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Hicexplorer hicpca (#2933) #2399

Hicexplorer hicpca (#2933)

Hicexplorer hicpca (#2933) #2399

Workflow file for this run

name: nf-test
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/nftest_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: bases2fastq
- 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: 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/cnnscorevariants
- profile: "conda"
tags: gatk4/determinegermlinecontigploidy
- 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: sentieon/bwaindex
- profile: "conda"
tags: sentieon/bwamem
- profile: "conda"
tags: universc
- profile: "singularity"
tags: universc
- profile: "conda"
tags: subworkflows/vcf_annotate_ensemblvep
env:
NXF_ANSI_LOG: false
SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
steps:
- uses: actions/checkout@v3
- 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: Cache nf-test installation
id: cache-software
uses: actions/cache@v3
with:
path: |
/usr/local/bin/nf-test
/home/runner/.nf-test/nf-test.jar
key: ${{ runner.os }}-nftest
- name: Install nf-test
if: steps.cache-software.outputs.cache-hit != 'true'
run: |
wget -qO- https://code.askimed.com/install/nf-test | bash
sudo mv nf-test /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 $SENTIEON_AUTH_DATA_BASE64
# Test the module
- name: Run nf-test
run: |
nf-test test \
--profile=${{ matrix.profile }} \
--tag ${{ matrix.tags }} \
--tap=test.tap
- uses: pcolby/tap-summary@v1
with:
path: >-
test.tap