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lDesireelDesiree
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Merge pull request #5 from ICGC-ARGO-Structural-Variation-CN-WG/seqz-preprocess@0.2.0
[release]
2 parents 490e9d2 + 2d36a28 commit 14eec91

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‎seqz-preprocess/.dockerignore‎

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.gitignore
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.nextflow*
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tests
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work
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outdir

‎seqz-preprocess/Dockerfile‎

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FROM continuumio/miniconda3:4.8.2
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# newer version results in conflicts.
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RUN apt-get update \
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&& apt-get install -y procps \
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&& /opt/conda/bin/conda install --yes -c bioconda samtools=1.9 tabix \
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&& /opt/conda/bin/conda install --yes -c bioconda sequenza-utils=3.0.0
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USER sequenza
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WORKDIR /home/sequenza
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CMD ["/bin/bash"]

‎seqz-preprocess/main.nf‎

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#!/usr/bin/env nextflow
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/*
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Copyright (c) 2021, ICGC ARGO
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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Authors:
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Desiree Schnidrig
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*/
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/********************************************************************/
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/* this block is auto-generated based on info from pkg.json where */
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/* changes can be made if needed, do NOT modify this block manually */
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nextflow.enable.dsl = 2
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version = '0.2.0' // package version
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container = [
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'ghcr.io': 'ghcr.io/icgc-argo-structural-variation-cn-wg/wfpm-demo.seqz-preprocess'
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]
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default_container_registry = 'ghcr.io'
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/********************************************************************/
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// universal params go here
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params.container_registry = ""
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params.container_version = ""
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params.container = ""
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params.cpus = 1
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params.mem = 1 // GB
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params.publish_dir = "output_dir/" // set to empty string will disable publishDir
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// tool specific parmas go here, add / change as needed
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params.tumor_bam = ""
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params.normal_bam = ""
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params.fasta = ""
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params.gcwiggle = "${baseDir}/resources/hg38.gc50Base.wig.gz"
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params.output_pattern = "*bin50.seqz.gz" // output file name pattern
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process seqzPreprocess {
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container "${params.container ?: container[params.container_registry ?: default_container_registry]}:${params.container_version ?: version}"
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publishDir "${params.publish_dir}/${task.process.replaceAll(':', '_')}", mode: "copy", enabled: params.publish_dir
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cpus params.cpus
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memory "${params.mem} GB"
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input: // input, make update as needed
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path tumor_bam
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path normal_bam
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path fasta
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path gcwiggle
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output: // output, make update as needed
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path "${params.output_pattern}", emit: seqz
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script:
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// add and initialize variables here as needed
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"""
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sequenza-utils bam2seqz --normal ${normal_bam} --tumor ${tumor_bam} --fasta ${fasta} -gc ${gcwiggle} --output sample.seqz.gz;
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sequenza-utils seqz_binning --seqz sample.seqz.gz --window 50 -o sample_bin50.seqz.gz
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"""
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}
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// this provides an entry point for this main script, so it can be run directly without clone the repo
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// using this command: nextflow run <git_acc>/<repo>/<pkg_name>/<main_script>.nf -r <pkg_name>.v<pkg_version> --params-file xxx
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workflow {
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seqzPreprocess(
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file(params.tumor_bam),
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file(params.normal_bam),
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file(params.fasta),
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file(params.gcwiggle)
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)
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}

‎seqz-preprocess/main.py‎

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#!/usr/bin/env python3
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# -*- coding: utf-8 -*-
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"""
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Copyright (c) 2021, ICGC ARGO
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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Authors:
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lDesiree
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"""
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import os
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import sys
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import argparse
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import subprocess
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def main():
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"""
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Python implementation of tool: seqz-preprocess
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This is auto-generated Python code, please update as needed!
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"""
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parser = argparse.ArgumentParser(description='Tool: seqz-preprocess')
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parser.add_argument('-i', '--input-file', dest='input_file', type=str,
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help='Input file', required=True)
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parser.add_argument('-o', '--output-dir', dest='output_dir', type=str,
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help='Output directory', required=True)
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args = parser.parse_args()
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if not os.path.isfile(args.input_file):
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sys.exit('Error: specified input file %s does not exist or is not accessible!' % args.input_file)
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if not os.path.isdir(args.output_dir):
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sys.exit('Error: specified output dir %s does not exist or is not accessible!' % args.output_dir)
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subprocess.run(f"fastqc -o {args.output_dir} {args.input_file}", shell=True, check=True)
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if __name__ == "__main__":
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main()

‎seqz-preprocess/nextflow.config‎

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docker {
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enabled = true
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runOptions = '-u \$(id -u):\$(id -g)'
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}

‎seqz-preprocess/pkg.json‎

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{
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"name": "seqz-preprocess",
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"version": "0.2.0",
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"description": "Sequenza preprocessing",
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"main": "main.nf",
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"deprecated": false,
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"keywords": [
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"bioinformatics",
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"seq",
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"qc metrics"
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],
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"repository": {
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"type": "git",
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"url": "https://github.com/icgc-argo-structural-variation-cn-wg/wfpm-demo.git"
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},
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"container": {
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"registries": [
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{
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"registry": "ghcr.io",
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"type": "docker",
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"org": "icgc-argo-structural-variation-cn-wg",
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"default": true
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}
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]
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},
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"dependencies": [],
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"devDependencies": [],
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"contributors": [
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{
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"name": "lDesiree",
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"email": "desiree.schnidrig@gmail.com"
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}
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],
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"license": "MIT",
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"bugReport": "https://github.com/icgc-argo-structural-variation-cn-wg/wfpm-demo/issues",
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"homepage": "https://github.com/icgc-argo-structural-variation-cn-wg/wfpm-demo#readme"
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}

‎seqz-preprocess/resources/hg38.gc50Base.wig.gz.md5‎

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e940cff9bff4e75960127201665e838f hg38.gc50Base.wig.gz

‎seqz-preprocess/resources/readme‎

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"# File 'hg38.gc50Base.wig.gz' is >100mb. Please download it from ''https://object.cancercollaboratory.org:9080/swift/v1/genomics-public-data/sequenza_references/hg38.gc50Base.wig.gz"" and compare it to the md5sum in this folder."

‎seqz-preprocess/tests/checker.nf‎

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#!/usr/bin/env nextflow
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/*
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Copyright (c) 2021, ICGC ARGO
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
10+
copies of the Software, and to permit persons to whom the Software is
11+
furnished to do so, subject to the following conditions:
12+
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
15+
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
17+
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
18+
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
19+
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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Authors:
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Desiree Schnidrig
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*/
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/*
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This is an auto-generated checker workflow to test the generated main template workflow, it's
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meant to illustrate how testing works. Please update to suit your own needs.
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*/
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/********************************************************************/
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/* this block is auto-generated based on info from pkg.json where */
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/* changes can be made if needed, do NOT modify this block manually */
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nextflow.enable.dsl = 2
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version = '0.2.0' // package version
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container = [
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'ghcr.io': 'ghcr.io/icgc-argo-structural-variation-cn-wg/wfpm-demo.seqz-preprocess'
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]
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default_container_registry = 'ghcr.io'
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/********************************************************************/
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// universal params
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params.container_registry = ""
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params.container_version = ""
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params.container = ""
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// tool specific parmas go here, add / change as needed
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params.tumor_bam = ""
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params.normal_bam = ""
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params.gcwiggle = ""
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params.fasta = ""
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params.expected_output = ""
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include { seqzPreprocess } from '../main'
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process file_smart_diff {
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container "${params.container ?: container[params.container_registry ?: default_container_registry]}:${params.container_version ?: version}"
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input:
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path seqz
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path expected_file
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output:
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stdout()
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script:
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"""
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zdiff ${seqz} ${expected_file} \
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&& ( echo "Test PASSED" && exit 0 ) || ( echo "Test FAILED, output file mismatch." && exit 1 )
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"""
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}
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workflow checker {
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take:
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tumor_bam
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normal_bam
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gcwiggle
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fasta
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expected_output
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main:
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seqzPreprocess(
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tumor_bam,
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normal_bam,
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gcwiggle,
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fasta
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)
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file_smart_diff(
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seqzPreprocess.out.seqz,
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expected_output
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)
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}
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workflow {
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checker(
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file(params.tumor_bam),
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file(params.normal_bam),
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file(params.fasta),
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file(params.gcwiggle),
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file(params.expected_output)
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)
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}

‎seqz-preprocess/tests/expected/expected_bin50.seqz.gz‎

4.63 KB
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