Skip to content

Latest commit

 

History

History
142 lines (101 loc) · 3.67 KB

seqsubmit_lint.md

File metadata and controls

142 lines (101 loc) · 3.67 KB

Nextflow lint results

  • Generated: 2026-03-17T00:28:25.509630919Z
  • Nextflow version: 26.02.0-edge
  • Summary: 1 error, 18 warnings

❌ Errors

  • Error: subworkflows/local/rna_detection.nf:29:24: fasta is already declared

            fasta.map {id, fasta -> [id, fasta, "bac"]}
                       ^^^^^

⚠️ Warnings

  • Warning: modules/local/generate_assembly_manifest/main.nf:20:9: Variable was declared but not used

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

  • Warning: modules/local/generate_assembly_manifest/main.nf:38:9: Variable was declared but not used

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

  • Warning: modules/local/generate_assembly_manifest/main.nf:39:9: Variable was declared but not used

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

  • Warning: modules/local/registerstudy/main.nf:22:9: Variable was declared but not used

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

  • Warning: modules/local/registerstudy/main.nf:46:9: Variable was declared but not used

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

  • Warning: modules/nf-core/barrnap/main.nf:45:9: Variable was declared but not used

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

  • Warning: subworkflows/local/genome_evaluation.nf:26:5: Variable was declared but not used

        ch_versions = channel.empty()
    ^^^^^^^^^^^

  • Warning: subworkflows/nf-core/fasta_classify_catpack/main.nf:39:19: Parameter was not used -- prefix with _ to suppress warning

            .branch { meta, db ->
                  ^^^^

  • Warning: workflows/genomesubmit.nf:32:5: Parameter was not used -- prefix with _ to suppress warning

        mags_or_bins_flag
    ^^^^^^^^^^^^^^^^^

  • Warning: workflows/genomesubmit.nf:78:25: Parameter was not used -- prefix with _ to suppress warning

            .branch { meta, fasta ->
                        ^^^^^

  • Warning: workflows/genomesubmit.nf:84:33: Parameter was not used -- prefix with _ to suppress warning

        genome_reads.filter { meta, reads -> meta.genome_coverage == null }
                                ^^^^^

  • Warning: workflows/genomesubmit.nf:109:25: Parameter was not used -- prefix with _ to suppress warning

            .branch { meta, fasta ->
                        ^^^^^

  • Warning: workflows/genomesubmit.nf:132:25: Parameter was not used -- prefix with _ to suppress warning

            .branch { meta, fasta ->
                        ^^^^^

  • Warning: workflows/genomesubmit.nf:163:25: Parameter was not used -- prefix with _ to suppress warning

            .branch { meta, fasta ->
                        ^^^^^

  • Warning: workflows/genomesubmit.nf:203:5: Variable was declared but not used

        genome_metadata_csv = fasta_updated_with_taxonomy
    ^^^^^^^^^^^^^^^^^^^

  • Warning: workflows/genomesubmit.nf:282:5: Variable was declared but not used

        ch_multiqc_config        = channel.fromPath(
    ^^^^^^^^^^^^^^^^^

  • Warning: workflows/genomesubmit.nf:284:5: Variable was declared but not used

        ch_multiqc_custom_config = params.multiqc_config ?
    ^^^^^^^^^^^^^^^^^^^^^^^^

  • Warning: workflows/genomesubmit.nf:287:5: Variable was declared but not used

        ch_multiqc_logo          = params.multiqc_logo ?
    ^^^^^^^^^^^^^^^