Nextflow lint results

Generated: 2026-03-07T00:19:44.000366043Z
Nextflow version: 26.02.0-edge
Summary: 26 errors, 55 warnings

❌ Errors

Error: conf/modules.config:125:1: If statements cannot be mixed with config statements
```
if (!params.skip_bbsplit && params.bbsplit_fasta_list) {
^
```
Error: conf/modules.config:138:1: If statements cannot be mixed with config statements
```
if (params.remove_ribo_rna && params.ribo_database_manifest) {
^
```
Error: conf/modules.config:176:1: If statements cannot be mixed with config statements
```
if (! params.skip_linting) {
^
```
Error: conf/modules.config:219:1: If statements cannot be mixed with config statements
```
if (!(params.skip_fastqc || params.skip_qc)) {
^
```
Error: conf/modules.config:270:1: If statements cannot be mixed with config statements
```
if (!params.skip_trimming) {
^
```
Error: conf/modules.config:356:1: If statements cannot be mixed with config statements
```
if (params.with_umi && !params.skip_umi_extract) {
^
```
Error: conf/modules.config:386:1: If statements cannot be mixed with config statements
```
if (!params.skip_bbsplit) {
^
```
Error: conf/modules.config:407:1: If statements cannot be mixed with config statements
```
if (params.remove_ribo_rna) {
^
```
Error: conf/modules.config:543:1: If statements cannot be mixed with config statements
```
if (!params.skip_alignment) {
^
```
Error: conf/modules.config:629:1: If statements cannot be mixed with config statements
```
if (!params.skip_alignment && params.aligner == 'star') {
^
```
Error: conf/modules.config:925:1: If statements cannot be mixed with config statements
```
if (!params.skip_coverage_tracks) {
^
```
Error: conf/modules.config:950:1: If statements cannot be mixed with config statements
```
if (!params.skip_multiqc) {
^
```
Error: conf/modules.config:967:1: If statements cannot be mixed with config statements
```
if (!params.skip_ribotish) {
^
```
Error: conf/modules.config:996:1: If statements cannot be mixed with config statements
```
if (!params.skip_ribotricer) {
^
```
Error: conf/modules.config:1027:1: If statements cannot be mixed with config statements
```
if (!params.skip_ribocode) {
^
```
Error: conf/modules.config:1064:1: If statements cannot be mixed with config statements
```
if (!params.skip_ribowaltz) {
^
```
Error: conf/modules.config:1077:1: If statements cannot be mixed with config statements
```
if (!params.skip_plastid) {
^
```
Error: conf/modules.config:1119:1: If statements cannot be mixed with config statements
```
if (params.contrasts) {
^
```
Error: main.nf:18:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/riboseq/workflows/riboseq/main.nf'
```
include { RIBOSEQ                 } from './workflows/riboseq'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: main.nf:103:5: RIBOSEQ is not defined
```
    RIBOSEQ (
    ^^^^^^^
```

Error: main.nf:120:35: RIBOSEQ is not defined

    ch_versions = ch_versions.mix(RIBOSEQ.out.versions)
                                  ^^^^^^^

Error: main.nf:123:22: RIBOSEQ is not defined

    multiqc_report = RIBOSEQ.out.multiqc_report // channel: /path/to/multiqc_report.html
                     ^^^^^^^

Error: subworkflows/local/prepare_genome/main.nf:119:42: fasta is already declared

            ch_fasta.combine(ch_gtf).map{fasta, gtf -> [[:], fasta, gtf]},
                                         ^^^^^

Error: subworkflows/local/prepare_genome/main.nf:119:49: gtf is already declared

            ch_fasta.combine(ch_gtf).map{fasta, gtf -> [[:], fasta, gtf]},
                                                ^^^

Error: subworkflows/local/prepare_genome/main.nf:175:32: fasta is already declared

                .flatMap { id, fasta -> [ [ 'id', id ], [ 'fasta', file(fasta, checkIfExists: true) ] ] } // Flatten entries to be able to groupTuple by a common key
                               ^^^^^

Error: workflows/riboseq/main.nf:303:64: Unexpected input: '\n'

                        [meta + [strand: strand, strand_filter:
                                                               ^

⚠️ Warnings

Warning: conf/modules.config:351:45: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { params.save_trimmed ? it : null }
                                            ^^

Warning: main.nf:54:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: main.nf:87:39: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .map { checkMaxContigSize(it) }
                                      ^^
```

Warning: main.nf:93:22: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_samplesheet = Channel.value(file(params.input, checkIfExists: true))
                     ^^^^^^^

Warning: main.nf:95:29: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_contrasts_file = Channel.value(file(params.contrasts))
                            ^^^^^^^

Warning: main.nf:101:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bowtie2_index = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/local/fastq_equalise_read_lengths/main.nf:68:25: Parameter was not used -- prefix with _ to suppress warning
```
        .filter { meta, reads -> meta.pair != null }
                        ^^^^^
```
Warning: subworkflows/local/fastq_equalise_read_lengths/main.nf:69:22: Parameter was not used -- prefix with _ to suppress warning
```
        .map { meta, reads -> meta.pair }
                     ^^^^^
```
Warning: subworkflows/local/fastq_equalise_read_lengths/main.nf:76:25: Parameter was not used -- prefix with _ to suppress warning
```
        .filter { meta, reads, pairs_needed ->
                        ^^^^^
```
Warning: subworkflows/local/fastq_equalise_read_lengths/main.nf:79:29: Parameter was not used -- prefix with _ to suppress warning
```
        .map { meta, reads, pairs_needed -> [ meta, reads ] }
                            ^^^^^^^^^^^^
```

Warning: subworkflows/local/fastq_equalise_read_lengths/main.nf:92:56: Implicit closure parameter is deprecated, declare an explicit parameter instead

                def avg_len_idx = header.findIndexOf { it == 'avg_len' }
                                                       ^^

Warning: subworkflows/local/fastq_equalise_read_lengths/main.nf:103:16: Parameter was not used -- prefix with _ to suppress warning
```
        .map { pair, meta, reads, riboseq_trim_len ->
               ^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:56:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:62:68: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_fasta    = GUNZIP_FASTA ( [ [:], fasta ] ).gunzip.map { it[1] }
                                                                   ^^

Warning: subworkflows/local/prepare_genome/main.nf:64:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_fasta = Channel.value(file(fasta))
                   ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:73:72: Implicit closure parameter is deprecated, declare an explicit parameter instead

                ch_gtf      = GUNZIP_GTF ( [ [:], gtf ] ).gunzip.map { it[1] }
                                                                       ^^

Warning: subworkflows/local/prepare_genome/main.nf:75:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
                ch_gtf = Channel.value(file(gtf))
                         ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:79:72: Implicit closure parameter is deprecated, declare an explicit parameter instead

                ch_gff      = GUNZIP_GFF ( [ [:], gff ] ).gunzip.map { it[1] }
                                                                       ^^

Warning: subworkflows/local/prepare_genome/main.nf:81:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
                ch_gff = Channel.value(file(gff))
                         ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:113:95: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_add_fasta = GUNZIP_ADDITIONAL_FASTA ( [ [:], additional_fasta ] ).gunzip.map { it[1] }
                                                                                              ^^

Warning: subworkflows/local/prepare_genome/main.nf:115:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_add_fasta = Channel.value(file(additional_fasta))
                           ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:120:36: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            ch_add_fasta.map{[[:], it]},
                                   ^^
```

Warning: subworkflows/local/prepare_genome/main.nf:123:63: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_fasta    = CUSTOM_CATADDITIONALFASTA.out.fasta.map{it[1]}.first()
                                                              ^^

Warning: subworkflows/local/prepare_genome/main.nf:124:61: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_gtf      = CUSTOM_CATADDITIONALFASTA.out.gtf.map{it[1]}.first()
                                                            ^^

Warning: subworkflows/local/prepare_genome/main.nf:133:102: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_transcript_fasta = GUNZIP_TRANSCRIPT_FASTA ( [ [:], transcript_fasta ] ).gunzip.map { it[1] }
                                                                                                     ^^

Warning: subworkflows/local/prepare_genome/main.nf:135:35: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_transcript_fasta = Channel.value(file(transcript_fasta))
                                  ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:149:44: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    SAMTOOLS_FAIDX ( ch_fasta.map { [ [:], it, [] ] }, true )
                                           ^^
```
Warning: subworkflows/local/prepare_genome/main.nf:150:51: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    ch_fai         = SAMTOOLS_FAIDX.out.fai.map { it[1] }
                                                  ^^
```
Warning: subworkflows/local/prepare_genome/main.nf:151:53: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    ch_chrom_sizes = SAMTOOLS_FAIDX.out.sizes.map { it[1] }
                                                    ^^
```
Warning: subworkflows/local/prepare_genome/main.nf:163:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bbsplit_index = Channel.empty()
                       ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:167:95: Implicit closure parameter is deprecated, declare an explicit parameter instead

                ch_bbsplit_index = UNTAR_BBSPLIT_INDEX ( [ [:], bbsplit_index ] ).untar.map { it[1] }
                                                                                              ^^

Warning: subworkflows/local/prepare_genome/main.nf:169:36: The use of Channel to access channel factories is deprecated -- use channel instead
```
                ch_bbsplit_index = Channel.value(file(bbsplit_index))
                                   ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:172:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel
            ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:178:30: Implicit closure parameter is deprecated, declare an explicit parameter instead

                .collect { [ it ] } // Collect entries as a list to pass as "tuple val(short_names), path(path_to_fasta)" to module
                             ^^

Warning: subworkflows/local/prepare_genome/main.nf:188:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_sortmerna_index = Channel.empty()
                         ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:189:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_rrna_fastas = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:194:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_rrna_fastas = Channel.from(ribo_db.readLines())
                         ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:202:101: Implicit closure parameter is deprecated, declare an explicit parameter instead

                ch_sortmerna_index = UNTAR_SORTMERNA_INDEX ( [ [:], sortmerna_index ] ).untar.map { it[1] }
                                                                                                    ^^

Warning: subworkflows/local/prepare_genome/main.nf:204:38: The use of Channel to access channel factories is deprecated -- use channel instead
```
                ch_sortmerna_index = Channel.value(file(sortmerna_index))
                                     ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:208:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
                Channel.of([ [],[] ]),
                ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:209:63: Implicit closure parameter is deprecated, declare an explicit parameter instead

                ch_rrna_fastas.collect().map { [ 'rrna_refs', it ] },
                                                              ^^

Warning: subworkflows/local/prepare_genome/main.nf:210:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
                Channel.of([ [],[] ])
                ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:219:21: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_star_index = Channel.empty()
                    ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:223:86: Implicit closure parameter is deprecated, declare an explicit parameter instead

                ch_star_index = UNTAR_STAR_INDEX ( [ [:], star_index ] ).untar.map { it[1] }
                                                                                     ^^

Warning: subworkflows/local/prepare_genome/main.nf:225:33: The use of Channel to access channel factories is deprecated -- use channel instead
```
                ch_star_index = Channel.value(file(star_index))
                                ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:238:77: Implicit closure parameter is deprecated, declare an explicit parameter instead

                ch_star_index = STAR_GENOMEGENERATE ( ch_fasta.map { [ [:], it ] }, ch_gtf.map { [ [:], it ] } ).index.map { it[1] }
                                                                            ^^

Warning: subworkflows/local/prepare_genome/main.nf:238:105: Implicit closure parameter is deprecated, declare an explicit parameter instead

                ch_star_index = STAR_GENOMEGENERATE ( ch_fasta.map { [ [:], it ] }, ch_gtf.map { [ [:], it ] } ).index.map { it[1] }
                                                                                                        ^^

Warning: subworkflows/local/prepare_genome/main.nf:238:126: Implicit closure parameter is deprecated, declare an explicit parameter instead

                ch_star_index = STAR_GENOMEGENERATE ( ch_fasta.map { [ [:], it ] }, ch_gtf.map { [ [:], it ] } ).index.map { it[1] }
                                                                                                                             ^^

Warning: subworkflows/local/prepare_genome/main.nf:246:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_salmon_index = Channel.empty()
                      ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:249:88: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_salmon_index = UNTAR_SALMON_INDEX ( [ [:], salmon_index ] ).untar.map { it[1] }
                                                                                       ^^

Warning: subworkflows/local/prepare_genome/main.nf:251:31: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_salmon_index = Channel.value(file(salmon_index))
                              ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:262:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_salmon_index_te = Channel.empty()
                         ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_riboseq_pipeline/main.nf:31:5: Parameter was not used -- prefix with _ to suppress warning
```
    monochrome_logs   // boolean: Do not use coloured log outputs
    ^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_riboseq_pipeline/main.nf:34:5: Parameter was not used -- prefix with _ to suppress warning
```
    input             //  string: Path to input samplesheet
    ^^^^^
```
Warning: subworkflows/local/utils_nfcore_riboseq_pipeline/main.nf:142:5: Parameter was not used -- prefix with _ to suppress warning
```
    hook_url        //  string: hook URL for notifications
    ^^^^^^^^
```

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Nextflow lint results

❌ Errors

⚠️ Warnings

FilesExpand file tree

riboseq_lint.md

Latest commit

History

riboseq_lint.md

File metadata and controls

Nextflow lint results

❌ Errors

⚠️ Warnings