Seqkit pair (#1348)

* add seqkit pair module

* local tests

* local tests

* fix workflow name

* fix workflow name

* fix version indentation

* fix version indentation

* fix version indentation

* fix review comments

* fix review comments

* fix github usernames

* minor fix

* add meta unpaired output

Co-authored-by: Peri <rrx8@cdc.gov>

modules/seqkit/pair/main.nf

@@ -0,0 +1,40 @@
+process SEQKIT_PAIR {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::seqkit=2.1.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0':
+        'quay.io/biocontainers/seqkit:2.1.0--h9ee0642_0' }"
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    tuple val(meta), path("*.paired.fastq.gz")                  , emit: reads
+    tuple val(meta), path("*.unpaired.fastq.gz"), optional: true, emit: unpaired_reads
+    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}"
+    """
+    seqkit \\
+        pair \\
+        -1 ${reads[0]} \\
+        -2 ${reads[1]} \\
+        $args \\
+        --threads $task.cpus
+
+    # gzip fastq
+    find . -maxdepth 1 -name "*.fastq" -exec gzip {} \;
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seqkit: \$( seqkit | sed '3!d; s/Version: //' )
+    END_VERSIONS
+    """
+}

modules/seqkit/pair/meta.yml

@@ -0,0 +1,48 @@
+name: seqkit_pair
+description: match up paired-end reads from two fastq files
+keywords:
+  - seqkit
+  - pair
+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: |
+        List of input paired-end FastQ files.
+
+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"
+  - reads:
+      type: file
+      description: Paired fastq reads
+      pattern: "*.paired.fastq.gz"
+  - unpaired_reads:
+      type: file
+      description: Unpaired reads (optional)
+      pattern: "*.unpaired.fastq.gz"
+
+authors:
+  - "@sateeshperi"
+  - "@mjcipriano"
+  - "@hseabolt"

tests/config/pytest_modules.yml

@@ -1445,6 +1445,10 @@ seacr/callpeak:
   - modules/seacr/callpeak/**
   - tests/modules/seacr/callpeak/**
 
+seqkit/pair:
+  - modules/seqkit/pair/**
+  - tests/modules/seqkit/pair/**
+
 seqkit/split2:
   - modules/seqkit/split2/**
   - tests/modules/seqkit/split2/**

tests/modules/seqkit/pair/main.nf

@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SEQKIT_PAIR } from '../../../../modules/seqkit/pair/main.nf'
+
+workflow test_seqkit_pair {
+    
+    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_PAIR ( input )
+}

tests/modules/seqkit/pair/nextflow.config

@@ -0,0 +1,6 @@
+process {
+
+    ext.args = "-u"
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}

tests/modules/seqkit/pair/test.yml

@@ -0,0 +1,12 @@
+- name: seqkit pair test_seqkit_pair
+  command: nextflow run tests/modules/seqkit/pair -entry test_seqkit_pair -c tests/config/nextflow.config
+  tags:
+    - seqkit/pair
+    - seqkit
+  files:
+    - path: output/seqkit/test_1.paired.fastq.gz
+      md5sum: fbfe7e8bdbc29abaaf58b6f1a32448e5
+    - path: output/seqkit/test_2.paired.fastq.gz
+      md5sum: 7d3c0912e5adc2674e8ecc1e647381b3
+    - path: output/seqkit/versions.yml
+      md5sum: 3086293bc986fc2ece38b1951d090819