Merge pull request #7 from ICGC-TCGA-PanCancer/[email protected]

[release]

fastqc-wf3/.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

fastqc-wf3/fastqc-wf3.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.output_pattern = "*.html"  // fastqc output html report
+params.another = ""
+
+
+// include section starts
+include { FastqcWf2 } from "./wfpr_modules/github.com/icgc-tcga-pancancer/awesome-wfpkgs2/[email protected]/fastqc-wf2"
+include { cleanupWorkdir } from "./wfpr_modules/github.com/icgc-argo/demo-wfpkgs/[email protected]/main"
+
+// include section ends
+
+
+workflow FastqcWf3 {
+  take:  // update as needed
+    // input section starts
+    input_file
+    // input section ends
+
+  main:  // update as needed
+    // main section starts
+    FastqcWf2(input_file)
+
+    cleanupWorkdir(FastqcWf2.out, true)
+    // main section ends
+
+  emit:  // update as needed
+    // output section starts
+    output_file = FastqcWf2.out.output_file
+    // output section ends
+}

fastqc-wf3/nextflow.config

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

fastqc-wf3/pkg.json

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+{
+    "name": "fastqc-wf3",
+    "version": "0.1.0",
+    "description": "FastQC workflow",
+    "main": "fastqc-wf3",
+    "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-wfpkgs2/[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"
+}

fastqc-wf3/tests/checker.nf

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+#!/usr/bin/env nextflow
+
+/*
+ This is an auto-generated checker workflow, please update as needed
+*/
+
+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 { FastqcWf3 } from '../fastqc-wf3'
+// include statements go here for dev dependencies
+
+Channel
+  .fromPath(params.input_file, checkIfExists: true)
+  .set { input_file }
+
+
+process file_diff {
+  input:
+    path output_file
+    path expected_gzip
+
+  output:
+    stdout()
+
+  script:
+    """
+    # 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/>test_rg_3.bam#"header_filename"><br/>test_rg_3.bam</div>#' ) \
+         <( gunzip -c ${expected_gzip} | sed -e 's#"header_filename">.*<br/>test_rg_3.bam#"header_filename"><br/>test_rg_3.bam</div>#' ) \
+    && ( echo "Test PASSED" && exit 0 ) || ( echo "Test FAILED, output file mismatch." && exit 1 )
+    """
+}
+
+
+workflow checker {
+  take:
+    input_file
+    expected_output
+
+  main:
+    FastqcWf3(
+      input_file
+    )
+
+    file_diff(
+      FastqcWf3.out.output_file,
+      expected_output
+    )
+}
+
+
+workflow {
+  checker(
+    file(params.input_file),
+    file(params.expected_output)
+  )
+}

fastqc-wf3/tests/expected/expected.input_file_name.txt

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+The input file name is README.md

fastqc-wf3/tests/input/README.md

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+This folder contains tiny data files for testing.

fastqc-wf3/tests/nextflow.config

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+includeConfig '../nextflow.config'

fastqc-wf3/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
+}

fastqc-wf3/tests/wfpr_modules

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+../wfpr_modules

fastqc-wf3/wfpr_modules

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+../wfpr_modules

wfpr_modules/github.com/icgc-tcga-pancancer/awesome-wfpkgs1/fastqc@0.2.0/wfpr_modules

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+../../../../../wfpr_modules

wfpr_modules/github.com/icgc-tcga-pancancer/awesome-wfpkgs2/fastqc-wf2@0.1.2/.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-wfpkgs2/fastqc-wf2@0.1.2/fastqc-wf2.nf

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+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+version = '0.1.2'
+
+// 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.output_pattern = "*.html"  // fastqc output html report
+
+include { fastqc } from "./wfpr_modules/github.com/icgc-tcga-pancancer/awesome-wfpkgs1/[email protected]/fastqc"
+include { FastqcWf } from "./wfpr_modules/github.com/icgc-tcga-pancancer/awesome-wfpkgs2/[email protected]/fastqc-wf"
+include { cleanupWorkdir } from "./wfpr_modules/github.com/icgc-argo/demo-wfpkgs/[email protected]/main"
+
+
+
+workflow FastqcWf2 {
+  take:  // input, make update as needed
+    input_file
+
+  main:
+    FastqcWf(input_file)
+
+    cleanupWorkdir(FastqcWf.out, true)
+
+  emit:
+    output_file = FastqcWf.out.output_file
+}

wfpr_modules/github.com/icgc-tcga-pancancer/awesome-wfpkgs2/fastqc-wf2@0.1.2/nextflow.config

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

wfpr_modules/github.com/icgc-tcga-pancancer/awesome-wfpkgs2/fastqc-wf2@0.1.2/pkg.json

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+{
+    "name": "fastqc-wf2",
+    "version": "0.1.2",
+    "description": "FastQC workflow",
+    "main": "fastqc-wf2",
+    "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-tcga-pancancer/awesome-wfpkgs2/[email protected]",
+        "github.com/icgc-argo/demo-wfpkgs/[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"
+}

wfpr_modules/github.com/icgc-tcga-pancancer/awesome-wfpkgs2/fastqc-wf2@0.1.2/wfpr_modules

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+../../../../../wfpr_modules