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Nextflow lint results

  • Generated: 2026-03-17T00:23:03.284476221Z
  • Nextflow version: 26.02.0-edge
  • Summary: 15 warnings

⚠️ Warnings

  • Warning: modules/nf-core/quast/main.nf:48:9: Variable was declared but not used

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

  • Warning: modules/nf-core/quast/main.nf:50:9: Variable was declared but not used

        def features  = gff             ? "--features $gff" : ''
        ^^^^^^^^

  • Warning: modules/nf-core/quast/main.nf:51:9: Variable was declared but not used

        def reference = fasta           ? "-r $fasta" : ''
        ^^^^^^^^^

  • Warning: modules/nf-core/toulligqc/main.nf:46:9: Variable was declared but not used

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

  • Warning: subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf:34:19: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_versions = Channel.empty()
                  ^^^^^^^

  • Warning: subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf:37:49: Parameter was not used -- prefix with _ to suppress warning

        ch_reads_only = ch_reads.map { meta, reads, adapter_fasta -> [ meta, reads ] }
                                                ^^^^^^^^^^^^^

  • Warning: subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf:39:26: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_fastqc_raw_html = Channel.empty()
                         ^^^^^^^

  • Warning: subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf:40:26: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_fastqc_raw_zip  = Channel.empty()
                         ^^^^^^^

  • Warning: subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf:50:28: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_trim_json         = Channel.empty()
                           ^^^^^^^

  • Warning: subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf:51:28: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_trim_html         = Channel.empty()
                           ^^^^^^^

  • Warning: subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf:52:28: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_trim_log          = Channel.empty()
                           ^^^^^^^

  • Warning: subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf:53:28: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_trim_reads_fail   = Channel.empty()
                           ^^^^^^^

  • Warning: subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf:54:28: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_trim_reads_merged = Channel.empty()
                           ^^^^^^^

  • Warning: subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf:55:28: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_fastqc_trim_html  = Channel.empty()
                           ^^^^^^^

  • Warning: subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf:56:28: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_fastqc_trim_zip   = Channel.empty()
                           ^^^^^^^