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Add AdapterRemovalFixPrefix (#1424)
* Add AdapterRemovalFixPrefix * Prettifying Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
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38
modules/adapterremovalfixprefix/main.nf
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38
modules/adapterremovalfixprefix/main.nf
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def VERSION = '0.05'
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process ADAPTERREMOVALFIXPREFIX {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::adapterremovalfixprefix=0.0.5" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/adapterremovalfixprefix:0.0.5--hdfd78af_2':
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'quay.io/biocontainers/adapterremovalfixprefix:0.0.5--hdfd78af_2' }"
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input:
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tuple val(meta), path(fastq)
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output:
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tuple val(meta), path("*.fq.gz"), emit: fixed_fastq
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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if ("$fastq" == "${prefix}.fq.gz") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
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"""
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AdapterRemovalFixPrefix \\
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$fastq \\
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$args \\
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| gzip > ${prefix}.fq.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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adapterremovalfixprefix: $VERSION
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END_VERSIONS
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"""
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}
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43
modules/adapterremovalfixprefix/meta.yml
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43
modules/adapterremovalfixprefix/meta.yml
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name: adapterremovalfixprefix
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description: Fixes prefixes from AdapterRemoval2 output to make sure no clashing read names are in the output. For use with DeDup.
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keywords:
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- adapterremoval
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- fastq
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- dedup
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tools:
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- adapterremovalfixprefix:
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description: Fixes adapter removal prefixes to make sure no clashing read names are in the output.
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homepage: https://github.com/apeltzer/AdapterRemovalFixPrefix
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documentation: None
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tool_dev_url: https://github.com/apeltzer/AdapterRemovalFixPrefix
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doi: "10.1186/s13059-016-0918-z"
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licence: ["GPL v3"]
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- fastq:
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type: file
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description: FASTQ file from AdapterRemoval2
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pattern: "*.{fq.gz,fastq.gz}"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- fixed_fastq:
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type: file
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description: FASTQ file with fixed read prefixes for DeDup
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pattern: "*.{fq.gz}"
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authors:
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- "@jfy133"
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@ -14,6 +14,10 @@ adapterremoval:
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- modules/adapterremoval/**
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- tests/modules/adapterremoval/**
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adapterremovalfixprefix:
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- modules/adapterremovalfixprefix/**
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- tests/modules/adapterremovalfixprefix/**
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agrvate:
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- modules/agrvate/**
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- tests/modules/agrvate/**
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19
tests/modules/adapterremovalfixprefix/main.nf
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19
tests/modules/adapterremovalfixprefix/main.nf
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { ADAPTERREMOVAL } from '../../../modules/adapterremoval/main.nf'
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include { ADAPTERREMOVALFIXPREFIX } from '../../../modules/adapterremovalfixprefix/main.nf'
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workflow test_adapterremovalfixprefix {
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input = [
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[ id:'test', single_end:false ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
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]
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]
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ADAPTERREMOVAL ( input, [] )
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ADAPTERREMOVALFIXPREFIX ( ADAPTERREMOVAL.out.collapsed )
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}
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9
tests/modules/adapterremovalfixprefix/nextflow.config
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9
tests/modules/adapterremovalfixprefix/nextflow.config
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process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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withName: ADAPTERREMOVAL {
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ext.args = "--collapse"
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}
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}
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9
tests/modules/adapterremovalfixprefix/test.yml
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9
tests/modules/adapterremovalfixprefix/test.yml
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- name: adapterremovalfixprefix test_adapterremovalfixprefix
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command: nextflow run tests/modules/adapterremovalfixprefix -entry test_adapterremovalfixprefix -c tests/config/nextflow.config
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tags:
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- adapterremovalfixprefix
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files:
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- path: output/adapterremovalfixprefix/test.fq.gz
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md5sum: ff956de3532599a56c3efe5369f0953f
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- path: output/adapterremovalfixprefix/versions.yml
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md5sum: 983cb58079bf015c1d489a7e48261746
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