           ^^

Warning: subworkflows/local/preprocessing/main.nf:42:76: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: subworkflows/local/samtools/main.nf:16:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_index_format = Channel.value("bai")
                          ^^^^^^^
```
Warning: subworkflows/local/star/main.nf:21:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_genome_name = Channel.of(params.genome_name)
                         ^^^^^^^
```

Warning: subworkflows/local/star/main.nf:23:52: Parameter was not used -- prefix with _ to suppress warning

        sample_meta = ch_reads_to_align.map{ meta, fastq ->
                                                   ^^^^^

Warning: subworkflows/local/star/main.nf:32:80: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_index = sample_meta.combine(STAR_GENOMEGENERATE.out.index.map { it[1] })
                                                                               ^^

Warning: subworkflows/local/star/main.nf:46:82: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_multiqc_files = ch_multiqc_files.mix(STAR_ALIGN.out.log_final.collect{it[1]})
                                                                                 ^^

Warning: subworkflows/local/star/main.nf:48:53: Parameter was not used -- prefix with _ to suppress warning

        ch_chrom_sizes_for_wig = ch_chrom_sizes.map{meta, sizes ->
                                                    ^^^^

Warning: subworkflows/local/utils_nfcore_customcage_pipeline/main.nf:28:5: Parameter was not used -- prefix with _ to suppress warning
```
    monochrome_logs   // boolean: Do not use coloured log outputs
    ^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_customcage_pipeline/main.nf:34:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_customcage_pipeline/main.nf:80:5: Parameter was not used -- prefix with _ to suppress warning
```
    hook_url        //  string: hook URL for notifications
    ^^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_customcage_pipeline/main.nf:81:5: Parameter was not used -- prefix with _ to suppress warning
```
    multiqc_report  //  string: Path to MultiQC report
    ^^^^^^^^^^^^^^
```

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/customcage.nf:98:5: Variable was declared but not used
```
def multiqc_report = []
    ^^^^^^^^^^^^^^
```
Warning: workflows/customcage.nf:108:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_gtf = Channel.fromPath(params.gtf, checkIfExists: true)
                     ^^^^^^^
```

Warning: workflows/customcage.nf:119:32: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_cager_sample_file = Channel.fromPath(params.cager_sample_file)
                               ^^^^^^^

Warning: workflows/customcage.nf:125:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_files = Channel.empty()
                       ^^^^^^^
```
Warning: workflows/customcage.nf:129:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_fasta = Channel.empty()
                   ^^^^^^^
```
Warning: workflows/customcage.nf:130:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_index = Channel.empty()
                   ^^^^^^^
```
Warning: workflows/customcage.nf:178:19: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .map{[it[3], it[4]]}
                  ^^
```
Warning: workflows/customcage.nf:178:26: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .map{[it[3], it[4]]}
                         ^^
```

Warning: workflows/customcage.nf:183:49: Parameter was not used -- prefix with _ to suppress warning

            mapped_files_ch = ch_for_cager.map{ meta, paths ->
                                                ^^^^

Warning: workflows/customcage.nf:187:49: Parameter was not used -- prefix with _ to suppress warning

            mapped_files_ch = ch_for_cager.map{ meta, paths ->
                                                ^^^^

Warning: workflows/customcage.nf:264:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_config        = Channel.fromPath(
                               ^^^^^^^
```
Warning: workflows/customcage.nf:267:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.multiqc_config, checkIfExists: true) :
        ^^^^^^^
```
Warning: workflows/customcage.nf:268:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.empty()
        ^^^^^^^
```
Warning: workflows/customcage.nf:270:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
        ^^^^^^^
```
Warning: workflows/customcage.nf:271:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.empty()
        ^^^^^^^
```
Warning: workflows/customcage.nf:275:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
                          ^^^^^^^
```

Warning: workflows/customcage.nf:281:45: The use of Channel to access channel factories is deprecated -- use channel instead

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

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