mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-20 23:32:05 +00:00
Faqcs (#1339)
* Initial module creation * Update test.yml * Update test.yml * Update test.yml * Update meta.yml Co-authored-by: Cipriano <rrn8@cdc.gov> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
This commit is contained in:
parent
a25423dbb9
commit
f144171ddc
6 changed files with 241 additions and 0 deletions
103
modules/faqcs/main.nf
Normal file
103
modules/faqcs/main.nf
Normal file
|
@ -0,0 +1,103 @@
|
|||
process FAQCS {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::faqcs=2.10" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/faqcs%3A2.10--r41h9a82719_2' :
|
||||
'quay.io/biocontainers/faqcs:2.10--r41h9a82719_2' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
|
||||
output:
|
||||
tuple val(meta), path('*.trimmed.fastq.gz') , emit: reads
|
||||
tuple val(meta), path('*.stats.txt') , emit: stats
|
||||
tuple val(meta), path('*_qc_report.pdf') , optional:true, emit: statspdf
|
||||
tuple val(meta), path('*.log') , emit: log
|
||||
tuple val(meta), path('*.discard.fastq.gz') , optional:true, emit: reads_fail
|
||||
tuple val(meta), path('*.trimmed.unpaired.fastq.gz') , optional:true, emit: reads_unpaired
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
// Added soft-links to original fastqs for consistent naming in MultiQC
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
if (meta.single_end) {
|
||||
"""
|
||||
[ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
|
||||
FaQCs \\
|
||||
-d . \\
|
||||
-u ${prefix}.fastq.gz \\
|
||||
--prefix ${prefix} \\
|
||||
-t $task.cpus \\
|
||||
$args \\
|
||||
2> ${prefix}.fastp.log
|
||||
|
||||
|
||||
if [[ -f ${prefix}.unpaired.trimmed.fastq ]]; then
|
||||
mv ${prefix}.unpaired.trimmed.fastq ${prefix}.trimmed.fastq
|
||||
gzip ${prefix}.trimmed.fastq
|
||||
fi
|
||||
if [[ -f ${prefix}.discard.trimmed.fastq ]]; then
|
||||
mv ${prefix}.discard.trimmed.fastq ${prefix}.trimmed.discard.fastq
|
||||
gzip ${prefix}.trimmed.discard.fastq
|
||||
fi
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
faqcs: \$(echo \$(FaQCs --version 2>&1) | sed 's/^.*Version: //;' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
} else {
|
||||
"""
|
||||
[ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
|
||||
[ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
|
||||
FaQCs \\
|
||||
-d . \\
|
||||
-1 ${prefix}_1.fastq.gz \\
|
||||
-2 ${prefix}_2.fastq.gz \\
|
||||
--prefix ${meta.id} \\
|
||||
-t $task.cpus \\
|
||||
$args \\
|
||||
2> ${prefix}.fastp.log
|
||||
|
||||
# Unpaired
|
||||
if [[ -f ${prefix}.unpaired.trimmed.fastq ]]; then
|
||||
# If it is empty remove it
|
||||
if [[ ! -s ${prefix}.unpaired.trimmed.fastq ]]; then
|
||||
rm ${prefix}.unpaired.trimmed.fastq
|
||||
else
|
||||
mv ${prefix}.unpaired.trimmed.fastq ${prefix}.trimmed.unpaired.fastq
|
||||
gzip ${prefix}.trimmed.unpaired.fastq
|
||||
fi
|
||||
fi
|
||||
|
||||
# R1
|
||||
if [[ -f ${prefix}.1.trimmed.fastq ]]; then
|
||||
mv ${prefix}.1.trimmed.fastq ${prefix}_1.trimmed.fastq
|
||||
gzip ${prefix}_1.trimmed.fastq
|
||||
fi
|
||||
|
||||
# R2
|
||||
if [[ -f ${prefix}.2.trimmed.fastq ]]; then
|
||||
mv ${prefix}.2.trimmed.fastq ${prefix}_2.trimmed.fastq
|
||||
gzip ${prefix}_2.trimmed.fastq
|
||||
fi
|
||||
|
||||
# Discarded: Created if --discard argument is passed
|
||||
if [[ -f ${prefix}.discard.trimmed.fastq ]]; then
|
||||
mv ${prefix}.discard.trimmed.fastq ${prefix}.trimmed.discard.fastq
|
||||
gzip ${prefix}.trimmed.discard.fastq
|
||||
fi
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
faqcs: \$(echo \$(FaQCs --version 2>&1) | sed 's/^.*Version: //;' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
}
|
||||
|
68
modules/faqcs/meta.yml
Normal file
68
modules/faqcs/meta.yml
Normal file
|
@ -0,0 +1,68 @@
|
|||
name: faqcs
|
||||
description: Perform adapter and quality trimming on sequencing reads with reporting
|
||||
keywords:
|
||||
- trimming
|
||||
- quality control
|
||||
- fastq
|
||||
- faqcs
|
||||
tools:
|
||||
- faqcs:
|
||||
description: |
|
||||
FaQCs combines several features of currently available applications into a single, user-friendly process, and includes additional unique capabilities such as filtering the PhiX control sequences, conversion of FASTQ formats, and multi-threading. The original data and trimmed summaries are reported within a variety of graphics and reports, providing a simple way to do data quality control and assurance.
|
||||
homepage: https://github.com/LANL-Bioinformatics/FaQCs
|
||||
documentation: https://github.com/LANL-Bioinformatics/FaQCs
|
||||
tool_dev_url: https://github.com/LANL-Bioinformatics/FaQCs
|
||||
doi: "https://doi.org/10.1186/s12859-014-0366-2"
|
||||
licence: ['GPLv3 License']
|
||||
|
||||
## TODO nf-core: Add a description of all of the variables used as input
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
|
||||
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: The trimmed/modified fastq reads
|
||||
pattern: "*trimmed.fastq.gz"
|
||||
- reads_fail:
|
||||
type: file
|
||||
description: Reads that failed the preprocessing (Optional with --discard args setting)
|
||||
pattern: "*discard.fastq.gz"
|
||||
- reads_unpaired:
|
||||
type: file
|
||||
description: Reads without matching mates in paired-end files (Optional)
|
||||
pattern: "*trimmed.unpaired.fastq.gz"
|
||||
- stats:
|
||||
type: file
|
||||
description: trimming/qc text stats file
|
||||
pattern: "*.stats.txt"
|
||||
- statspdf:
|
||||
type: file
|
||||
description: trimming/qc pdf report file
|
||||
pattern: "*_qc_report.pdf"
|
||||
- log:
|
||||
type: file
|
||||
description: fastq log file
|
||||
pattern: "*.log"
|
||||
authors:
|
||||
- "@mjcipriano"
|
||||
- "@sateeshperi"
|
||||
- "@hseabolt"
|
|
@ -504,6 +504,10 @@ expansionhunter:
|
|||
- modules/expansionhunter/**
|
||||
- tests/modules/expansionhunter/**
|
||||
|
||||
faqcs:
|
||||
- modules/faqcs/**
|
||||
- tests/modules/faqcs/**
|
||||
|
||||
fargene:
|
||||
- modules/fargene/**
|
||||
- tests/modules/fargene/**
|
||||
|
|
30
tests/modules/faqcs/main.nf
Normal file
30
tests/modules/faqcs/main.nf
Normal file
|
@ -0,0 +1,30 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { FAQCS } from '../../../modules/faqcs/main.nf'
|
||||
|
||||
|
||||
//
|
||||
// Test with single-end data
|
||||
//
|
||||
workflow test_fastp_single_end {
|
||||
input = [ [ id:'test', single_end:true ], // meta map
|
||||
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
|
||||
]
|
||||
|
||||
FAQCS ( input )
|
||||
}
|
||||
|
||||
//
|
||||
// Test with paired-end data
|
||||
//
|
||||
workflow test_fastp_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) ]
|
||||
]
|
||||
|
||||
FAQCS ( input )
|
||||
}
|
||||
|
5
tests/modules/faqcs/nextflow.config
Normal file
5
tests/modules/faqcs/nextflow.config
Normal file
|
@ -0,0 +1,5 @@
|
|||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
}
|
31
tests/modules/faqcs/test.yml
Normal file
31
tests/modules/faqcs/test.yml
Normal file
|
@ -0,0 +1,31 @@
|
|||
- name: faqcs test_fastp_single_end
|
||||
command: nextflow run tests/modules/faqcs -entry test_fastp_single_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- faqcs
|
||||
files:
|
||||
- path: output/faqcs/test.fastp.log
|
||||
md5sum: be79dc893f87de1f82faf749cdfb848c
|
||||
- path: output/faqcs/test.stats.txt
|
||||
md5sum: ea20e93706b2e4c676004253baa3cec6
|
||||
- path: output/faqcs/test.trimmed.fastq.gz
|
||||
md5sum: 875863b402f67403dac63ef59b9c9a8a
|
||||
- path: output/faqcs/test_qc_report.pdf
|
||||
- path: output/faqcs/versions.yml
|
||||
md5sum: 2a38d7e7ab5299336e9669c393c9da6c
|
||||
|
||||
- name: faqcs test_fastp_paired_end
|
||||
command: nextflow run tests/modules/faqcs -entry test_fastp_paired_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- faqcs
|
||||
files:
|
||||
- path: output/faqcs/test.fastp.log
|
||||
md5sum: be79dc893f87de1f82faf749cdfb848c
|
||||
- path: output/faqcs/test.stats.txt
|
||||
md5sum: 9a693f8af94ab8c485519d9a523aa622
|
||||
- path: output/faqcs/test_1.trimmed.fastq.gz
|
||||
md5sum: 875863b402f67403dac63ef59b9c9a8a
|
||||
- path: output/faqcs/test_2.trimmed.fastq.gz
|
||||
md5sum: 375aeb74819ca3d72203135ac80df78c
|
||||
- path: output/faqcs/test_qc_report.pdf
|
||||
- path: output/faqcs/versions.yml
|
||||
md5sum: 208d54c0cf6dfc54e719b81b990afac9
|
Loading…
Reference in a new issue