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nfmicrofinder_lint.md

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Nextflow lint results

  • Generated: 2026-03-24T10:46:39.500469395Z
  • Nextflow version: 26.03.0-edge
  • Summary: 21 warnings

⚠️ Warnings

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

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

  • Warning: modules/local/microfinder_filter/main.nf:23:9: Variable was declared but not used

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

  • Warning: modules/local/microfinder_filter/main.nf:35:9: Variable was declared but not used

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

  • Warning: modules/local/sort_fasta/main.nf:23:9: Variable was declared but not used

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

  • Warning: modules/local/sort_fasta/main.nf:24:9: Variable was declared but not used

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

  • Warning: modules/local/sort_fasta/main.nf:25:9: Variable was declared but not used

        def VERSION     = "2.2.3"
        ^^^^^^^

  • Warning: modules/local/sort_fasta/main.nf:36:9: Variable was declared but not used

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

  • Warning: modules/local/sort_fasta/main.nf:37:9: Variable was declared but not used

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

  • Warning: subworkflows/local/microfinder_map/main.nf:27:19: The use of Channel to access channel factories is deprecated -- use channel instead

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

  • Warning: subworkflows/local/microfinder_map/main.nf:45:41: Parameter was not used -- prefix with _ to suppress warning

            .multiMap { pep_meta, pep_file, miniprot_meta, miniprot_index ->
                                        ^^^^^^^^^^^^^

  • Warning: subworkflows/local/microfinder_map/main.nf:101:56: Parameter was not used -- prefix with _ to suppress warning

            tsv_branched.has_content.map { meta, tsv_file, ref_meta, ref_file -> tuple(meta, tsv_file) },
                                                       ^^^^^^^^

  • Warning: subworkflows/local/microfinder_map/main.nf:101:66: Parameter was not used -- prefix with _ to suppress warning

            tsv_branched.has_content.map { meta, tsv_file, ref_meta, ref_file -> tuple(meta, tsv_file) },
                                                                 ^^^^^^^^

  • Warning: subworkflows/local/microfinder_map/main.nf:102:40: Parameter was not used -- prefix with _ to suppress warning

            tsv_branched.has_content.map { meta, tsv_file, ref_meta, ref_file -> ref_file },
                                       ^^^^

  • Warning: subworkflows/local/microfinder_map/main.nf:102:46: Parameter was not used -- prefix with _ to suppress warning

            tsv_branched.has_content.map { meta, tsv_file, ref_meta, ref_file -> ref_file },
                                             ^^^^^^^^

  • Warning: subworkflows/local/microfinder_map/main.nf:102:56: Parameter was not used -- prefix with _ to suppress warning

            tsv_branched.has_content.map { meta, tsv_file, ref_meta, ref_file -> ref_file },
                                                       ^^^^^^^^

  • Warning: subworkflows/local/utils_nfcore_nfmicrofinder_pipeline/main.nf:32:5: Parameter was not used -- prefix with _ to suppress warning

        monochrome_logs   // boolean: Do not use coloured log outputs
    ^^^^^^^^^^^^^^^

  • Warning: subworkflows/local/utils_nfcore_nfmicrofinder_pipeline/main.nf:85:5: The use of Channel to access channel factories is deprecated -- use channel instead

        Channel
    ^^^^^^^

  • Warning: subworkflows/local/utils_nfcore_nfmicrofinder_pipeline/main.nf:89:5: The use of Channel to access channel factories is deprecated -- use channel instead

        Channel
    ^^^^^^^

  • Warning: subworkflows/local/utils_nfcore_nfmicrofinder_pipeline/main.nf:94:5: The use of Channel to access channel factories is deprecated -- use channel instead

        Channel
    ^^^^^^^

  • Warning: subworkflows/local/utils_nfcore_nfmicrofinder_pipeline/main.nf:98:5: The use of Channel to access channel factories is deprecated -- use channel instead

        Channel
    ^^^^^^^

  • Warning: workflows/nfmicrofinder.nf:49:26: The use of Channel to access channel factories is deprecated -- use channel instead

        def topic_versions = Channel.topic("versions")
                         ^^^^^^^