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Merge pull request #2 from ICGC-ARGO-Structural-Variation-CN-WG/demo-fastqc-wf@0.2.0
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‎demo-fastqc-wf/local_modules/demo-copy-file.nf‎

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#!/usr/bin/env nextflow
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/*
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This is an example process as a local module. Using local module is optional, in general
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is discouraged. A process can pentially be reused in different workflows should be developed
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in an independent package, so that it can be imported by anyone into any workflow.
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*/
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nextflow.enable.dsl = 2
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params.input_file = ""
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params.publish_dir = ""
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process demoCopyFile {
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publishDir "${params.publish_dir}/${task.process.replaceAll(':', '_')}", mode: "copy", enabled: params.publish_dir
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input:
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path input_file
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output:
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path "output_dir/*", emit: output_file
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script:
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"""
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mkdir output_dir
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cp ${input_file} output_dir/
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"""
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}

‎demo-fastqc-wf/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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Junjun Zhang
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*/
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nextflow.enable.dsl = 2
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version = '0.2.0' // package version
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// universal params go here, change default value as needed
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params.container = ""
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params.container_registry = ""
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params.container_version = ""
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params.cpus = 1
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params.mem = 1 // GB
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params.publish_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.input_file = ""
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params.cleanup = true
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include { cleanupWorkdir; getSecondaryFiles; getBwaSecondaryFiles } from './wfpr_modules/github.com/icgc-argo/demo-wfpkgs/demo-utils@1.3.0/main.nf' params([*:params, 'cleanup': false])
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include { demoFastqc } from './wfpr_modules/github.com/icgc-argo-structural-variation-cn-wg/wfpm-demo/demo-fastqc@0.2.0/main.nf' params([*:params, 'cleanup': false])
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// please update workflow code as needed
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workflow DemoFastqcWf {
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take: // update as needed
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input_file
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main: // update as needed
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demoFastqc(input_file)
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if (params.cleanup) { cleanupWorkdir(demoFastqc.out, true) }
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emit: // update as needed
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output_file = demoFastqc.out.output_file
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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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DemoFastqcWf(
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file(params.input_file)
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)
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}

‎demo-fastqc-wf/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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}

‎demo-fastqc-wf/pkg.json‎

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{
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"name": "demo-fastqc-wf",
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"version": "0.2.0",
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"description": "FastQC workflow",
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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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"dependencies": [
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"github.com/icgc-argo/demo-wfpkgs/demo-utils@1.3.0",
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"github.com/icgc-argo-structural-variation-cn-wg/wfpm-demo/demo-fastqc@0.2.0"
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],
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"devDependencies": [],
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"contributors": [
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{
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"name": "Junjun Zhang",
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"email": "junjun.ca@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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}

‎demo-fastqc-wf/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
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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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Junjun Zhang
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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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nextflow.enable.dsl = 2
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version = '0.2.0' // package version
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// universal params
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params.publish_dir = ""
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params.container = ""
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params.container_registry = ""
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params.container_version = ""
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// tool specific parmas go here, add / change as needed
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params.input_file = ""
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params.expected_output = ""
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params.cleanup = false
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include { DemoFastqcWf } from '../main'
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// include section starts
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// include section ends
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process file_smart_diff {
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input:
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path output_file
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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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# Note: this is only for demo purpose, please write your own 'diff' according to your own needs.
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# in this example, we need to remove date field before comparison eg, <div id="header_filename">Tue 19 Jan 2021<br/>test_rg_3.bam</div>
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# sed -e 's#"header_filename">.*<br/>test_rg_3.bam#"header_filename"><br/>test_rg_3.bam</div>#'
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cat ${output_file} \
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| sed -e 's#"header_filename">.*<br/>#"header_filename"><br/>#' > normalized_output
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([[ '${expected_file}' == *.gz ]] && gunzip -c ${expected_file} || cat ${expected_file}) \
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| sed -e 's#"header_filename">.*<br/>#"header_filename"><br/>#' > normalized_expected
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diff normalized_output normalized_expected \
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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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input_file
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expected_output
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main:
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DemoFastqcWf(
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input_file
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)
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file_smart_diff(
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DemoFastqcWf.out.output_file,
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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.input_file),
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file(params.expected_output)
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)
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}

‎demo-fastqc-wf/tests/expected/expected.test_rg_3.bam‎

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‎demo-fastqc-wf/tests/expected/expected.test_rg_3_fastqc.out.gz‎

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‎demo-fastqc-wf/tests/input/README.md‎

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This folder contains tiny data files for testing.

‎demo-fastqc-wf/tests/input/test_rg_3.bam‎

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‎demo-fastqc-wf/tests/nextflow.config‎

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includeConfig '../nextflow.config'

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