feat: add module for seqkit stats (#1466)

modules/seqkit/stats/main.nf

@@ -0,0 +1,34 @@
+process SEQKIT_STATS {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::seqkit=2.2.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/seqkit:2.2.0--h9ee0642_0':
+        'quay.io/biocontainers/seqkit:2.2.0--h9ee0642_0' }"
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    tuple val(meta), path("*.tsv"), emit: stats
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: '--all'
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    seqkit stats \\
+        --tabular \\
+        $args \\
+        $reads > '${prefix}.tsv'
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seqkit: \$( seqkit version | sed 's/seqkit v//' )
+    END_VERSIONS
+    """
+}

modules/seqkit/stats/meta.yml

@@ -0,0 +1,44 @@
+name: "seqkit_stats"
+description: simple statistics of FASTA/Q files
+keywords:
+  - seqkit
+  - stats
+tools:
+  - "seqkit":
+      description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
+      homepage: https://bioinf.shenwei.me/seqkit/usage/
+      documentation: https://bioinf.shenwei.me/seqkit/usage/
+      tool_dev_url: https://github.com/shenwei356/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 ]
+  - reads:
+      type: file
+      description: >
+        Either FASTA or FASTQ files.
+      pattern: "*.{fa,fna,faa,fasta,fq,fastq}[.gz]"
+
+output:
+  - meta:
+      type: map
+      description: >
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - stats:
+      type: file
+      description: >
+        Tab-separated output file with basic sequence statistics.
+      pattern: "*.tsv"
+
+authors:
+  - "@Midnighter"

tests/config/pytest_modules.yml

@@ -1591,6 +1591,10 @@ seqkit/split2:
   - modules/seqkit/split2/**
   - tests/modules/seqkit/split2/**
 
+seqkit/stats:
+  - modules/seqkit/stats/**
+  - tests/modules/seqkit/stats/**
+
 seqsero2:
   - modules/seqsero2/**
   - tests/modules/seqsero2/**

tests/modules/seqkit/stats/main.nf

@@ -0,0 +1,58 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SEQKIT_STATS } from '../../../../modules/seqkit/stats/main.nf'
+
+workflow test_seqkit_stats_single_end {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+
+    SEQKIT_STATS ( input )
+}
+
+workflow test_seqkit_stats_paired_end {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    SEQKIT_STATS ( input )
+}
+
+workflow test_seqkit_stats_nanopore {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true),
+    ]
+
+    SEQKIT_STATS ( input )
+}
+
+workflow test_seqkit_stats_genome_fasta {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+    ]
+
+    SEQKIT_STATS ( input )
+}
+
+workflow test_seqkit_stats_transcriptome_fasta {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true),
+    ]
+
+    SEQKIT_STATS ( input )
+}

tests/modules/seqkit/stats/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}

tests/modules/seqkit/stats/test.yml

@@ -0,0 +1,54 @@
+- name: seqkit stats test_seqkit_stats_single_end
+  command: nextflow run tests/modules/seqkit/stats -entry test_seqkit_stats_single_end -c tests/config/nextflow.config
+  tags:
+    - seqkit/stats
+    - seqkit
+  files:
+    - path: output/seqkit/test.tsv
+      md5sum: e23227d089a7e04b0ec0cb547c4aadff
+    - path: output/seqkit/versions.yml
+      md5sum: d67f0c16feb9df77b11f6c91bbdf9926
+
+- name: seqkit stats test_seqkit_stats_paired_end
+  command: nextflow run tests/modules/seqkit/stats -entry test_seqkit_stats_paired_end -c tests/config/nextflow.config
+  tags:
+    - seqkit/stats
+    - seqkit
+  files:
+    - path: output/seqkit/test.tsv
+      md5sum: 9de20dc39fb01285e3f0c382fda9db52
+    - path: output/seqkit/versions.yml
+      md5sum: bd8881933b953d07f2600e2e6a88ebf3
+
+- name: seqkit stats test_seqkit_stats_nanopore
+  command: nextflow run tests/modules/seqkit/stats -entry test_seqkit_stats_nanopore -c tests/config/nextflow.config
+  tags:
+    - seqkit/stats
+    - seqkit
+  files:
+    - path: output/seqkit/test.tsv
+      md5sum: 5da1709eb5ae64fa3b2d624bffe2e7aa
+    - path: output/seqkit/versions.yml
+      md5sum: 565632701fbe048f7ba99f1865bd48ca
+
+- name: seqkit stats test_seqkit_stats_genome_fasta
+  command: nextflow run tests/modules/seqkit/stats -entry test_seqkit_stats_genome_fasta -c tests/config/nextflow.config
+  tags:
+    - seqkit/stats
+    - seqkit
+  files:
+    - path: output/seqkit/test.tsv
+      md5sum: f64489767a4e769539ef3faf83260184
+    - path: output/seqkit/versions.yml
+      md5sum: 782fcdeaa922c8bb532ffa5808849d87
+
+- name: seqkit stats test_seqkit_stats_transcriptome_fasta
+  command: nextflow run tests/modules/seqkit/stats -entry test_seqkit_stats_transcriptome_fasta -c tests/config/nextflow.config
+  tags:
+    - seqkit/stats
+    - seqkit
+  files:
+    - path: output/seqkit/test.tsv
+      md5sum: fbb975b665a08c8862fcd1268613a945
+    - path: output/seqkit/versions.yml
+      md5sum: db99b016d986d26102ec398264a58410