Add seqkit/fx2tab module

modules/nf-core/seqkit/fx2tab/main.nf

@@ -0,0 +1,37 @@
+process SEQKIT_FX2TAB {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "bioconda::seqkit=2.1.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0' :
+        'biocontainers/seqkit:2.1.0--h9ee0642_0' }"
+
+    input:
+    tuple val(meta), path(fastx)
+
+    output:
+    tuple val(meta), path("*.txt*"), emit: text
+    path "versions.yml", emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args   = task.ext.args   ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def suffix = task.ext.suffix ?: "txt.zst"
+    """
+    seqkit \\
+        fx2tab \\
+        $args \\
+        --threads $task.cpus \\
+        $fastx \\
+        -o ${prefix}.${suffix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seqkit: \$( seqkit | sed '3!d; s/Version: //' )
+    END_VERSIONS
+    """
+}

modules/nf-core/seqkit/fx2tab/meta.yml

@@ -0,0 +1,42 @@
+name: seqkit_fx2tab
+description: Convert FASTA/Q to tabular format, and provide various information, like sequence length, GC content/GC skew.
+keywords:
+  - fasta
+  - fastq
+  - text
+  - tabular
+  - convert
+tools:
+  - seqkit:
+      description: |
+        Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
+      homepage: https://github.com/shenwei356/seqkit
+      documentation: https://bioinf.shenwei.me/seqkit/
+      doi: 10.1371/journal.pone.0163962
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fastx:
+      type: file
+      description: Sequence file in fasta/q format
+      pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}[.gz,.zst]"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - text:
+      type: file
+      description: Text file in tabular format
+      pattern: "*.txt[.gz,.zstd,.zst]"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@heuermh"

tests/config/pytest_modules.yml

@@ -3243,6 +3243,10 @@ sentieon/varcal:
   - modules/nf-core/sentieon/varcal/**
   - tests/modules/nf-core/sentieon/varcal/**
 
+seqkit/fx2tab:
+  - modules/nf-core/seqkit/fx2tab/**
+  - tests/modules/nf-core/seqkit/fx2tab/**
+
 seqkit/grep:
   - modules/nf-core/seqkit/grep/**
   - tests/modules/nf-core/seqkit/grep/**

tests/modules/nf-core/seqkit/fx2tab/main.nf

@@ -0,0 +1,25 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SEQKIT_FX2TAB                            } from '../../../../../modules/nf-core/seqkit/fx2tab/main.nf'
+
+workflow test_seqkit_fx2tab_fasta {
+
+    input = [ [ id:'test' ],   // meta map
+              [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+            ]
+
+    SEQKIT_FX2TAB ( input )
+
+}
+
+workflow test_seqkit_fx2tab_fastq {
+
+    input = [ [ id:'test' ],   // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    SEQKIT_FX2TAB ( input )
+
+}

tests/modules/nf-core/seqkit/fx2tab/nextflow.config

@@ -0,0 +1,7 @@
+process {
+
+    withName: 'SEQKIT_FX2TAB' {
+        ext.args        = ""
+        publishDir      = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    }
+}

tests/modules/nf-core/seqkit/fx2tab/test.yml

@@ -0,0 +1,18 @@
+- name: seqkit fx2tab test_seqkit_fx2tab_fasta
+  command: nextflow run ./tests/modules/nf-core/seqkit/fx2tab -entry test_seqkit_fx2tab_fasta -c ./tests/config/nextflow.config
+  tags:
+    - seqkit/fx2tab
+    - seqkit
+  files:
+    - path: output/seqkit/test.txt.zst
+      md5sum: 9d6751134b38b57b1d2f76f508b610fa
+    - path: output/seqkit/versions.yml
+- name: seqkit fx2tab test_seqkit_fx2tab_fastq
+  command: nextflow run ./tests/modules/nf-core/seqkit/fx2tab -entry test_seqkit_fx2tab_fastq -c ./tests/config/nextflow.config
+  tags:
+    - seqkit/fx2tab
+    - seqkit
+  files:
+    - path: output/seqkit/test.txt.zst
+      md5sum: df053f44dbaa8576e93426274e73c2b5
+    - path: output/seqkit/versions.yml