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Updates #567

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Updates

Updates #567

Workflow file for this run

.github/workflows/ci.yml at 55dac76
name: nf-core CI
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
on:
push:
branches:
- dev
pull_request:
release:
types: [published]
# Cancel if a newer run is started
concurrency:
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
cancel-in-progress: true
jobs:
##############################
### SMALL INTEGRATION TEST ###
##############################
test:
name: Run standard 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:
NXF_VER: ${{ matrix.NXF_VER }}
NXF_ANSI_LOG: false
CAPSULE_LOG: none
strategy:
matrix:
NXF_VER: ["23.04.0", ""]
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
- name: Install Nextflow
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
# Work around for the unexpected end of file error that github actions seems to get when downloading compressed
# files during pipeline execution
- name: Download data
run: |
wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz
wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-bowtie2.tar.gz
wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz
wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.bed.gz
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
uses: Wandalen/wretry.action@v1.0.11
with:
command: nextflow run ${GITHUB_WORKSPACE} -profile docker,test_local_zip
attempt_limit: 2
##############################
### 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)
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/cutandrun') }}
runs-on: ubuntu-latest
env:
NXF_VER: ${{ matrix.nxf_ver }}
NXF_ANSI_LOG: false
CAPSULE_LOG: none
strategy:
matrix:
# Nextflow versions: check pipeline minimum and current latest
NXF_VER: ["23.04.0", ""]
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
- name: Install Nextflow
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
# Work around for the unexpected end of file error that github actions seems to get when downloading compressed
# files during pipeline execution
- name: Download data
run: |
wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz
wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-bowtie2.tar.gz
wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz
wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.bed.gz
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
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 ###
#####################################
test_edge:
name: Run standard pipeline test (edge version)
# 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:
NXF_ANSI_LOG: false
CAPSULE_LOG: none
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "latest-everything"
# Work around for the unexpected end of file error that github actions seems to get when downloading compressed
# files during pipeline execution
- name: Download data
run: |
wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz
wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-bowtie2.tar.gz
wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz
wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.bed.gz
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
uses: Wandalen/wretry.action@v1.0.11
with:
command: nextflow run ${GITHUB_WORKSPACE} -profile docker,test_local_zip
attempt_limit: 2
##############################
### UNIT TESTS ###
##############################
unit_tests:
name: ${{ matrix.NXF_VER }} ${{ matrix.tags }}
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/cutandrun') }}
runs-on: ubuntu-20.04
env:
NXF_VER: ${{ matrix.NXF_VER }}
NXF_ANSI_LOG: false
CAPSULE_LOG: none
strategy:
fail-fast: false
matrix:
NXF_VER: ["23.04.0", ""]
tags:
- test_genome_options
- test_genome_options_spikein
- test_samplesheet
- test_samplesheet_2
- test_samplesheet_3
- test_filtering_noqfilter
- test_filtering_withqfilter
- test_bam_scale_none
- test_bam_scale_spikein
- test_bam_scale_cpm
- test_bam_scale_rpkm
- test_bam_scale_bpm
- test_bam_scale_cpm_iggscale
- 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_peak_callers_ctrl_tests
- test_consensus_peaks_group
- test_consensus_peaks_all
- test_consensus_peaks_invalid
- verify_output_only_input
- verify_output_save_merged
- verify_output_save_trimmed
- verify_output_skip_trimming
- verify_output_skip_fastqc
- verify_output_save_ref
- verify_output_align_only_align
- verify_output_align_only_align_end_to_end
- verify_output_align_only_align_local
- verify_output_align_intermed
- verify_output_align_save_spikein_align
- verify_output_align_save_unaligned
- verify_output_align_duplicates_mark
- verify_output_align_duplicates_remove
- verify_output_align_duplicates_remove_target
- verify_output_align_linear_duplicates_remove
- verify_output_align_linear_duplicates_remove_target
- verify_output_only_filtering
- verify_output_only_filtering_with_mitochondrial_reads
- verify_output_only_filtering_without_mitochondrial_reads
- verify_output_only_filtering_without_mitochondrial_reads_mito_name_null
- verify_output_peak_calling_only_peak_calling
- verify_output_reporting_skip_preseq_false
- verify_output_reporting_skip_preseq_true
- verify_output_reporting_skip_dtqc_false
- verify_output_reporting_skip_dtqc_true
- verify_output_reporting_skip_heatmaps_false
- verify_output_reporting_skip_heatmaps_true
- verify_output_reporting_skip_heatmaps_grouped
- verify_output_reporting_skip_igv_false
- verify_output_reporting_skip_igv_true
- verify_output_reporting_skip_multiqc_false
- verify_output_reporting_skip_multiqc_true
- verify_output_reporting_skip_peak_qc_false
- verify_output_reporting_skip_peak_qc_true
- verify_output_reporting_skip_reporting
steps:
- name: Checkout Code
uses: actions/checkout@v3
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Setup Pip Cache
uses: actions/cache@v3
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
restore-keys: |
${{ runner.os }}-pip-
- name: Install Python dependencies
run: python -m pip install --upgrade pip pytest-workflow
- name: Restore Keys
uses: actions/cache@v3
with:
path: /usr/local/bin/nextflow
key: ${{ runner.os }}-nextflow-${{ matrix.nxf_version }}
restore-keys: |
${{ runner.os }}-nextflow-
- name: Install Nextflow
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Run pytest-workflow
uses: Wandalen/wretry.action@v1.0.11
with:
command: TMPDIR=~ PROFILE=docker pytest --tag ${{ matrix.tags }} --symlink --kwdof --color=yes
attempt_limit: 3
- name: Output log on failure
if: failure()
run: |
sudo apt install bat > /dev/null
batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err}
- name: Upload logs on failure
if: failure()
uses: actions/upload-artifact@v2
with:
name: logs-unit-tests
path: |
/home/runner/pytest_workflow_*/*/.nextflow.log
/home/runner/pytest_workflow_*/*/log.out
/home/runner/pytest_workflow_*/*/log.err
/home/runner/pytest_workflow_*/*/work
!/home/runner/pytest_workflow_*/*/work/conda
!/home/runner/pytest_workflow_*/*/work/singularity