Merge branch 'dev' into chris-feat (ff14edcc) · Commits · Chaos / Cutandrun

.github/workflows/awsfulltest.yml

+0 −3

Original line number	Diff line number	Diff line
		@@ -15,9 +15,6 @@ jobs:
		steps:
		- name: Launch workflow via tower
		uses: nf-core/tower-action@v2
		# TODO nf-core: You can customise AWS full pipeline tests as required
		# Add full size test data (but still relatively small datasets for few samples)
		# on the `test_full.config` test runs with only one set of parameters

		with:
		workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}

.github/workflows/ci.yml

+37 −19

Original line number	Diff line number	Diff line
		@@ -49,9 +49,11 @@ jobs:
		wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz
		wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz

		- name: Run pipeline
		run: \|
		nextflow run ${GITHUB_WORKSPACE} -profile docker,test_local_zip
		- name: Run Pipeline
		uses: Wandalen/wretry.action@v1.0.11
		with:
		command: nextflow run ${GITHUB_WORKSPACE} -profile docker,test_local_zip
		attempt_limit: 2

		##############################
		### LARGE INTEGRATION TEST ###
		@@ -89,9 +91,11 @@ jobs:
		wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz
		wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz

		- name: Run pipeline with test data
		run: \|
		nextflow run ${GITHUB_WORKSPACE} -profile docker,test_full_small_local_zip
		- name: Run Pipeline
		uses: Wandalen/wretry.action@v1.0.11
		with:
		command: nextflow run ${GITHUB_WORKSPACE} -profile docker,test_full_small_local_zip
		attempt_limit: 2

		#####################################
		### EDGE VERSION INTEGRATION TEST ###
		@@ -127,9 +131,11 @@ jobs:
		wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz
		wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz

		- name: Run pipeline with test data
		run: \|
		nextflow run ${GITHUB_WORKSPACE} -profile docker,test_local_zip
		- name: Run Pipeline
		uses: Wandalen/wretry.action@v1.0.11
		with:
		command: nextflow run ${GITHUB_WORKSPACE} -profile docker,test_local_zip
		attempt_limit: 2

		##############################
		### UNIT TESTS ###
		@@ -169,39 +175,47 @@ jobs:
		- test_bam_scale_rpkm
		- test_bam_scale_bpm
		- test_bam_scale_cpm_iggscale
		- test_peak_callers
		- test_peak_callers_seacr
		- test_peak_callers_macs2
		- test_peak_callers_invalid
		- test_peak_callers_seacr_macs2
		- test_peak_callers_macs2_seacr
		- test_peak_callers_seacr_macs2_noigg
		- test_conseneus_peaks_group
		- test_conseneus_peaks_all
		- test_conseneus_peaks_invalid
		- verify_output_reporting
		- verify_output_reporting_skip_reporting
		- verify_output_reporting_skip_igv
		- verify_output_reporting_skip_heatmaps
		- verify_output_reporting_skip_multiqc
		steps:
		- uses: actions/checkout@v2
		- name: Checkout Code
		uses: actions/checkout@v2

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

		- uses: actions/cache@v2
		- name: Setup Pip Cache
		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
		- name: Restore Keys
		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 }}
		@@ -209,8 +223,12 @@ jobs:
		run: \|
		wget -qO- get.nextflow.io \| bash
		sudo mv nextflow /usr/local/bin/

		- name: Run pytest-workflow
		run: pytest --tag ${{ matrix.tags }} --kwdof
		uses: Wandalen/wretry.action@v1.0.11
		with:
		command: pytest --tag ${{ matrix.tags }} --kwdof
		attempt_limit: 3

		- name: Upload logs on failure
		if: failure()

modules.json

+8 −8

Original line number	Diff line number	Diff line
		@@ -28,7 +28,7 @@
		"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
		},
		"custom/getchromsizes": {
		"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
		"git_sha": "950700bcdc0e9a2b6883d40d2c51c6fc435cd714"
		},
		"deeptools/computematrix": {
		"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
		@@ -49,22 +49,22 @@
		"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
		},
		"samtools/flagstat": {
		"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
		"git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"
		},
		"samtools/idxstats": {
		"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
		"git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"
		},
		"samtools/index": {
		"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
		"git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"
		},
		"samtools/sort": {
		"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
		"git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"
		},
		"samtools/stats": {
		"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
		"git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"
		},
		"samtools/view": {
		"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
		"git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"
		},
		"seacr/callpeak": {
		"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
		@@ -76,7 +76,7 @@
		"git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
		},
		"untar": {
		"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
		"git_sha": "7ec09d0ef4df89617baacc9b2dafcddb7cd4b05a"
		}
		}
		}

modules/nf-core/modules/custom/getchromsizes/main.nf

+3 −3

Original line number	Diff line number	Diff line
		@@ -2,10 +2,10 @@ process CUSTOM_GETCHROMSIZES {
		tag "$fasta"
		label 'process_low'

		conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
		conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
		container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
		'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
		'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
		'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
		'quay.io/biocontainers/samtools:1.15--h1170115_1' }"

		input:
		path fasta

modules/nf-core/modules/samtools/flagstat/main.nf

+3 −3

Original line number	Diff line number	Diff line
		@@ -2,10 +2,10 @@ process SAMTOOLS_FLAGSTAT {
		tag "$meta.id"
		label 'process_low'

		conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
		conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
		container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
		'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
		'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
		'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
		'quay.io/biocontainers/samtools:1.15--h1170115_1' }"

		input:
		tuple val(meta), path(bam), path(bai)

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