Nextflow lint results

Generated: 2026-01-16T10:26:39.790798200Z
Nextflow version: 25.12.0-edge
Summary: 45 errors, 42 warnings

❌ Errors

Error: conf/base.config:13:16: check_max is not defined

    cpus   = { check_max( 3    * task.attempt, 'cpus'   ) }
               ^^^^^^^^^

Error: conf/base.config:14:16: check_max is not defined

    memory = { check_max( 6.GB * task.attempt, 'memory' ) }
               ^^^^^^^^^

Error: conf/base.config:15:16: check_max is not defined

    time   = { check_max( 4.h  * task.attempt, 'time'   ) }
               ^^^^^^^^^

Error: conf/base.config:29:20: check_max is not defined

        cpus   = { check_max( 1                  , 'cpus'    ) }
                   ^^^^^^^^^

Error: conf/base.config:30:20: check_max is not defined

        memory = { check_max( 15.GB * task.attempt, 'memory'  ) }
                   ^^^^^^^^^

Error: conf/base.config:31:20: check_max is not defined

        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
                   ^^^^^^^^^

Error: conf/base.config:34:20: check_max is not defined

        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
                   ^^^^^^^^^

Error: conf/base.config:35:20: check_max is not defined

        memory = { check_max( 1.GB * task.attempt, 'memory'  ) }
                   ^^^^^^^^^

Error: conf/base.config:36:20: check_max is not defined

        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
                   ^^^^^^^^^

Error: conf/base.config:39:20: check_max is not defined

        cpus   = { check_max( 5     * task.attempt, 'cpus'    ) }
                   ^^^^^^^^^

Error: conf/base.config:40:20: check_max is not defined

        memory = { check_max( 5.GB * task.attempt, 'memory'  ) }
                   ^^^^^^^^^

Error: conf/base.config:41:20: check_max is not defined

        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
                   ^^^^^^^^^

Error: conf/base.config:44:20: check_max is not defined

        cpus   = { check_max( 6     * task.attempt, 'cpus'    ) }
                   ^^^^^^^^^

Error: conf/base.config:45:20: check_max is not defined

        memory = { check_max( 15.GB * task.attempt, 'memory'  ) }
                   ^^^^^^^^^

Error: conf/base.config:46:20: check_max is not defined

        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
                   ^^^^^^^^^

Error: conf/base.config:49:20: check_max is not defined

        cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
                   ^^^^^^^^^

Error: conf/base.config:50:20: check_max is not defined

        memory = { check_max( 55.GB * task.attempt, 'memory'  ) }
                   ^^^^^^^^^

Error: conf/base.config:51:20: check_max is not defined

        time   = { check_max( 16.h  * task.attempt, 'time'    ) }
                   ^^^^^^^^^

Error: conf/base.config:54:20: check_max is not defined

        cpus   = { check_max( 1    * task.attempt, 'cpus'    ) }
                   ^^^^^^^^^

Error: conf/base.config:55:20: check_max is not defined

        memory = { check_max( 100.GB * task.attempt, 'memory'  ) }
                   ^^^^^^^^^

Error: conf/base.config:56:20: check_max is not defined

        time   = { check_max( 16.h  * task.attempt, 'time'    ) }
                   ^^^^^^^^^

Error: conf/base.config:59:20: check_max is not defined

        time   = { check_max( 20.h  * task.attempt, 'time'    ) }
                   ^^^^^^^^^

Error: conf/base.config:62:20: check_max is not defined

        memory = { check_max( 200.GB * task.attempt, 'memory' ) }
                   ^^^^^^^^^

Error: conf/base.config:63:20: check_max is not defined

        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
                   ^^^^^^^^^

Error: main.nf:28:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
WorkflowMain.initialise(workflow, params, log)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```

Error: main.nf:28:1: WorkflowMain is not defined

WorkflowMain.initialise(workflow, params, log)
^^^^^^^^^^^^

Error: main.nf:36:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/radseq/workflows/radseq.nf'
```
include { RADSEQ } from './workflows/radseq'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: main.nf:42:5: RADSEQ is not defined
```
    RADSEQ ()
    ^^^^^^
```

Error: modules/local/bcftools/main.nf:78:23: extension is not defined

    touch ${prefix}.${extension}
                      ^^^^^^^^^

Error: modules/local/prepare_forward_reads.nf:91:86: assembled_fastq is not defined

        awk 'BEGIN{P=1}{if(P==1||P==2){gsub(/^[@]/,">");print}; if(P==4)P=0; P++}' ${assembled_fastq} | \\
                                                                                     ^^^^^^^^^^^^^^^

Error: modules/local/rbmerge2fasta.nf:12:16: meta is already declared
```
    tuple val (meta), path (rbmerge)
               ^^^^
```
Error: modules/nf-core/bcftools/view/main.nf:57:23: extension is not defined
```
    touch ${prefix}.${extension}
                      ^^^^^^^^^
```

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

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

Error: modules/nf-core/fgbio/zipperbams/main.nf:12:15: meta is already declared
```
    tuple val(meta), path(mapped_bam)
              ^^^^
```

Error: modules/nf-core/freebayes/main.nf:27:9: targets_file is already declared

    def targets_file     = target_bed     ? "--target ${target_bed}"       : ""
        ^^^^^^^^^^^^

Error: nextflow.config:190:5: Unexpected input: 'includeConfig'

    includeConfig "${params.custom_config_base}/nfcore_custom.config"
    ^

Error: subworkflows/local/bam_intervals_bedtools.nf:30:36: WorkflowRadseq is not defined

    ch_bed_to_merge = ch_bed.map { WorkflowRadseq.groupMetaID(it) }.groupTuple() // [meta, bed]
                                   ^^^^^^^^^^^^^^

Error: subworkflows/local/bam_intervals_bedtools.nf:44:37: WorkflowRadseq is not defined

        ch_cov_to_merge = cov.map { WorkflowRadseq.groupMetaID(it) }.groupTuple()
                                    ^^^^^^^^^^^^^^

Error: subworkflows/local/bam_intervals_bedtools.nf:69:41: WorkflowRadseq is not defined

        ch_intervals = ch_fai_bed.map { WorkflowRadseq.splitBedFile(params, log, it) }.transpose()
                                        ^^^^^^^^^^^^^^

Error: subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf:43:5: Incorrect number of call arguments, expected 1 but received 2
```
    BAM_STATS_SAMTOOLS ( ch_bam_bai, [] )
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```

Error: subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf:83:9: Incorrect number of call arguments, expected 4 but received 5

        BWAMEM1_MEM_PRE ( BAM2FASTQ_PRE.out.fastq, bwaindex, true, params.sequence_type, read_lengths.collect() )
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf:100:9: Incorrect number of call arguments, expected 4 but received 5

        BWAMEM2_MEM_PRE ( BAM2FASTQ_PRE.out.fastq, bwaindex, true, params.sequence_type, read_lengths.collect() ) // reads, BWAMEM2_INDEX.out.index.first(), true, params.sequence_type, read_lengths.collect()
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf:182:9: Incorrect number of call arguments, expected 4 but received 5

        BWAMEM1_MEM_POST ( BAM2FASTQ_POST.out.fastq, bwaindex, false, params.sequence_type, read_lengths.collect() )
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf:187:9: Incorrect number of call arguments, expected 4 but received 5

        BWAMEM2_MEM_POST ( BAM2FASTQ_POST.out.fastq, bwaindex, false, params.sequence_type, read_lengths.collect() )
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/radseq.nf:92:26: Unexpected input: '\n'

        case 'reference':
                         ^

⚠️ Warnings

Warning: modules/local/rbmerge2fasta.nf:11:16: Variable was declared but not used
```
    tuple val (meta), path (rbdiv)
               ^^^^
```
Warning: modules/nf-core/custom/dumpsoftwareversions/main.nf:22:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/fastqc/main.nf:27:48: Parameter was not used -- prefix with _ to suppress warning

    def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
                                               ^^^^^^^^

Warning: modules/nf-core/fgbio/zipperbams/main.nf:11:15: Variable was declared but not used
```
    tuple val(meta), path(unmapped_bam)
              ^^^^
```
Warning: modules/nf-core/fgbio/zipperbams/main.nf:25:9: Variable was declared but not used
```
    def args2 = task.ext.args2 ?: ''
        ^^^^^
```
Warning: modules/nf-core/samtools/flagstat/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/samtools/idxstats/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/samtools/stats/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/tabix/tabix/main.nf:33:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: subworkflows/local/bam_intervals_bedtools.nf:20:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/local/bam_intervals_bedtools.nf:30:63: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_bed_to_merge = ch_bed.map { WorkflowRadseq.groupMetaID(it) }.groupTuple() // [meta, bed]
                                                              ^^

Warning: subworkflows/local/bam_intervals_bedtools.nf:37:60: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_sorted_mbed = BEDTOOLS_SORT (ch_mbed, faidx.map{it[1]}).sorted
                                                           ^^

Warning: subworkflows/local/bam_intervals_bedtools.nf:41:68: Implicit closure parameter is deprecated, declare an explicit parameter instead

        cov = BEDTOOLS_COVERAGE (ch_bed.combine(ch_sorted_mbed.map{it[1]}).map{meta,bed,mbed -> [meta,mbed,bed]}, faidx.map{it[1]}).bed
                                                                   ^^

Warning: subworkflows/local/bam_intervals_bedtools.nf:41:125: Implicit closure parameter is deprecated, declare an explicit parameter instead

        cov = BEDTOOLS_COVERAGE (ch_bed.combine(ch_sorted_mbed.map{it[1]}).map{meta,bed,mbed -> [meta,mbed,bed]}, faidx.map{it[1]}).bed
                                                                                                                            ^^

Warning: subworkflows/local/bam_intervals_bedtools.nf:44:64: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_cov_to_merge = cov.map { WorkflowRadseq.groupMetaID(it) }.groupTuple()
                                                               ^^

Warning: subworkflows/local/bam_intervals_bedtools.nf:47:66: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_mcov = BEDTOOLS_MERGE_COV (ch_cov_to_merge, faidx.map{it[1]}).cov
                                                                 ^^

Warning: subworkflows/local/bam_intervals_bedtools.nf:69:82: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_intervals = ch_fai_bed.map { WorkflowRadseq.splitBedFile(params, log, it) }.transpose()
                                                                                 ^^

Warning: subworkflows/local/fastq_unzip.nf:9:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/fastq_unzip.nf:15:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_fasta    = Channel.fromPath(fasta).map{[ [:], it ]}
                      ^^^^^^^
```

Warning: subworkflows/local/fastq_unzip.nf:15:58: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_fasta    = Channel.fromPath(fasta).map{[ [:], it ]}
                                                         ^^

Warning: subworkflows/local/input_check.nf:15:38: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { create_fastq_channels(it) }
                                     ^^
```
Warning: subworkflows/local/vcf_bcftools_radseq_filters.nf:15:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/vcf_bcftools_radseq_filters.nf:24:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_miss = Channel.fromList(params.fraction_missingness_list)
              ^^^^^^^
```
Warning: subworkflows/local/vcf_bcftools_radseq_filters.nf:25:14: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_mac = Channel.fromList(params.minor_allele_count_list)
             ^^^^^^^
```
Warning: subworkflows/nf-core/bam_dedup_stats_samtools_umitools/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:14:19: 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:19:56: Parameter was not used -- prefix with _ to suppress warning

    SAMTOOLS_FLAGSTAT ( bam_bai_fasta.map{meta,bam,bai,fasta-> [meta,bam,bai]} )
                                                       ^^^^^

Warning: subworkflows/nf-core/bam_stats_samtools/main.nf:22:56: Parameter was not used -- prefix with _ to suppress warning

    SAMTOOLS_IDXSTATS ( bam_bai_fasta.map{meta,bam,bai,fasta-> [meta,bam,bai]} )
                                                       ^^^^^

Warning: subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf:40:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf:57:5: Variable was declared but not used
```
    check_bam = FASTQTOBAM.out.bam.dump(tag: 'fastq_to_bam')
    ^^^^^^^^^
```
Warning: subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf:64:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    aligned_bam = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf:71:13: Variable was declared but not used

            check_module_out = BWAMEM1_INDEX.out.index.dump(tag: 'index_out')
            ^^^^^^^^^^^^^^^^

Warning: subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf:75:48: The use of Channel to access channel factories is deprecated -- use channel instead

        bwaindex    = fasta_meta ? bwa_index ? Channel.fromPath(bwa_index).collect().map{ it -> [[id:it[0].baseName], it] } : BWAMEM1_INDEX.out.index : []
                                               ^^^^^^^

Warning: subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf:94:48: The use of Channel to access channel factories is deprecated -- use channel instead

        bwaindex    = fasta_meta ? bwa_index ? Channel.fromPath(bwa_index).collect().map{ it -> [[id:it[0].baseName], it] } : BWAMEM2_INDEX.out.index : []
                                               ^^^^^^^

Warning: subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf:107:65: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ZIPPERBAMS_PRE ( FASTQTOBAM.out.bam, aligned_bam, fasta.map{it[1]}, dict.map{it[1]} )
                                                                ^^

Warning: subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf:107:82: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ZIPPERBAMS_PRE ( FASTQTOBAM.out.bam, aligned_bam, fasta.map{it[1]}, dict.map{it[1]} )
                                                                                 ^^

Warning: subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf:114:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    groupready_bam = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf:125:9: Variable was declared but not used
```
        check_dummy_bam_bai = dummy_bam_bai.dump(tag: 'dummy_index')
        ^^^^^^^^^^^^^^^^^^^
```
Warning: subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf:151:21: The use of Channel to access channel factories is deprecated -- use channel instead
```
    consensus_bam = Channel.empty()
                    ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf:172:48: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    FILTERCONSENSUS ( consensus_bam, fasta.map{it[1]} )
                                               ^^
```

Warning: subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf:194:66: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ZIPPERBAMS_POST ( consensus_bam, aligned_bam_post, fasta.map{it[1]}, dict.map{it[1]} )
                                                                 ^^

Warning: subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf:194:83: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ZIPPERBAMS_POST ( consensus_bam, aligned_bam_post, fasta.map{it[1]}, dict.map{it[1]} )
                                                                                  ^^

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