added module seqkit replace (#1382)

* added module seqkit replace

* added when

* removed extra line

* Update modules/seqkit/replace/main.nf

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>

* Updated meta

* updated indents

Co-authored-by: Cipriano <rrn8@cdc.gov>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>

modules/seqkit/replace/main.nf

@@ -0,0 +1,41 @@
+process SEQKIT_REPLACE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::seqkit=2.1.0" : null)
+    container "${ 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(fastx)
+
+    output:
+    tuple val(meta), path("*.fast*"), emit: fastx
+    path "versions.yml"             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def extension = "fastq"
+    if ("$fastx" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz/) {
+        extension = "fasta"
+    }
+    def endswith = task.ext.suffix ?: "${extension}.gz"
+    """
+    seqkit \\
+        replace \\
+        ${args} \\
+        --threads ${task.cpus} \\
+        -i ${fastx} \\
+        -o ${prefix}.${endswith}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seqkit: \$( seqkit | sed '3!d; s/Version: //' )
+    END_VERSIONS
+    """
+}

modules/seqkit/replace/meta.yml

@@ -0,0 +1,41 @@
+name: seqkit_replace
+description: Use seqkit to find/replace strings within sequences and sequence headers
+keywords:
+  - seqkit
+  - replace
+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.016396"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fastx:
+      type: file
+      description: fasta/q file
+      pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}*"
+
+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"
+  - fastx:
+      type: file
+      description: fasta/q file with replaced values
+      pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}*"
+
+authors:
+  - "@mjcipriano"

tests/config/pytest_modules.yml

@@ -1481,6 +1481,10 @@ seqkit/pair:
   - modules/seqkit/pair/**
   - tests/modules/seqkit/pair/**
 
+seqkit/replace:
+  - modules/seqkit/replace/**
+  - tests/modules/seqkit/replace/**
+
 seqkit/split2:
   - modules/seqkit/split2/**
   - tests/modules/seqkit/split2/**

tests/modules/seqkit/replace/main.nf

@@ -0,0 +1,24 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SEQKIT_REPLACE } from '../../../../modules/seqkit/replace/main.nf'
+include { SEQKIT_REPLACE as SEQKIT_REPLACEUNCOMP } from '../../../../modules/seqkit/replace/main.nf'
+
+workflow test_seqkit_replace {
+
+    input = [ [ id:'test' ],   // meta map
+              [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+            ]
+
+    SEQKIT_REPLACE ( input )
+}
+
+workflow test_seqkit_replace_uncomp {
+
+    input = [ [ id:'test' ],   // meta map
+              [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+            ]
+
+    SEQKIT_REPLACEUNCOMP ( input )
+}

tests/modules/seqkit/replace/nextflow.config

@@ -0,0 +1,14 @@
+process {
+
+    withName: 'SEQKIT_REPLACE' {
+        ext.args   = "-s -p 'A' -r 'N'"
+        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    }
+
+    withName: 'SEQKIT_REPLACEUNCOMP' {
+        ext.args          = "-s -p 'T' -r 'N'"
+        ext.suffix        = ".fasta"
+        publishDir        = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    }
+
+}

tests/modules/seqkit/replace/test.yml

@@ -0,0 +1,21 @@
+- name: seqkit replace test_seqkit_replace
+  command: nextflow run tests/modules/seqkit/replace -entry test_seqkit_replace -c tests/config/nextflow.config
+  tags:
+    - seqkit
+    - seqkit/replace
+  files:
+    - path: output/seqkit/test.fasta.gz
+      md5sum: 053847219695c0a923d02352442d7abf
+    - path: output/seqkit/versions.yml
+      md5sum: dc9d18b7836c9db00a3032fd191bd831
+
+- name: seqkit replace test_seqkit_replace_uncomp
+  command: nextflow run tests/modules/seqkit/replace -entry test_seqkit_replace_uncomp -c tests/config/nextflow.config
+  tags:
+    - seqkit
+    - seqkit/replace
+  files:
+    - path: output/seqkit/test..fasta
+      md5sum: 05d3294a62c72f5489f067c1da3c2f6c
+    - path: output/seqkit/versions.yml
+      md5sum: 3b88128487ec949f0bdeecebc375c407