Merge pull request #33 from luslab/dev (68ad0534) · Commits · Chaos / Cutandrun

.github/workflows/ci.yml

+71 −3

Original line number	Diff line number	Diff line
		@@ -9,6 +9,9 @@ on:
		types: [published]

		jobs:
		##############################
		### SMALL INTEGRATION TEST ###
		##############################
		test:
		name: Run standard pipeline test
		# Only run on push if this is the nf-core dev branch (merged PRs)
		@@ -33,6 +36,9 @@ jobs:
		- name: Run pipeline with test data
		run: \|
		nextflow run ${GITHUB_WORKSPACE} -profile docker,test
		##############################
		### LARGE INTEGRATION TEST ###
		##############################
		test_full_small:
		name: Run extended pipeline test
		# Only run on push if this is the nf-core dev branch (merged PRs)
		@@ -43,8 +49,8 @@ jobs:
		NXF_ANSI_LOG: false
		strategy:
		matrix:
		# Nextflow versions: check pipeline minimum and current latest
		nxf_ver: ['21.04.0', '']
		# We only run this on the specified nextflow version for the pipeline
		nxf_ver: ['21.04.0']
		steps:
		- name: Check out pipeline code
		uses: actions/checkout@v2
		@@ -57,3 +63,65 @@ jobs:
		- name: Run pipeline with test data
		run: \|
		nextflow run ${GITHUB_WORKSPACE} -profile docker,test_full_small
		##############################
		### UNIT TESTS ###
		##############################
		unit_tests:
		name: ${{ matrix.nxf_version }} ${{ matrix.tags }}
		if: ${{ github.event_name != 'push' \|\| (github.event_name == 'push' && github.repository == 'nf-core/cutandrun') }}
		runs-on: ubuntu-20.04
		env:
		NXF_ANSI_LOG: false
		strategy:
		fail-fast: false
		matrix:
		nxf_version: ["21.04.0"]
		tags: ["samplesheet", "verify_output_input", "verify_output_align_short", "verify_output_align_long", "verify_output_peak_calling", "verify_output_reporting", "verify_output_save", "verify_output_skip"]
		steps:
		- uses: actions/checkout@v2

		- name: Set up Python
		uses: actions/setup-python@v2
		with:
		python-version: "3.x"

		- uses: actions/cache@v2
		with:
		path: ~/.cache/pip
		key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
		restore-keys: \|
		${{ runner.os }}-pip-
		- name: Set up Python
		uses: actions/setup-python@v2
		with:
		python-version: "3.x"

		- name: Install Python dependencies
		run: python -m pip install --upgrade pip pytest-workflow

		- uses: actions/cache@v2
		with:
		path: /usr/local/bin/nextflow
		key: ${{ runner.os }}-nextflow-${{ matrix.nxf_version }}
		restore-keys: \|
		${{ runner.os }}-nextflow-
		- name: Install Nextflow
		env:
		NXF_VER: ${{ matrix.nxf_version }}
		CAPSULE_LOG: none
		run: \|
		wget -qO- get.nextflow.io \| bash
		sudo mv nextflow /usr/local/bin/
		- name: Run pytest-workflow
		run: pytest --tag ${{ matrix.tags }} --kwdof

		- name: Upload logs on failure
		if: failure()
		uses: actions/upload-artifact@v2
		with:
		name: logs-${{ matrix.tags }}-${{ matrix.profile }}-${{ matrix.nxf_version }}
		path: \|
		/tmp/pytest_workflow_//.nextflow.log
		/tmp/pytest_workflow_//log.out
		/tmp/pytest_workflow_//log.err
		/tmp/pytest_workflow_//work

assets/multiqc_config.yaml

+0 −6

Original line number	Diff line number	Diff line
		@@ -47,12 +47,6 @@ module_order:
		- picard
		- custom_content

		report_section_order:
		software_versions:
		order: -1000
		nf-core-cutandrun-summary:
		order: -1001

		# Don't show % Dups in the General Stats table (we have this from Picard)
		table_columns_visible:
		FastQC:

assets/samplesheet.csv

+7 −3

Original line number	Diff line number	Diff line
		sample,fastq_1,fastq_2
		SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz
		SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,
		group,replicate,control_group,fastq_1,fastq_2
		h3k27me3,1,1,READ1_FASTQ,READ2_FASTQC
		h3k27me3,2,1,READ1_FASTQ,READ2_FASTQC
		h3k4me3,1,2,READ1_FASTQ,READ2_FASTQC
		h3k4me3,2,2,READ1_FASTQ,READ2_FASTQC
		igg,1,1,READ1_FASTQ,READ2_FASTQC
		igg,2,2,READ1_FASTQ,READ2_FASTQC

assets/schema_input.json

+19 −14

Original line number	Diff line number	Diff line
		@@ -7,10 +7,20 @@
		"items": {
		"type": "object",
		"properties": {
		"sample": {
		"group": {
		"type": "string",
		"pattern": "^\\S+$",
		"errorMessage": "Sample name must be provided and cannot contain spaces"
		"errorMessage": "Sample group must be provided and cannot contain spaces"
		},
		"replicate": {
		"type": "integer",
		"pattern": "^[0-9]*$",
		"errorMessage": "Biological Replicate number within the group - technical replicates must have the same replicate number"
		},
		"control_group": {
		"type": "integer",
		"pattern": "^[0-9]*$",
		"errorMessage": "Group ID that matches to the IgG control group (if provided) - otherwise set to 0"
		},
		"fastq_1": {
		"type": "string",
		@@ -18,22 +28,17 @@
		"errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
		},
		"fastq_2": {
		"errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
		"anyOf": [
		{
		"type": "string",
		"pattern": "^\\S+\\.f(ast)?q\\.gz$"
		},
		{
		"type": "string",
		"maxLength": 0
		}
		]
		"pattern": "^\\S+\\.f(ast)?q\\.gz$",
		"errorMessage": "FastQ file for reads 2 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
		}
		},
		"required": [
		"sample",
		"fastq_1"
		"replicate",
		"control_group",
		"fastq_1",
		"fastq_2"
		]
		}
		}

docs/output.md

+0 −2

Original line number	Diff line number	Diff line
		@@ -257,8 +257,6 @@ Additional QC and analysis pertaining particularly to CUT&Run and CUT&Tag data a

		> NB: The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.

		### MultiQC

		<details markdown="1">
		<summary>Output files</summary>

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