Nextflow lint results

Generated: 2026-01-16T10:29:59.227134598Z
Nextflow version: 25.12.0-edge
Summary: 11 errors, 74 warnings

❌ Errors

Error: modules/local/format_fasta_mirna/main.nf:1:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
def VERSION = '0.0.14'
^^^^^^^^^^^^^^^^^^^^^^
```

Error: modules/local/format_fasta_mirna/main.nf:28:34: VERSION is not defined

        fastx_toolkit:  \$(echo "$VERSION")
                                 ^^^^^^^^

Error: subworkflows/local/prepare_genome/main.nf:24:5: for loops are no longer supported
```
    for (file_path in files) {
    ^^^
```
Error: subworkflows/local/prepare_genome/main.nf:24:10: file_path is not defined
```
    for (file_path in files) {
         ^^^^^^^^^
```

Error: subworkflows/local/prepare_genome/main.nf:25:25: file_path is not defined

        def file_name = file_path.getName()
                        ^^^^^^^^^

Error: subworkflows/local/prepare_genome/main.nf:28:13: break is not allowed as an identifier because it is a Groovy keyword
```
            break
            ^^^^^
```
Error: subworkflows/local/prepare_genome/main.nf:28:13: break is not defined
```
            break
            ^^^^^
```

Error: workflows/smrnaseq.nf:34:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_multiqc_config                     = channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/smrnaseq.nf:35:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_multiqc_custom_config              = params.multiqc_config ? channel.fromPath( params.multiqc_config, checkIfExists: true ) : channel.empty()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/smrnaseq.nf:36:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_multiqc_logo                       = params.multiqc_logo   ? channel.fromPath( params.multiqc_logo, checkIfExists: true ) : channel.empty()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/smrnaseq.nf:37:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_fastp_adapters                     = channel.fromPath(params.fastp_known_mirna_adapters, checkIfExists: true).collect() // collect to consume for all incoming samples to FASTP
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

⚠️ Warnings

Warning: modules/local/format_fasta_mirna/main.nf:1:5: Variable was declared but not used
```
def VERSION = '0.0.14'
    ^^^^^^^
```
Warning: modules/nf-core/blat/main.nf:52:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/cat/fastq/main.nf:22:60: 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:58:60: 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/mirdeep2/mapper/main.nf:41:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/mirdeep2/mirdeep2/main.nf:51:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/mirtop/counts/main.nf:24:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/nf-core/mirtop/counts/main.nf:42:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/mirtop/counts/main.nf:43:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/nf-core/mirtop/export/main.nf:26:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/nf-core/mirtop/export/main.nf:44:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/mirtop/gff/main.nf:44:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/mirtop/gff/main.nf:45:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/nf-core/mirtop/stats/main.nf:24:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/nf-core/mirtop/stats/main.nf:39:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/mirtrace/qc/main.nf:26:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/mirtrace/qc/main.nf:27:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/nf-core/mirtrace/qc/main.nf:45:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/seqcluster/collapse/main.nf:41:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/seqkit/grep/main.nf:45:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: subworkflows/local/contaminant_filter/main.nf:59:5: Variable was declared but not used
```
    ch_mqc_results  = channel.empty()
    ^^^^^^^^^^^^^^
```
Warning: subworkflows/local/contaminant_filter/main.nf:135:24: Parameter was not used -- prefix with _ to suppress warning
```
                .map { meta, file -> file.text.readLines() }
                       ^^^^
```
Warning: subworkflows/local/contaminant_filter/main.nf:181:24: Parameter was not used -- prefix with _ to suppress warning
```
                .map { meta, file -> file.text.readLines() }
                       ^^^^
```
Warning: subworkflows/local/contaminant_filter/main.nf:227:24: Parameter was not used -- prefix with _ to suppress warning
```
                .map { meta, file -> file.text.readLines() }
                       ^^^^
```
Warning: subworkflows/local/contaminant_filter/main.nf:273:24: Parameter was not used -- prefix with _ to suppress warning
```
                .map { meta, file -> file.text.readLines() }
                       ^^^^
```
Warning: subworkflows/local/mirna_quant/main.nf:53:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { add_suffix(it, "mature") }
                          ^^
```
Warning: subworkflows/local/mirna_quant/main.nf:59:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { add_suffix(it, "hairpin") }
                          ^^
```

Warning: subworkflows/local/mirna_quant/main.nf:81:60: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_edger_input = BAM_STATS_MATURE.out.idxstats.collect{it[1]}
                                                           ^^

Warning: subworkflows/local/mirna_quant/main.nf:82:53: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .mix(BAM_STATS_HAIRPIN.out.idxstats.collect{it[1]})
                                                    ^^
```
Warning: subworkflows/local/mirna_quant/main.nf:106:5: Variable was declared but not used
```
    ch_tsvs = BAM_STATS_MIRNA_MIRTOP.out.counts
    ^^^^^^^
```
Warning: subworkflows/local/mirna_quant/main.nf:107:18: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .collect{it[1]}
                 ^^
```
Warning: subworkflows/local/mirna_quant/main.nf:114:16: Parameter was not used -- prefix with _ to suppress warning
```
        .map { meta, file -> file }
               ^^^^
```
Warning: subworkflows/local/mirna_quant/main.nf:127:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { add_suffix(it, "genome") }
                          ^^
```

Warning: subworkflows/local/prepare_genome/main.nf:98:27: Parameter was not used -- prefix with _ to suppress warning

                    .map{ meta, index_dir ->
                          ^^^^

Warning: subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf:34:5: Parameter was not used -- prefix with _ to suppress warning
```
    monochrome_logs         // boolean: Do not use coloured log outputs
    ^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf:37:5: Parameter was not used -- prefix with _ to suppress warning
```
    input                   //  string: Path to input samplesheet
    ^^^^^
```
Warning: subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf:246:35: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        fastqs = fastqs.collect { it.take(1) }
                                  ^^
```
Warning: subworkflows/nf-core/bam_sort_stats_samtools/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_mirna_mirtop/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:15:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:33:22: Parameter was not used -- prefix with _ to suppress warning
```
    catch (Exception ex) {
                     ^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:51:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:52:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    fastqc_raw_html = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:53:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    fastqc_raw_zip = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:54:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
    umi_log = Channel.empty()
              ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:55:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trim_json = Channel.empty()
                ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:56:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trim_html = Channel.empty()
                ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:57:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trim_log = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:58:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trim_reads_fail = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:59:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trim_reads_merged = Channel.empty()
                        ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:60:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    fastqc_trim_html = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:61:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    fastqc_trim_zip = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:62:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trim_read_count = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:63:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    adapter_seq = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:66:49: Parameter was not used -- prefix with _ to suppress warning

    reads_only = reads.map { meta, reads_files, adapter_fasta -> [ meta, reads_files ] }
                                                ^^^^^^^^^^^^^

Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:104:20: Parameter was not used -- prefix with _ to suppress warning

            .map { sample_id, meta, umi_reads_files, adapter_fasta -> [meta, umi_reads_files, adapter_fasta] }
                   ^^^^^^^^^

Warning: subworkflows/nf-core/fastq_find_mirna_mirdeep2/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/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/smrnaseq.nf:34:1: Variable was declared but not used

ch_multiqc_config                     = channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
^^^^^^^^^^^^^^^^^

Warning: workflows/smrnaseq.nf:35:1: Variable was declared but not used

ch_multiqc_custom_config              = params.multiqc_config ? channel.fromPath( params.multiqc_config, checkIfExists: true ) : channel.empty()
^^^^^^^^^^^^^^^^^^^^^^^^

Warning: workflows/smrnaseq.nf:36:1: Variable was declared but not used

ch_multiqc_logo                       = params.multiqc_logo   ? channel.fromPath( params.multiqc_logo, checkIfExists: true ) : channel.empty()
^^^^^^^^^^^^^^^

Warning: workflows/smrnaseq.nf:37:1: Variable was declared but not used

ch_fastp_adapters                     = channel.fromPath(params.fastp_known_mirna_adapters, checkIfExists: true).collect() // collect to consume for all incoming samples to FASTP
^^^^^^^^^^^^^^^^^

Warning: workflows/smrnaseq.nf:295:9: Variable was declared but not used

        ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Warning: workflows/smrnaseq.nf:314:104: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/smrnaseq.nf:315:105: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/smrnaseq.nf:316:99: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/smrnaseq.nf:318:87: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/smrnaseq.nf:321:71: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_multiqc_files = ch_multiqc_files.mix(genome_stats.collect({it[1]}).ifEmpty([]))
                                                                      ^^

Warning: workflows/smrnaseq.nf:322:87: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/smrnaseq.nf:323:88: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/smrnaseq.nf:324:86: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/smrnaseq.nf:326:83: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/smrnaseq.nf:327:83: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/smrnaseq.nf:328:82: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Nextflow lint results

❌ Errors

⚠️ Warnings

FilesExpand file tree

smrnaseq_lint.md

Latest commit

History

smrnaseq_lint.md

File metadata and controls

Nextflow lint results

❌ Errors

⚠️ Warnings