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added starting template for song-score-upload@0.2.6
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‎song-score-upload/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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}

‎song-score-upload/main.nf‎

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#!/usr/bin/env nextflow
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/*
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Copyright (c) 2020-2021, Ontario Institute for Cancer Research
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Licensed under the Apache License, Version 2.0 (the "License");
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you may not use this file except in compliance with the License.
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You may obtain a copy of the License at
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http://www.apache.org/licenses/LICENSE-2.0
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Unless required by applicable law or agreed to in writing, software
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distributed under the License is distributed on an "AS IS" BASIS,
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WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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See the License for the specific language governing permissions and
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limitations under the License.
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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 = '0.2.6' // 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 { demoCopyFile } from "./local_modules/demo-copy-file"
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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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// please update workflow code as needed
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workflow SongScoreUpload {
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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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demoCopyFile(input_file)
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if (params.cleanup) { cleanupWorkdir(demoCopyFile.out, true) }
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emit: // update as needed
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output_file = demoCopyFile.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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SongScoreUpload(
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file(params.input_file)
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)
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}

‎song-score-upload/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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}

‎song-score-upload/pkg.json‎

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{
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"name": "song-score-upload",
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"version": "0.2.6",
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"description": "SONG/SCORE upload",
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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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"data",
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"metadata",
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"upload"
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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/nextflow-data-processing-utility-tools.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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],
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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": "Apache License 2.0",
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"bugReport": "https://github.com/icgc-argo/nextflow-data-processing-utility-tools/issues",
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"homepage": "https://github.com/icgc-argo/nextflow-data-processing-utility-tools#readme"
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}

‎song-score-upload/tests/checker.nf‎

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#!/usr/bin/env nextflow
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/*
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Copyright (c) 2020-2021, Ontario Institute for Cancer Research
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Licensed under the Apache License, Version 2.0 (the "License");
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you may not use this file except in compliance with the License.
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You may obtain a copy of the License at
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http://www.apache.org/licenses/LICENSE-2.0
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Unless required by applicable law or agreed to in writing, software
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distributed under the License is distributed on an "AS IS" BASIS,
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WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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See the License for the specific language governing permissions and
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limitations under the License.
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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 = '0.2.6' // 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 { SongScoreUpload } 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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# 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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diff <( cat ${output_file} | sed -e 's#"header_filename">.*<br/>#"header_filename"><br/>#' ) \
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<( ([[ '${expected_file}' == *.gz ]] && gunzip -c ${expected_file} || cat ${expected_file}) | sed -e 's#"header_filename">.*<br/>#"header_filename"><br/>#' ) \
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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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SongScoreUpload(
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input_file
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)
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file_smart_diff(
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SongScoreUpload.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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}

‎song-score-upload/tests/expected/expected.test_rg_3.bam‎

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‎song-score-upload/tests/expected/expected.test_rg_3_fastqc.out.gz‎

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‎song-score-upload/tests/nextflow.config‎

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includeConfig '../nextflow.config'

‎song-score-upload/tests/test-job-1.json‎

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{
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"input_file": "input/test_rg_3.bam",
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"expected_output": "expected/expected.test_rg_3.bam",
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"publish_dir": "outdir",
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"cleanup": true,
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"cpus": 1,
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"mem": 0.5
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}

‎song-score-upload/tests/test-job-2.json‎

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{
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"input_file": "input/test_rg_3.bam",
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"expected_output": "expected/expected.test_rg_3.bam",
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"publish_dir": "outdir",
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"container_registry": "ghcr.io",
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"cpus": 1,
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"mem": 0.5
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}

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