Nextflow lint results

Generated: 2026-03-07T00:18:41.564775322Z
Nextflow version: 26.02.0-edge
Summary: 13 errors, 45 warnings

❌ Errors

Error: main.nf:36:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/crisprseq/workflows/crisprseq_targeted.nf'
```
include { CRISPRSEQ_TARGETED  } from './workflows/crisprseq_targeted'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```

Error: main.nf:56:9: CRISPRSEQ_TARGETED is not defined

        CRISPRSEQ_TARGETED (
        ^^^^^^^^^^^^^^^^^^

Error: main.nf:62:29: CRISPRSEQ_TARGETED is not defined

        multiqc_report_ch = CRISPRSEQ_TARGETED.out.multiqc_report
                            ^^^^^^^^^^^^^^^^^^

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/vsearch/sort/main.nf:40:13: prefix is not defined
```
    touch ${prefix}.fasta
            ^^^^^^
```

Error: subworkflows/local/utils_nfcore_crisprseq_pipeline/main.nf:115:41: reference is already declared

                meta, fastq_1, fastq_2, reference, protospacer, template ->
                                        ^^^^^^^^^

Error: subworkflows/local/utils_nfcore_crisprseq_pipeline/main.nf:115:52: protospacer is already declared

                meta, fastq_1, fastq_2, reference, protospacer, template ->
                                                   ^^^^^^^^^^^

Error: subworkflows/local/utils_nfcore_crisprseq_pipeline/main.nf:115:65: template is already declared

                meta, fastq_1, fastq_2, reference, protospacer, template ->
                                                                ^^^^^^^^

Error: subworkflows/local/utils_nfcore_crisprseq_pipeline/main.nf:117:25: Variables in a closure should be declared with def
```
                        files = [ fastq_1, fastq_2 ]
                        ^^^^^
```

Error: subworkflows/local/utils_nfcore_crisprseq_pipeline/main.nf:501:9: warning is not defined

        warning "mle_design_matrix will only be used for the MAGeCK MLE computations"
        ^^^^^^^

Error: subworkflows/local/utils_nfcore_crisprseq_pipeline/main.nf:513:9: warning is not defined

        warning "MAGeCK MLE module will be run twice, once with the design matrix and once with day0-label"
        ^^^^^^^

Error: subworkflows/local/utils_nfcore_crisprseq_pipeline/main.nf:517:9: warning is not defined

        warning "mle_design_matrix will only be used for the MAGeCK MLE computations"
        ^^^^^^^

Error: workflows/crisprseq_targeted.nf:61:22: Unexpected input: '='

        while ( line1=it.readLine() ) {
                     ^

⚠️ Warnings

Warning: modules/local/bagel2/bf.nf:26:9: Variable was declared but not used

    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^

Warning: modules/local/bagel2/fc.nf:23:9: Variable was declared but not used

    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^

Warning: modules/local/bagel2/graph.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/bagel2/graph.nf:22:9: Variable was declared but not used

    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^

Warning: modules/local/bagel2/pr.nf:23:9: Variable was declared but not used

    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^

Warning: modules/local/extract_umis.nf:19:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/find_adapters.nf:18:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/hitselection.nf:26:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/hitselection.nf:246:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/mageck/flutemle.nf:25:5: Variable was declared but not used
```
    args = task.ext.args ?: ' '
    ^^^^
```
Warning: modules/local/mageck/graphrra.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/orient_reference.nf:19:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/venndiagram.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/cat/fastq/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/cat/fastq/main.nf:23:59: 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:54:59: 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/crisprcleanr/normalize/main.nf:26:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/mageck/count/main.nf:53:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/mageck/count/main.nf:55:9: Variable was declared but not used

    def sample_label = ("$fastq1".endsWith(".fastq.gz") || "$fastq1".endsWith(".fq.gz")) ? "--sample-label ${meta.id}" : ''
        ^^^^^^^^^^^^

Warning: modules/nf-core/mageck/test/main.nf:42:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: subworkflows/local/utils_nfcore_crisprseq_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_crisprseq_pipeline/main.nf:35:5: Parameter was not used -- prefix with _ to suppress warning
```
    input             //  string: Path to input samplesheet
    ^^^^^
```
Warning: subworkflows/local/utils_nfcore_crisprseq_pipeline/main.nf:101:5: Variable was declared but not used
```
    reads_screening  = channel.empty()
    ^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_crisprseq_pipeline/main.nf:106:5: Variable was declared but not used
```
    versions         = channel.empty()
    ^^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_crisprseq_pipeline/main.nf:244:14: Parameter was not used -- prefix with _ to suppress warning
```
    .filter{ meta, sequence -> sequence instanceof String }
             ^^^^
```
Warning: subworkflows/local/utils_nfcore_crisprseq_pipeline/main.nf:252:21: Parameter was not used -- prefix with _ to suppress warning
```
        .map{ meta, reference ->
                    ^^^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_crisprseq_pipeline/main.nf:256:11: Parameter was not used -- prefix with _ to suppress warning
```
    .map{ metaid, new_file, meta ->
          ^^^^^^
```
Warning: subworkflows/local/utils_nfcore_crisprseq_pipeline/main.nf:267:14: Parameter was not used -- prefix with _ to suppress warning
```
    .filter{ meta, sequence -> sequence instanceof String }
             ^^^^
```
Warning: subworkflows/local/utils_nfcore_crisprseq_pipeline/main.nf:275:21: Parameter was not used -- prefix with _ to suppress warning
```
        .map{ meta, template ->
                    ^^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_crisprseq_pipeline/main.nf:279:11: Parameter was not used -- prefix with _ to suppress warning
```
    .map{ metaid, new_file, meta ->
          ^^^^^^
```

Warning: subworkflows/local/utils_nfcore_crisprseq_pipeline/main.nf:310:25: Parameter was not used -- prefix with _ to suppress warning

            .map{ meta, fastqs, reference, protospacer -> [ meta, reference, protospacer ]} // Don't add fastqs to the channel
                        ^^^^^^

Warning: subworkflows/local/utils_nfcore_crisprseq_pipeline/main.nf:395:39: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def reference_ok = metas.collect{ it.self_reference }.unique().size == 1
                                      ^^

Warning: subworkflows/local/utils_nfcore_crisprseq_pipeline/main.nf:401:38: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def template_ok = metas.collect{ it.template }.unique().size == 1
                                     ^^

Warning: workflows/crisprseq_screening.nf:91:72: 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/crisprseq_screening.nf:106:89: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/crisprseq_screening.nf:115:90: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/crisprseq_screening.nf:196:82: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_multiqc_files = ch_multiqc_files.mix(MAGECK_COUNT.out.summary.collect{it[1]})
                                                                                 ^^

Warning: workflows/crisprseq_screening.nf:242:68: Implicit closure parameter is deprecated, declare an explicit parameter instead

            .map { condition, metas -> [condition, metas.collect { it.id }]}
                                                                   ^^

Warning: workflows/crisprseq_screening.nf:261:63: Implicit closure parameter is deprecated, declare an explicit parameter instead

                def treatment_samples = all_conditions.find { it[0] in contrast_meta.treatment }  // Find samples for each condition
                                                              ^^

Warning: workflows/crisprseq_screening.nf:262:63: Implicit closure parameter is deprecated, declare an explicit parameter instead

                def reference_samples = all_conditions.find { it[0] in contrast_meta.reference }
                                                              ^^

Warning: workflows/crisprseq_screening.nf:359:56: Implicit closure parameter is deprecated, declare an explicit parameter instead

            MATRICESCREATION(ch_contrasts_counts.map { it[0] })
                                                       ^^

Warning: workflows/crisprseq_screening.nf:543:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    def topic_versions = Channel.topic("versions")
                         ^^^^^^^
```

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