Merge pull request #8 from ICGC-TCGA-PanCancer/[email protected]

[release] [email protected]

demo-fastqc-wf/.gitignore

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+*.py[cod]
+
+# C extensions
+*.so
+
+# Packages
+*.egg
+*.egg-info
+dist
+build
+eggs
+.eggs
+parts
+bin
+var
+sdist
+develop-eggs
+.installed.cfg
+lib
+lib64
+venv*/
+pyvenv*/
+
+# Installer logs
+pip-log.txt
+
+# Unit test / coverage reports
+.coverage
+.tox
+.coverage.*
+nosetests.xml
+coverage.xml
+htmlcov
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+.idea
+*.iml
+*.komodoproject
+
+# Complexity
+output/*.html
+output/*/index.html
+
+# Sphinx
+docs/_build
+
+.DS_Store
+*~
+.*.sw[po]
+.build
+.ve
+.env
+.cache
+.pytest
+.bootstrap
+.appveyor.token
+*.bak
+*.log
+.vscode
+.python-version
+.nextflow*
+work
+outdir

demo-fastqc-wf/demo-fastqc-wf.nf

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+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+version = '0.1.0'  // package version
+
+// universal params go here, change default value as needed
+params.container_version = ""
+params.cpus = 1
+params.mem = 1  // GB
+params.publish_dir = ""  // set to empty string will disable publishDir
+
+// tool specific parmas go here, add / change as needed
+params.input_file = ""
+params.cleanup = true
+
+include { demoFastqc } from './wfpr_modules/github.com/icgc-tcga-pancancer/awesome-wfpkgs1/[email protected]/demo-fastqc'
+include { cleanupWorkdir; getSecondaryFiles; getBwaSecondaryFiles } from './wfpr_modules/github.com/icgc-argo/demo-wfpkgs/[email protected]/main.nf'
+
+
+// please update workflow code as needed
+workflow DemoFastqcWf {
+  take:  // update as needed
+    input_file
+
+
+  main:  // update as needed
+    demoFastqc(input_file)
+    if (params.cleanup) { cleanupWorkdir(demoFastqc.out, true) }
+
+  emit:  // update as needed
+    output_file = demoFastqc.out.output_file
+}

demo-fastqc-wf/local_modules/demo-copy-file.nf

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

demo-fastqc-wf/nextflow.config

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

demo-fastqc-wf/pkg.json

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+{
+    "name": "demo-fastqc-wf",
+    "version": "0.1.0",
+    "description": "FastQC workflow",
+    "main": "demo-fastqc-wf",
+    "scripts": {
+        "test": "wfpm test"
+    },
+    "deprecated": false,
+    "keywords": [
+        "bioinformatics",
+        "seq",
+        "qc metrics"
+    ],
+    "repository": {
+        "type": "git",
+        "url": "https://github.com/icgc-tcga-pancancer/awesome-wfpkgs2.git"
+    },
+    "dependencies": [
+        "github.com/icgc-argo/demo-wfpkgs/[email protected]",
+        "github.com/icgc-tcga-pancancer/awesome-wfpkgs1/[email protected]"
+    ],
+    "devDependencies": [],
+    "contributors": [
+        {
+            "name": "Junjun Zhang",
+            "email": "[email protected]"
+        }
+    ],
+    "license": "MIT",
+    "bugReport": "https://github.com/icgc-tcga-pancancer/awesome-wfpkgs2/issues",
+    "homepage": "https://github.com/icgc-tcga-pancancer/awesome-wfpkgs2#readme"
+}

demo-fastqc-wf/tests/checker.nf

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+#!/usr/bin/env nextflow
+
+/*
+ This is an auto-generated checker workflow to test the generated main template workflow, it's
+ meant to illustrate how testing works. Please update to suit your own needs.
+*/
+
+nextflow.enable.dsl = 2
+version = '0.1.0'  // package version
+
+// universal params
+params.publish_dir = ""
+params.container_version = ""
+
+// tool specific parmas go here, add / change as needed
+params.input_file = ""
+params.expected_output = ""
+
+include { DemoFastqcWf } from '../demo-fastqc-wf' params(['cleanup': false])
+// include section starts
+// include section ends
+
+Channel
+  .fromPath(params.input_file, checkIfExists: true)
+  .set { input_file }
+
+
+process file_smart_diff {
+  input:
+    path output_file
+    path expected_file
+
+  output:
+    stdout()
+
+  script:
+    """
+    # Note: this is only for demo purpose, please write your own 'diff' according to your own needs.
+    # remove date field before comparison eg, <div id="header_filename">Tue 19 Jan 2021<br/>test_rg_3.bam</div>
+    # sed -e 's#"header_filename">.*<br/>test_rg_3.bam#"header_filename"><br/>test_rg_3.bam</div>#'
+
+    diff <( cat ${output_file} | sed -e 's#"header_filename">.*<br/>#"header_filename"><br/>#' ) \
+         <( ([[ '${expected_file}' == *.gz ]] && gunzip -c ${expected_file} || cat ${expected_file}) | sed -e 's#"header_filename">.*<br/>#"header_filename"><br/>#' ) \
+    && ( echo "Test PASSED" && exit 0 ) || ( echo "Test FAILED, output file mismatch." && exit 1 )
+    """
+}
+
+
+workflow checker {
+  take:
+    input_file
+    expected_output
+
+  main:
+    DemoFastqcWf(
+      input_file
+    )
+
+    file_smart_diff(
+      DemoFastqcWf.out.output_file,
+      expected_output
+    )
+}
+
+
+workflow {
+  checker(
+    file(params.input_file),
+    file(params.expected_output)
+  )
+}

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

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+This folder contains tiny data files for testing.

demo-fastqc-wf/tests/nextflow.config

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+includeConfig '../nextflow.config'

demo-fastqc-wf/tests/test-job-1.json

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+{
+    "input_file": "input/test_rg_3.bam",
+    "expected_output": "expected/expected.test_rg_3_fastqc.out.gz",
+    "publish_dir": "outdir",
+    "cpus": 1,
+    "mem": 0.5
+}

demo-fastqc-wf/tests/wfpr_modules

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+../wfpr_modules

demo-fastqc-wf/wfpr_modules

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+../wfpr_modules

wfpr_modules/github.com/icgc-tcga-pancancer/awesome-wfpkgs1/demo-fastqc@0.1.0/.dockerignore

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+.gitignore
+.nextflow*
+tests
+work
+outdir

wfpr_modules/github.com/icgc-tcga-pancancer/awesome-wfpkgs1/demo-fastqc@0.1.0/.gitignore

@@ -0,0 +1,69 @@
+*.py[cod]
+
+# C extensions
+*.so
+
+# Packages
+*.egg
+*.egg-info
+dist
+build
+eggs
+.eggs
+parts
+bin
+var
+sdist
+develop-eggs
+.installed.cfg
+lib
+lib64
+venv*/
+pyvenv*/
+
+# Installer logs
+pip-log.txt
+
+# Unit test / coverage reports
+.coverage
+.tox
+.coverage.*
+nosetests.xml
+coverage.xml
+htmlcov
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+.idea
+*.iml
+*.komodoproject
+
+# Complexity
+output/*.html
+output/*/index.html
+
+# Sphinx
+docs/_build
+
+.DS_Store
+*~
+.*.sw[po]
+.build
+.ve
+.env
+.cache
+.pytest
+.bootstrap
+.appveyor.token
+*.bak
+*.log
+.vscode
+.python-version
+.nextflow*
+work
+outdir

wfpr_modules/github.com/icgc-tcga-pancancer/awesome-wfpkgs1/demo-fastqc@0.1.0/Dockerfile

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+FROM pegi3s/fastqc:0.11.9
+
+LABEL org.opencontainers.image.source https://github.com/icgc-tcga-pancancer/awesome-wfpkgs1
+
+ENV PATH="/tools:${PATH}"
+
+COPY *.py /tools/
+
+CMD ["/bin/bash"]