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CNVKit 0.9.10 update #18001

CNVKit 0.9.10 update

CNVKit 0.9.10 update #18001

Workflow file for this run

name: Pytest-workflow
on:
push:
branches: [master]
pull_request:
branches: [master]
merge_group:
types: [checks_requested]
branches: [master]
# Cancel if a newer run is started
concurrency:
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
cancel-in-progress: true
jobs:
changes:
name: Check for changes
runs-on: ubuntu-latest
outputs:
# Expose matched filters as job 'modules' output variable
modules: ${{ steps.filter.outputs.changes }}
steps:
- uses: actions/checkout@v3
- uses: dorny/paths-filter@v2
id: filter
with:
filters: "tests/config/pytest_modules.yml"
test:
runs-on: ubuntu-20.04
name: ${{ matrix.tags }} ${{ matrix.profile }}
needs: changes
if: needs.changes.outputs.modules != '[]'
strategy:
fail-fast: false
matrix:
tags: ["${{ fromJson(needs.changes.outputs.modules) }}"]
profile: ["docker", "singularity", "conda"]
exclude:
- profile: "conda"
tags: annotsv
- profile: "conda"
tags: cellpose
- profile: "conda"
tags: mcquant
- profile: "conda"
tags: bases2fastq
- profile: "conda"
tags: backsub
- profile: "conda"
tags: basicpy
- profile: "conda"
tags: bcl2fastq
- profile: "conda"
tags: bclconvert
- profile: "conda"
tags: cellranger/count
- profile: "conda"
tags: cellranger/mkfastq
- profile: "conda"
tags: cellranger/mkgtf
- profile: "conda"
tags: cellranger/mkref
- profile: "conda"
tags: cellranger/mkvdjref
- profile: "conda"
tags: cellranger/multi
- profile: "conda"
tags: cellranger/vdj
- profile: "conda"
tags: coreograph
- profile: "conda"
tags: deepcell/mesmer
- profile: "conda"
tags: deepvariant
- profile: "conda"
tags: ensemblvep/vep
- profile: "conda"
tags: fastk/fastk
- profile: "conda"
tags: fastk/histex
- profile: "conda"
tags: fastk/merge
- profile: "conda"
tags: fcs/fcsadaptor
- profile: "conda"
tags: fcs/fcsgx
- profile: "conda"
tags: gatk4/baserecalibratorspark
- profile: "conda"
tags: gatk4/cnnscorevariants
- profile: "conda"
tags: gatk4/determinegermlinecontigploidy
- profile: "conda"
tags: gatk4/germlinecnvcaller
- profile: "conda"
tags: gatk4/markduplicatesspark
- profile: "conda"
tags: gatk4/postprocessgermlinecnvcalls
- profile: "conda"
tags: genescopefk
- profile: "conda"
tags: ilastik/multicut
- profile: "conda"
tags: ilastik/pixelclassification
- profile: "conda"
tags: imputeme/vcftoprs
- profile: "conda"
tags: merquryfk/katcomp
- profile: "conda"
tags: merquryfk/katgc
- profile: "conda"
tags: merquryfk/merquryfk
- profile: "conda"
tags: merquryfk/ploidyplot
- profile: "conda"
tags: mitohifi/findmitoreference
- profile: "conda"
tags: scimap/mcmicro
- profile: "conda"
tags: sentieon/applyvarcal
- profile: "conda"
tags: sentieon/bwaindex
- profile: "conda"
tags: sentieon/bwamem
- profile: "conda"
tags: sentieon/dedup
- profile: "conda"
tags: sentieon/gvcftyper
- profile: "conda"
tags: sentieon/haplotyper
- profile: "conda"
tags: sentieon/varcal
- profile: "conda"
tags: spaceranger/count
- profile: "conda"
tags: spaceranger/mkgtf
- profile: "conda"
tags: spaceranger/mkref
- profile: "conda"
tags: universc
- profile: "singularity"
tags: universc
- profile: "singularity"
tags: gatk4/determinegermlinecontigploidy
- profile: "conda"
tags: subworkflows/bcl_demultiplex
- profile: "conda"
tags: subworkflows/vcf_annotate_ensemblvep_snpeff
- profile: "conda"
tags: subworkflows/vcf_annotate_ensemblvep
- profile: "conda"
tags: subworkflows/fasta_clean_fcs
- profile: "conda"
tags: islandpath
env:
NXF_ANSI_LOG: false
SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
steps:
- uses: actions/checkout@v3
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- 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 cryptography
- uses: actions/cache@v3
with:
path: /usr/local/bin/nextflow
key: ${{ runner.os }}
restore-keys: |
${{ runner.os }}-nextflow-
- name: Install Nextflow
env:
CAPSULE_LOG: none
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Set up Singularity
if: matrix.profile == 'singularity'
uses: eWaterCycle/setup-singularity@v5
with:
singularity-version: 3.7.1
- name: Set up miniconda
if: matrix.profile == 'conda'
uses: conda-incubator/setup-miniconda@v2
with:
auto-update-conda: true
channels: conda-forge,bioconda,defaults
python-version: ${{ matrix.python-version }}
- name: Conda setup
if: matrix.profile == 'conda'
run: |
conda clean -a
conda install -n base conda-libmamba-solver
conda config --set solver libmamba
# Set up secrets
- name: Set up nextflow secrets
if: env.SENTIEON_LICENSE_BASE64 != null
run: |
nextflow secrets set SENTIEON_LICENSE_BASE64 ${{ secrets.SENTIEON_LICENSE_BASE64 }}
nextflow secrets set SENTIEON_AUTH_MECH_BASE64 ${{ secrets.SENTIEON_AUTH_MECH_BASE64 }}
SENTIEON_ENCRYPTION_KEY=$(echo -n "${{ secrets.ENCRYPTION_KEY_BASE64 }}" | base64 -d)
SENTIEON_LICENSE_MESSAGE=$(echo -n "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d)
SENTIEON_AUTH_DATA=$(python tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0)
nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64
# Test the module
- name: Run pytest-workflow
# only use one thread for pytest-workflow to avoid race condition on conda cache.
run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes
- name: Output log on failure
if: failure()
run: |
sudo apt-get update > /dev/null
sudo apt-get install bat > /dev/null
batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err}
- name: Setting global variables
uses: actions/github-script@v6
id: parsed
with:
script: |
return '${{ matrix.tags }}'.toLowerCase().replaceAll(/\//g, '-').trim('-').trim('"')
result-encoding: string
- name: Upload logs on failure
if: failure()
uses: actions/upload-artifact@v2
with:
name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }}
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