mag_lint.md

Nextflow lint results

• Generated: 2026-03-17T00:24:24.754616180Z
• Nextflow version: 26.02.0-edge
• Summary: 28 warnings

⚠️ Warnings

• Warning: modules/nf-core/bcftools/consensus/main.nf:40:9: Variable was declared but not used

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

• Warning: modules/nf-core/bcftools/consensus/main.nf:42:9: Variable was declared but not used

      def masking = mask ? "-m $mask" : ""
          ^^^^^^^

• Warning: modules/nf-core/bcftools/index/main.nf:23:9: Variable was declared but not used

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

• Warning: modules/nf-core/bcftools/index/main.nf:40:9: Variable was declared but not used

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

• 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/comebin/runcomebin/main.nf:59:9: Variable was declared but not used

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

• Warning: modules/nf-core/concoct/concoct/main.nf:43:9: Variable was declared but not used

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

• Warning: modules/nf-core/concoct/concoctcoveragetable/main.nf:37:9: Variable was declared but not used

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

• Warning: modules/nf-core/concoct/cutupfasta/main.nf:43:9: Variable was declared but not used

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

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

      def bedfile = bed ? "-b ${prefix}.bed" : ""
          ^^^^^^^

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

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

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

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

• Warning: modules/nf-core/gunzip/main.nf:43:9: Variable was declared but not used

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

• Warning: modules/nf-core/megahit/main.nf:52:9: Variable was declared but not used

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

• Warning: modules/nf-core/megahit/main.nf:53:9: Variable was declared but not used

      def args2 = task.ext.args2 ?: ''
          ^^^^^

• Warning: modules/nf-core/megahit/main.nf:55:9: Variable was declared but not used

      def reads_command = meta.single_end || !reads2 ? "-r ${reads1}" : "-1 ${reads1.join(',')} -2 ${reads2.join(',')}"
          ^^^^^^^^^^^^^

• Warning: modules/nf-core/metamdbg/asm/main.nf:47:9: Variable was declared but not used

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

• Warning: modules/nf-core/nanolyse/main.nf:23:9: Variable was declared but not used

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

• Warning: modules/nf-core/nanoq/main.nf:38:9: Variable was declared but not used

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

• Warning: modules/nf-core/porechop/abi/main.nf:44:9: Variable was declared but not used

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

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

      def adapters_list = custom_adapters ? "--custom_adapters ${custom_adapters}" : ""
          ^^^^^^^^^^^^^

• Warning: modules/nf-core/prodigal/main.nf:49:9: Variable was declared but not used

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

• Warning: modules/nf-core/spades/main.nf:80:9: Variable was declared but not used

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

• Warning: modules/nf-core/spades/main.nf:82:9: Variable was declared but not used

      def maxmem = task.memory.toGiga()
          ^^^^^^

• Warning: modules/nf-core/spades/main.nf:86:9: Variable was declared but not used

      def custom_hmms = hmm ? "--custom-hmms $hmm" : ""
          ^^^^^^^^^^^

• Warning: modules/nf-core/spades/main.nf:87:9: Variable was declared but not used

      def reads = yml ? "--dataset $yml" : "$illumina_reads $pacbio_reads $nanopore_reads"
          ^^^^^

• Warning: subworkflows/nf-core/fasta_binning_concoct/main.nf:14:19: The use of Channel to access channel factories is deprecated -- use channel instead

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