Nextflow lint results

Generated: 2026-01-16T10:19:36.419202544Z
Nextflow version: 25.12.0-edge
Summary: 31 errors, 51 warnings

❌ Errors

Error: conf/modules.config:22:21: Unexpected input: ':'

            withName: '.*FASTQC_RAW' {
                    ^

Error: modules/local/orp_transrate/main.nf:12:15: meta is already declared

    tuple val(meta), path(reads)         // processed reads
              ^^^^

Error: modules/nf-core/salmon/quant/main.nf:30:20: Unexpected input: ','
```
    def reads1 = [], reads2 = []
                   ^
```
Error: modules/nf-core/trinity/main.nf:26:20: Unexpected input: ','
```
    def reads1 = [], reads2 = []
                   ^
```

Error: nextflow.config:317:40: manifest is not defined

\033[0;35m  nf-core/denovotranscript ${manifest.version}\033[0m
                                       ^^^^^^^^

Error: nextflow.config:320:26: manifest is not defined

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

Error: nextflow.config:320:69: manifest is not defined

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

Error: nextflow.config:320:186: manifest is not defined

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

Error: nextflow.config:329:22: validation is not defined

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

Error: nextflow.config:330:21: validation is not defined

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

Error: subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf:15:26: Unexpected input: 'new'

    def Map json = (Map) new JsonSlurper().parseText(json_file.text).get('summary')
                         ^

Error: workflows/denovotranscript.nf:8:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
if (params.remove_ribo_rna) {
^
```
Error: workflows/denovotranscript.nf:53:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/denovotranscript/modules/nf-core/trinity/main.nf'
```
include { TRINITY                     } from '../modules/nf-core/trinity/main'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/denovotranscript.nf:54:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/denovotranscript/modules/nf-core/trinity/main.nf'
```
include { TRINITY as TRINITY_NO_NORM  } from '../modules/nf-core/trinity/main'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/denovotranscript.nf:56:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/denovotranscript/modules/nf-core/salmon/quant/main.nf'
```
include { SALMON_QUANT                } from '../modules/nf-core/salmon/quant/main'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/denovotranscript.nf:61:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/denovotranscript/subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf'
```
include { FASTQ_TRIM_FASTP_FASTQC     } from '../subworkflows/nf-core/fastq_trim_fastp_fastqc/main'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/denovotranscript.nf:83:5: FASTQ_TRIM_FASTP_FASTQC is not defined
```
    FASTQ_TRIM_FASTP_FASTQC (
    ^^^^^^^^^^^^^^^^^^^^^^^
```

Error: workflows/denovotranscript.nf:91:45: FASTQ_TRIM_FASTP_FASTQC is not defined

    ch_multiqc_files = ch_multiqc_files.mix(FASTQ_TRIM_FASTP_FASTQC.out.fastqc_raw_zip.collect{it[1]})
                                            ^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/denovotranscript.nf:92:45: FASTQ_TRIM_FASTP_FASTQC is not defined

    ch_multiqc_files = ch_multiqc_files.mix(FASTQ_TRIM_FASTP_FASTQC.out.fastqc_trim_zip.collect{it[1]})
                                            ^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/denovotranscript.nf:93:35: FASTQ_TRIM_FASTP_FASTQC is not defined

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

Error: workflows/denovotranscript.nf:94:25: FASTQ_TRIM_FASTP_FASTQC is not defined

    ch_filtered_reads = FASTQ_TRIM_FASTP_FASTQC.out.reads
                        ^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/denovotranscript.nf:97:44: ch_ribo_db is not defined

        ch_sortmerna_fastas = Channel.from(ch_ribo_db.readLines()).map { row -> file(row, checkIfExists: true) }.collect()
                                           ^^^^^^^^^^

Error: workflows/denovotranscript.nf:142:17: TRINITY is not defined

                TRINITY (
                ^^^^^^^

Error: workflows/denovotranscript.nf:145:47: TRINITY is not defined

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

Error: workflows/denovotranscript.nf:146:51: TRINITY is not defined

                ch_assemblies = ch_assemblies.mix(TRINITY.out.transcript_fasta)
                                                  ^^^^^^^

Error: workflows/denovotranscript.nf:153:17: TRINITY_NO_NORM is not defined

                TRINITY_NO_NORM (
                ^^^^^^^^^^^^^^^

Error: workflows/denovotranscript.nf:156:47: TRINITY_NO_NORM is not defined

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

Error: workflows/denovotranscript.nf:157:51: TRINITY_NO_NORM is not defined

                ch_assemblies = ch_assemblies.mix(TRINITY_NO_NORM.out.transcript_fasta)
                                                  ^^^^^^^^^^^^^^^

Error: workflows/denovotranscript.nf:276:9: SALMON_QUANT is not defined
```
        SALMON_QUANT (
        ^^^^^^^^^^^^
```

Error: workflows/denovotranscript.nf:282:49: SALMON_QUANT is not defined

        ch_multiqc_files = ch_multiqc_files.mix(SALMON_QUANT.out.results.collect{it[1]})
                                                ^^^^^^^^^^^^

Error: workflows/denovotranscript.nf:283:39: SALMON_QUANT is not defined

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

⚠️ Warnings

Warning: modules/local/orp_transrate/main.nf:11:15: Variable was declared but not used

    tuple val(meta), path(fasta)         // assembly file
              ^^^^

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/evigene/tr2aacds/main.nf:68:9: Variable was declared but not used
```
    def args        = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/evigene/tr2aacds/main.nf:70:9: Variable was declared but not used
```
    def max_memory  = 7*1024
        ^^^^^^^^^^
```

Warning: modules/nf-core/sortmerna/main.nf:25:70: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def reads_input = reads instanceof List ? reads.collect{"--reads $it"}.join(' ') : "--reads $reads"
                                                                     ^^

Warning: modules/nf-core/sortmerna/main.nf:62:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/sortmerna/main.nf:64:9: Variable was declared but not used

    def reads_input = reads instanceof List ? reads.collect{"--reads $it"}.join(' ') : "--reads $reads"
        ^^^^^^^^^^^

Warning: modules/nf-core/sortmerna/main.nf:64:70: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def reads_input = reads instanceof List ? reads.collect{"--reads $it"}.join(' ') : "--reads $reads"
                                                                     ^^

Warning: modules/nf-core/spades/main.nf:88:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/spades/main.nf:90:9: Variable was declared but not used
```
    def maxmem = task.memory.toGiga()
        ^^^^^^
```

Warning: modules/nf-core/spades/main.nf:94:9: Variable was declared but not used

    def custom_hmms = hmm ? "--custom-hmms $hmm" : ""
        ^^^^^^^^^^^

Warning: modules/nf-core/spades/main.nf:95:9: Variable was declared but not used

    def reads = yml ? "--dataset $yml" : "$illumina_reads $pacbio_reads $nanopore_reads"
        ^^^^^

Warning: modules/nf-core/spades/main.nf:96:9: Variable was declared but not used

    def ss = params.ss ? "--ss ${params.ss}" : ""
        ^^

Warning: nextflow.config:320:129: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: subworkflows/local/utils_nfcore_denovotranscript_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_denovotranscript_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_denovotranscript_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_denovotranscript_pipeline/main.nf:75:5: The use of Channel to access channel factories is deprecated -- use channel instead
```
    Channel
    ^^^^^^^
```

Warning: subworkflows/local/utils_nfcore_denovotranscript_pipeline/main.nf:183:55: Implicit closure parameter is deprecated, declare an explicit parameter instead

        def invalid_assemblers = assemblers.findAll { it != "trinity" && it != "trinity_no_norm" && it != "rnaspades" }
                                                      ^^

Warning: subworkflows/local/utils_nfcore_denovotranscript_pipeline/main.nf:183:74: Implicit closure parameter is deprecated, declare an explicit parameter instead

        def invalid_assemblers = assemblers.findAll { it != "trinity" && it != "trinity_no_norm" && it != "rnaspades" }
                                                                         ^^

Warning: subworkflows/local/utils_nfcore_denovotranscript_pipeline/main.nf:183:101: Implicit closure parameter is deprecated, declare an explicit parameter instead

        def invalid_assemblers = assemblers.findAll { it != "trinity" && it != "trinity_no_norm" && it != "rnaspades" }
                                                                                                    ^^

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/denovotranscript.nf:12:18: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_ribo_db = Channel.empty()
                 ^^^^^^^
```
Warning: workflows/denovotranscript.nf:77:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: workflows/denovotranscript.nf:78:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_files = Channel.empty()
                       ^^^^^^^
```

Warning: workflows/denovotranscript.nf:91:96: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_multiqc_files = ch_multiqc_files.mix(FASTQ_TRIM_FASTP_FASTQC.out.fastqc_raw_zip.collect{it[1]})
                                                                                               ^^

Warning: workflows/denovotranscript.nf:92:97: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_multiqc_files = ch_multiqc_files.mix(FASTQ_TRIM_FASTP_FASTQC.out.fastqc_trim_zip.collect{it[1]})
                                                                                                ^^

Warning: workflows/denovotranscript.nf:97:31: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_sortmerna_fastas = Channel.from(ch_ribo_db.readLines()).map { row -> file(row, checkIfExists: true) }.collect()
                              ^^^^^^^

Warning: workflows/denovotranscript.nf:106:75: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/denovotranscript.nf:115:78: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/denovotranscript.nf:124:51: Parameter was not used -- prefix with _ to suppress warning

            ch_pool = ch_filtered_reads.collect { meta, fastq -> fastq }.map { [[id:'pooled_reads', single_end:false], it] }
                                                  ^^^^

Warning: workflows/denovotranscript.nf:124:120: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_pool = ch_filtered_reads.collect { meta, fastq -> fastq }.map { [[id:'pooled_reads', single_end:false], it] }
                                                                                                                       ^^

Warning: workflows/denovotranscript.nf:134:29: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_assemblies = Channel.empty()
                            ^^^^^^^
```
Warning: workflows/denovotranscript.nf:185:28: Parameter was not used -- prefix with _ to suppress warning
```
                .collect { meta, fasta -> fasta }
                           ^^^^
```

Warning: workflows/denovotranscript.nf:186:65: Implicit closure parameter is deprecated, declare an explicit parameter instead

                .map { [[id:'all_assembled', single_end:false], it ] }
                                                                ^^

Warning: workflows/denovotranscript.nf:205:56: Implicit closure parameter is deprecated, declare an explicit parameter instead

                def mrna_file = dir.listFiles().find { it.name.endsWith('.okay.mrna') }
                                                       ^^

Warning: workflows/denovotranscript.nf:211:58: Implicit closure parameter is deprecated, declare an explicit parameter instead

                def pubids_file = dir.listFiles().find { it.name.endsWith('.pubids') }
                                                         ^^

Warning: workflows/denovotranscript.nf:234:97: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_multiqc_files = ch_multiqc_files.mix(BUSCO_BUSCO.out.short_summaries_txt.collect{it[1]})
                                                                                                ^^

Warning: workflows/denovotranscript.nf:262:58: Parameter was not used -- prefix with _ to suppress warning

            ch_transcripts_fa = ch_transcripts.collect { meta, fasta -> fasta }
                                                         ^^^^

Warning: workflows/denovotranscript.nf:282:82: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_multiqc_files = ch_multiqc_files.mix(SALMON_QUANT.out.results.collect{it[1]})
                                                                                 ^^

Warning: workflows/denovotranscript.nf:302:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_config        = Channel.fromPath(
                               ^^^^^^^
```
Warning: workflows/denovotranscript.nf:305:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.multiqc_config, checkIfExists: true) :
        ^^^^^^^
```
Warning: workflows/denovotranscript.nf:306:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.empty()
        ^^^^^^^
```
Warning: workflows/denovotranscript.nf:308:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
        ^^^^^^^
```
Warning: workflows/denovotranscript.nf:309:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.empty()
        ^^^^^^^
```
Warning: workflows/denovotranscript.nf:313:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
                          ^^^^^^^
```

Warning: workflows/denovotranscript.nf:319:45: The use of Channel to access channel factories is deprecated -- use channel instead

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

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