Nextflow lint results

Generated: 2026-01-16T10:23:09.062046754Z
Nextflow version: 25.12.0-edge
Summary: 37 errors, 64 warnings

❌ Errors

Error: modules/local/qc/report/main.nf:15:15: meta is already declared
```
    tuple val(meta), path(pdf)
              ^^^^
```
Error: modules/nf-core/star/starsolo/main.nf:33:30: Unexpected input: '\n'
```
        case "CB_UMI_Simple":
                             ^
```

Error: nextflow.config:211:1: Variable declarations cannot be mixed with config statements

def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: nextflow.config:214:68: trace_timestamp is not defined

    file    = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
                                                                   ^^^^^^^^^^^^^^^

Error: nextflow.config:218:66: trace_timestamp is not defined

    file    = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
                                                                 ^^^^^^^^^^^^^^^

Error: nextflow.config:222:65: trace_timestamp is not defined

    file    = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
                                                                ^^^^^^^^^^^^^^^

Error: nextflow.config:226:62: trace_timestamp is not defined

    file    = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
                                                             ^^^^^^^^^^^^^^^

Error: nextflow.config:249:34: manifest is not defined

        command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
                                 ^^^^^^^^

Error: nextflow.config:259:15: manifest is not defined

\033[0;35m  ${manifest.name} ${manifest.version}\033[0m
              ^^^^^^^^

Error: nextflow.config:259:32: manifest is not defined

\033[0;35m  ${manifest.name} ${manifest.version}\033[0m
                               ^^^^^^^^

Error: nextflow.config:262:26: manifest is not defined

        afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "  https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                         ^^^^^^^^

Error: nextflow.config:262:67: manifest is not defined

        afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "  https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                                                                  ^^^^^^^^

Error: nextflow.config:262:182: manifest is not defined

        afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "  https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                                                                                                                                                                                     ^^^^^^^^

Error: nextflow.config:267:26: manifest is not defined

    https://github.com/${manifest.name}/blob/master/CITATIONS.md
                         ^^^^^^^^

Error: nextflow.config:271:22: validation is not defined

        beforeText = validation.help.beforeText
                     ^^^^^^^^^^

Error: nextflow.config:272:21: validation is not defined

        afterText = validation.help.afterText
                    ^^^^^^^^^^

Error: subworkflows/local/align_reads.nf:19:22: reads is already declared

        .map { meta, reads -> [ [ "id": meta.id, "single_end": true, "filename": reads.baseName ], reads ]}
                     ^^^^^

Error: subworkflows/local/demultiplex_reads.nf:26:47: reads is already declared

        .map { amp_batch, pool_barcode, meta, reads -> [
                                              ^^^^^

Error: subworkflows/local/prepare_genome.nf:38:31: fasta is already declared

    ch_fasta = ch_fasta.map { fasta -> [ [id: fasta.baseName], fasta ] }
                              ^^^^^

Error: subworkflows/local/prepare_genome.nf:49:27: gtf is already declared

    ch_gtf = ch_gtf.map { gtf -> [ [id: gtf.baseName], gtf ] }
                          ^^^

Error: subworkflows/local/prepare_genome.nf:64:29: fasta is already declared

                .map{ meta, fasta, ercc -> [ [id:"${meta.id}_ercc"], [fasta, ercc] ] }
                            ^^^^^

Error: subworkflows/local/velocity.nf:9:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/marsseq/modules/nf-core/star/starsolo/main.nf'

include { STARSOLO                        } from '../../modules/nf-core/star/starsolo/main'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: subworkflows/local/velocity.nf:23:22: reads is already declared

        .map { meta, reads -> return [ meta, reads.sort().collate(2) ] }
                     ^^^^^

Error: subworkflows/local/velocity.nf:30:69: reads is already declared

    CAT_FASTQ ( VELOCITY_CONVERT.out.reads.groupTuple().map { meta, reads -> [ meta, reads.flatten() ] } )
                                                                    ^^^^^

Error: subworkflows/local/velocity.nf:43:15: reads is already declared
```
        meta, reads -> [
              ^^^^^
```

Error: subworkflows/local/velocity.nf:54:5: STARSOLO is not defined

    STARSOLO ( ch_reads, VELOCITY_WHITELIST.out.whitelist, index )
    ^^^^^^^^

Error: subworkflows/local/velocity.nf:55:35: STARSOLO is not defined

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

Error: subworkflows/local/velocity.nf:59:24: STARSOLO is not defined

    star_multiqc     = STARSOLO.out.log_final
                       ^^^^^^^^

Error: workflows/marsseq.nf:29:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ercc_regions            = file("$projectDir/data/ercc-regions.tsv")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/marsseq.nf:30:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_oligos               = Channel.fromPath("$projectDir/data/oligos.txt", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/marsseq.nf:31:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_spike_seq            = Channel.fromPath("$projectDir/data/spike-seq.txt", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/marsseq.nf:32:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_spike_concentrations = Channel.fromPath("$projectDir/data/spike-concentrations.txt", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/marsseq.nf:63:9: ercc_regions is not defined
```
        ercc_regions,
        ^^^^^^^^^^^^
```

Error: workflows/marsseq.nf:71:13: ch_oligos is not defined

            ch_oligos,
            ^^^^^^^^^

Error: workflows/marsseq.nf:97:13: ch_spike_seq is not defined

            ch_spike_seq,
            ^^^^^^^^^^^^

Error: workflows/marsseq.nf:98:13: ch_spike_concentrations is not defined

            ch_spike_concentrations,
            ^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/marsseq.nf:99:13: ch_oligos is not defined
```
            ch_oligos
            ^^^^^^^^^
```

⚠️ Warnings

Warning: modules/local/ercc/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/extract/main.nf:26:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/extract/main.nf:52:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/qc/align/main.nf:25:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/qc/report/main.nf:14:15: Variable was declared but not used
```
    tuple val(meta), path(rds)
              ^^^^
```
Warning: modules/local/wget/main.nf:37:9: Variable was declared but not used
```
    def args = task.ext.args ?: ""
        ^^^^
```
Warning: modules/nf-core/cat/cat/main.nf:23:40: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def file_list = files_in.collect { it.toString() }
                                       ^^
```
Warning: modules/nf-core/cat/cat/main.nf:58:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def file_list   = files_in.collect { it.toString() }
                                         ^^
```
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/custom/dumpsoftwareversions/main.nf:22:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/gunzip/main.nf:43:9: Variable was declared but not used

    def args        = task.ext.args ?: ''
        ^^^^

Warning: nextflow.config:262:125: Implicit closure parameter is deprecated, declare an explicit parameter instead

        afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "  https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                                                                                                                            ^^

Warning: subworkflows/local/align_reads.nf:17:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/demultiplex_reads.nf:20:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:23:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions      = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:24:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_fasta         = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:25:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_gtf           = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:26:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bowtie2_index = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:27:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_star_index    = Channel.empty()
                       ^^^^^^^
```

Warning: subworkflows/local/prepare_genome.nf:33:95: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: subworkflows/local/prepare_genome.nf:36:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_fasta = Channel.value(file(fasta, checkIfExists: true))
                   ^^^^^^^
```

Warning: subworkflows/local/prepare_genome.nf:44:91: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: subworkflows/local/prepare_genome.nf:47:18: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_gtf = Channel.value(file(gtf, checkIfExists: true))
                 ^^^^^^^
```

Warning: subworkflows/local/prepare_genome.nf:71:32: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_bowtie2_index = Channel.fromPath(bowtie2_index, checkIfExists: true).map { index -> [ [id:"target_index"], index ] }
                               ^^^^^^^

Warning: subworkflows/local/prepare_genome.nf:80:29: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_star_index = Channel.fromPath(star_index, checkIfExists: true).map { index -> [ [id:"target_index"], index ] }
                            ^^^^^^^

Warning: subworkflows/local/prepare_pipeline.nf:19:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_reads = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/prepare_pipeline.nf:20:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/prepare_pipeline.nf:27:19: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        gtf.map { it[1] },
                  ^^
```
Warning: subworkflows/local/utils_nfcore_marsseq_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_marsseq_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_marsseq_pipeline/main.nf:38:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_marsseq_pipeline/main.nf:75:5: The use of Channel to access channel factories is deprecated -- use channel instead
```
    Channel
    ^^^^^^^
```
Warning: subworkflows/local/velocity.nf:19:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/nf-core/utils_nextflow_pipeline/main.nf:94:33: Parameter was not used -- prefix with _ to suppress warning
```
    catch (NullPointerException e) {
                                ^
```
Warning: subworkflows/nf-core/utils_nextflow_pipeline/main.nf:98:24: Parameter was not used -- prefix with _ to suppress warning
```
    catch (IOException e) {
                       ^
```

Warning: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:116:98: 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: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:264:22: Parameter was not used -- prefix with _ to suppress warning
```
    catch (Exception all) {
                     ^^^
```
Warning: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:361:26: Parameter was not used -- prefix with _ to suppress warning
```
        catch (Exception all) {
                         ^^^
```

Warning: workflows/marsseq.nf:29:1: Variable was declared but not used

ercc_regions            = file("$projectDir/data/ercc-regions.tsv")
^^^^^^^^^^^^

Warning: workflows/marsseq.nf:30:1: Variable was declared but not used

ch_oligos               = Channel.fromPath("$projectDir/data/oligos.txt", checkIfExists: true)
^^^^^^^^^

Warning: workflows/marsseq.nf:30:27: The use of Channel to access channel factories is deprecated -- use channel instead

ch_oligos               = Channel.fromPath("$projectDir/data/oligos.txt", checkIfExists: true)
                          ^^^^^^^

Warning: workflows/marsseq.nf:31:1: Variable was declared but not used

ch_spike_seq            = Channel.fromPath("$projectDir/data/spike-seq.txt", checkIfExists: true)
^^^^^^^^^^^^

Warning: workflows/marsseq.nf:31:27: The use of Channel to access channel factories is deprecated -- use channel instead

ch_spike_seq            = Channel.fromPath("$projectDir/data/spike-seq.txt", checkIfExists: true)
                          ^^^^^^^

Warning: workflows/marsseq.nf:32:1: Variable was declared but not used

ch_spike_concentrations = Channel.fromPath("$projectDir/data/spike-concentrations.txt", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^

Warning: workflows/marsseq.nf:32:27: The use of Channel to access channel factories is deprecated -- use channel instead

ch_spike_concentrations = Channel.fromPath("$projectDir/data/spike-concentrations.txt", checkIfExists: true)
                          ^^^^^^^

Warning: workflows/marsseq.nf:47:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_files = Channel.empty()
                       ^^^^^^^
```

Warning: workflows/marsseq.nf:55:68: 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/marsseq.nf:59:30: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_samplesheet.map { it[0].amp_batches },
                             ^^
```
Warning: workflows/marsseq.nf:60:30: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_samplesheet.map { it[0].seq_batches },
                             ^^
```
Warning: workflows/marsseq.nf:61:30: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_samplesheet.map { it[0].well_cells },
                             ^^
```
Warning: workflows/marsseq.nf:84:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .groupTuple(by: [0], sort: { it.name })
                                         ^^
```
Warning: workflows/marsseq.nf:119:34: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            ch_samplesheet.map { it[0].amp_batches },
                                 ^^
```
Warning: workflows/marsseq.nf:120:34: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            ch_samplesheet.map { it[0].well_cells },
                                 ^^
```

Warning: workflows/marsseq.nf:126:87: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/marsseq.nf:127:83: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/marsseq.nf:145:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_config        = Channel.fromPath(
                               ^^^^^^^
```
Warning: workflows/marsseq.nf:148:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.multiqc_config, checkIfExists: true) :
        ^^^^^^^
```
Warning: workflows/marsseq.nf:149:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.empty()
        ^^^^^^^
```
Warning: workflows/marsseq.nf:151:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
        ^^^^^^^
```
Warning: workflows/marsseq.nf:152:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.empty()
        ^^^^^^^
```

Warning: workflows/marsseq.nf:156:27: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
                          ^^^^^^^

Warning: workflows/marsseq.nf:162:45: The use of Channel to access channel factories is deprecated -- use channel instead

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

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