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ampliseq_lint.md

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Nextflow lint results

  • Generated: 2026-03-20T00:22:54.359890738Z
  • Nextflow version: 26.03.0-edge
  • Summary: 16 warnings

⚠️ Warnings

  • Warning: modules/local/hmmer/hmmextract/main.nf:50:9: Variable was declared but not used

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

  • Warning: modules/nf-core/kraken2/kraken2/main.nf:59:9: Variable was declared but not used

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

  • Warning: modules/nf-core/kraken2/kraken2/main.nf:61:9: Variable was declared but not used

        def paired       = meta.single_end ? "" : "--paired"
        ^^^^^^

  • Warning: modules/nf-core/kraken2/kraken2/main.nf:64:9: Variable was declared but not used

        def readclassification_option = save_reads_assignment ? "--output ${prefix}.kraken2.classifiedreads.txt" : "--output /dev/null"
        ^^^^^^^^^^^^^^^^^^^^^^^^^

  • Warning: modules/nf-core/kraken2/kraken2/main.nf:65:9: Variable was declared but not used

        def compress_reads_command = save_output_fastqs ? "pigz -p $task.cpus *.fastq" : ""
        ^^^^^^^^^^^^^^^^^^^^^^

  • Warning: modules/nf-core/pigz/uncompress/main.nf:39:9: Variable was declared but not used

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

  • Warning: modules/nf-core/vsearch/cluster/main.nf:78:9: Variable was declared but not used

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

  • Warning: subworkflows/local/utils_nfcore_ampliseq_pipeline/main.nf:358:63: Implicit closure parameter is deprecated, declare an explicit parameter instead

            if (sectionValue instanceof Map && sectionValue.any { it.value instanceof Map && it.value.containsKey('file') }) {
                                                              ^^

  • Warning: subworkflows/local/utils_nfcore_ampliseq_pipeline/main.nf:358:90: Implicit closure parameter is deprecated, declare an explicit parameter instead

            if (sectionValue instanceof Map && sectionValue.any { it.value instanceof Map && it.value.containsKey('file') }) {
                                                                                         ^^

  • Warning: subworkflows/local/utils_nfcore_ampliseq_pipeline/main.nf:392:46: Implicit closure parameter is deprecated, declare an explicit parameter instead

                        occurrences.collect { "${it.section}['${it.key}']" }.join(", ")
                                             ^^

  • Warning: subworkflows/local/utils_nfcore_ampliseq_pipeline/main.nf:392:61: Implicit closure parameter is deprecated, declare an explicit parameter instead

                        occurrences.collect { "${it.section}['${it.key}']" }.join(", ")
                                                            ^^

  • Warning: workflows/ampliseq.nf:191:27: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_pplace_sheet = Channel.fromPath(params.pplace_sheet)
                          ^^^^^^^

  • Warning: workflows/ampliseq.nf:793:19: Implicit closure parameter is deprecated, declare an explicit parameter instead

            .filter { it.data.extract_hmm }
                  ^^

  • Warning: workflows/ampliseq.nf:794:18: Implicit closure parameter is deprecated, declare an explicit parameter instead

            .map { [ it.meta, it.data.hmm, it.data.extract_hmm ] }
                 ^^

  • Warning: workflows/ampliseq.nf:794:27: Implicit closure parameter is deprecated, declare an explicit parameter instead

            .map { [ it.meta, it.data.hmm, it.data.extract_hmm ] }
                          ^^

  • Warning: workflows/ampliseq.nf:794:40: Implicit closure parameter is deprecated, declare an explicit parameter instead

            .map { [ it.meta, it.data.hmm, it.data.extract_hmm ] }
                                       ^^