Add AdapterRemovalFixPrefix (#1424)

* Add AdapterRemovalFixPrefix

* Prettifying

Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>

modules/adapterremovalfixprefix/main.nf

@@ -0,0 +1,38 @@
+def VERSION = '0.05'
+
+process ADAPTERREMOVALFIXPREFIX {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::adapterremovalfixprefix=0.0.5" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/adapterremovalfixprefix:0.0.5--hdfd78af_2':
+        'quay.io/biocontainers/adapterremovalfixprefix:0.0.5--hdfd78af_2' }"
+
+    input:
+    tuple val(meta), path(fastq)
+
+    output:
+    tuple val(meta), path("*.fq.gz"), emit: fixed_fastq
+    path "versions.yml"             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if ("$fastq" == "${prefix}.fq.gz") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+
+    """
+    AdapterRemovalFixPrefix \\
+        $fastq \\
+        $args \\
+        | gzip > ${prefix}.fq.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        adapterremovalfixprefix: $VERSION
+    END_VERSIONS
+    """
+}

modules/adapterremovalfixprefix/meta.yml

@@ -0,0 +1,43 @@
+name: adapterremovalfixprefix
+description: Fixes prefixes from AdapterRemoval2 output to make sure no clashing read names are in the output. For use with DeDup.
+keywords:
+  - adapterremoval
+  - fastq
+  - dedup
+tools:
+  - adapterremovalfixprefix:
+      description: Fixes adapter removal prefixes to make sure no clashing read names are in the output.
+      homepage: https://github.com/apeltzer/AdapterRemovalFixPrefix
+      documentation: None
+      tool_dev_url: https://github.com/apeltzer/AdapterRemovalFixPrefix
+      doi: "10.1186/s13059-016-0918-z"
+      licence: ["GPL v3"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fastq:
+      type: file
+      description: FASTQ file from AdapterRemoval2
+      pattern: "*.{fq.gz,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"
+  - fixed_fastq:
+      type: file
+      description: FASTQ file with fixed read prefixes for DeDup
+      pattern: "*.{fq.gz}"
+
+authors:
+  - "@jfy133"

tests/config/pytest_modules.yml

@@ -14,6 +14,10 @@ adapterremoval:
   - modules/adapterremoval/**
   - tests/modules/adapterremoval/**
 
+adapterremovalfixprefix:
+  - modules/adapterremovalfixprefix/**
+  - tests/modules/adapterremovalfixprefix/**
+
 agrvate:
   - modules/agrvate/**
   - tests/modules/agrvate/**

tests/modules/adapterremovalfixprefix/main.nf

@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ADAPTERREMOVAL          } from '../../../modules/adapterremoval/main.nf'
+include { ADAPTERREMOVALFIXPREFIX } from '../../../modules/adapterremovalfixprefix/main.nf'
+
+workflow test_adapterremovalfixprefix {
+
+    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)
+        ]
+    ]
+
+    ADAPTERREMOVAL ( input, [] )
+    ADAPTERREMOVALFIXPREFIX ( ADAPTERREMOVAL.out.collapsed )
+}

tests/modules/adapterremovalfixprefix/nextflow.config

@@ -0,0 +1,9 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: ADAPTERREMOVAL {
+        ext.args = "--collapse"
+    }
+
+}

tests/modules/adapterremovalfixprefix/test.yml

@@ -0,0 +1,9 @@
+- name: adapterremovalfixprefix test_adapterremovalfixprefix
+  command: nextflow run tests/modules/adapterremovalfixprefix -entry test_adapterremovalfixprefix -c tests/config/nextflow.config
+  tags:
+    - adapterremovalfixprefix
+  files:
+    - path: output/adapterremovalfixprefix/test.fq.gz
+      md5sum: ff956de3532599a56c3efe5369f0953f
+    - path: output/adapterremovalfixprefix/versions.yml
+      md5sum: 983cb58079bf015c1d489a7e48261746