Merge pull request #32 from luslab/dev (4d44e59f) · Commits · Chaos / Cutandrun

.github/workflows/ci.yml

+6 −7

Original line number	Diff line number	Diff line
		@@ -32,11 +32,10 @@ jobs:

		- name: Run pipeline with test data
		run: \|
		nextflow run ${GITHUB_WORKSPACE} -profile test_all_exp_one_igg_small,docker --skip_deseq2
		# ---------------------------------------------------------------------
		test_one_exp_all_igg_small:
		name: Run pipeline test with 2 groups of 2 replicate and one replicate of igg
		# Only run on push if this is the luslab dev branch (merged PRs)
		nextflow run ${GITHUB_WORKSPACE} -profile docker,test
		test_full_small:
		name: Run extended pipeline test
		# Only run on push if this is the nf-core dev branch (merged PRs)
		if: ${{ github.event_name != 'push' \|\| (github.event_name == 'push' && github.repository == 'nf-core/cutandrun') }}
		runs-on: ubuntu-latest
		env:
		@@ -45,7 +44,7 @@ jobs:
		strategy:
		matrix:
		# Nextflow versions: check pipeline minimum and current latest
		nxf_ver: ["21.04.0", ""]
		nxf_ver: ['21.04.0', '']
		steps:
		- name: Check out pipeline code
		uses: actions/checkout@v2
		@@ -57,4 +56,4 @@ jobs:

		- name: Run pipeline with test data
		run: \|
		nextflow run ${GITHUB_WORKSPACE} -profile test_one_exp_all_igg_small,docker --skip_deseq2
		nextflow run ${GITHUB_WORKSPACE} -profile docker,test_full_small
		No newline at end of file

+6 −4

Original line number	Diff line number	Diff line
		@@ -14,7 +14,7 @@ jobs:
		- uses: actions/checkout@v2
		- uses: actions/setup-node@v1
		with:
		node-version: "10"
		node-version: '10'
		- name: Install markdownlint
		run: npm install -g markdownlint-cli
		- name: Run Markdownlint
		@@ -67,7 +67,7 @@ jobs:
		- uses: actions/checkout@v1
		- uses: actions/setup-node@v1
		with:
		node-version: "10"
		node-version: '10'
		- name: Install yaml-lint
		run: npm install -g yaml-lint
		- name: Run yaml-lint
		@@ -101,6 +101,7 @@ jobs:
		nf-core:
		runs-on: ubuntu-latest
		steps:

		- name: Check out pipeline code
		uses: actions/checkout@v2

		@@ -113,8 +114,8 @@ jobs:

		- uses: actions/setup-python@v1
		with:
		python-version: "3.6"
		architecture: "x64"
		python-version: '3.6'
		architecture: 'x64'

		- name: Install dependencies
		run: \|
		@@ -141,3 +142,4 @@ jobs:
		lint_log.txt
		lint_results.md
		PR_number.txt

+0 −0

File moved.

+7 −24

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		@@ -2,34 +2,17 @@ report_comment: >
		This report has been generated by the <a href="https://github.com/nf-core/cutandrun" target="_blank">nf-core/cutandrun</a>
		analysis pipeline. For information about how to interpret these results, please see the
		<a href="https://github.com/nf-core/cutandrun" target="_blank">documentation</a>.
		report_section_order:
		software_versions:
		order: -1000
		nf-core-cutandrun-summary:
		order: -1001

		export_plots: true

		report_header_info:
		- Contact E-mail: "chris.cheshire@crick.ac.uk"
		- Application Type: "CUT&RUN"
		- Project Type: "Application"
		# - Sequencing Platform: "HiSeq 2500 High Output V4"
		# - Sequencing Setup: "2x50"

		# show_analysis_paths: True
		# show_analysis_time: True

		# show_hide_buttons:
		# - Read Group 1
		# - Read Group 2
		# - Controls
		# - Conditions
		# show_hide_mode:
		# - show
		# - show
		# - show
		# - show
		# show_hide_patterns:
		# - _r1
		# - _r2
		# - igg_
		# - ["h3k4me3_", "h3k27me3_"]

		# export_plots: true

		# Run only these modules
		run_modules:

+4 −3

Original line number	Diff line number	Diff line
		@@ -15,10 +15,11 @@ for version_file in version_files:
		results[software] = version

		# Dump to YAML
		print ('''
		print(
		"""
		id: 'software_versions'
		section_name: 'nf-core/rnaseq Software Versions'
		section_href: 'https://github.com/nf-core/rnaseq'
		section_name: 'nf-core/cutandrun Software Versions'
		section_href: 'https://github.com/nf-core/cutandrun'
		plot_type: 'html'
		description: 'are collected at run time from the software output.'
		data: \|