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simplify default tests + add conda/singularity #736

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merged 13 commits into from
Sep 8, 2022
Merged

simplify default tests + add conda/singularity #736

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59b60bc
simplify default tests + add conda/singularity
maxulysse Sep 7, 2022
34c7eff
update CHANGELOG
maxulysse Sep 7, 2022
d0375ce
fix conda test
maxulysse Sep 7, 2022
b162417
fix scope for fixOwnership + sort items
maxulysse Sep 7, 2022
dd3b5cb
fix indent + sort
maxulysse Sep 7, 2022
05333ee
add timeout for conda
maxulysse Sep 7, 2022
ff38247
better comments
maxulysse Sep 7, 2022
5b307f9
enhance installation
maxulysse Sep 7, 2022
e3e6cdc
exclude latest version for conda
maxulysse Sep 7, 2022
2d0e91f
Merge remote-tracking branch 'upstream/dev' into dev_complete_CI
maxulysse Sep 8, 2022
dd5faeb
remove docker.fixOwnership
maxulysse Sep 8, 2022
3856599
prettier again
maxulysse Sep 8, 2022
349e1d6
fix checksum
maxulysse Sep 8, 2022
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50 changes: 43 additions & 7 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -26,28 +26,63 @@ jobs:
- "latest-everything"
test:
- "default"
profile: ["docker"]
profile: ["docker", "singularity", "conda"]
exclude:
- NXF_VER: "latest-everything"
profile: "conda"
steps:
- name: Check out pipeline code
uses: actions/checkout@v2

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

- uses: actions/cache@v2
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

- uses: actions/cache@v2
with:
path: /usr/local/bin/nextflow
key: ${{ runner.os }}
restore-keys: |
${{ runner.os }}-nextflow-

- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"

- name: Set up Python
uses: actions/setup-python@v2
- name: Set up Singularity
if: matrix.profile == 'singularity'
uses: eWaterCycle/setup-singularity@v5
with:
python-version: "3.x"
singularity-version: 3.7.1
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- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow
- 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 clean
if: matrix.profile == 'conda'
run: conda clean -a

- name: Run pipeline with tests settings
uses: Wandalen/wretry.action@v1.0.11
with:
command: PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.test }} --symlink --kwdof --git-aware --color=yes
command: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.test }} --symlink --kwdof --git-aware --color=yes
attempt_limit: 3

- name: Output log on failure
Expand Down Expand Up @@ -91,6 +126,7 @@ jobs:
- "freebayes"
- "gatk4_spark"
- "haplotypecaller"
- "intervals"
- "manta"
- "markduplicates"
- "mpileup"
Expand Down
1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -27,6 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#731](https://github.com/nf-core/sarek/pull/731) - Run the somatic test as default on `-profile test_full`, the germline can be tested with `-profile test_full_somatic`
- [#733](https://github.com/nf-core/sarek/pull/733) - Add description for params.cf_chrom_len
- [#734](https://github.com/nf-core/sarek/pull/734) - nf-core modules update -a
- [#736](https://github.com/nf-core/sarek/pull/736) - More extensive CI for default test

### Fixed

Expand Down
43 changes: 23 additions & 20 deletions conf/test.config
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Original file line number Diff line number Diff line change
Expand Up @@ -253,29 +253,32 @@ process {
}
}

// ENABLE CI containers for testing
// Enable container engines/virtualisation envs for CI testing
// only works when specified with the profile ENV
// otherwise tests can be done with the regular provided profiles
if (System.getenv('PROFILE')) {
if ("$PROFILE" == "conda") {
params.enable_conda = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
conda.createTimeout = "120 min"
params.enable_conda = true
charliecloud.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
singularity.enabled = false
} else if ("$PROFILE" == "docker") {
docker.enabled = true
docker.userEmulation = { params.use_gatk_spark ? false : true }.call()
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
fixOwnership = true
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Decided to remove that instead of fixing it, as it was causing the strelkabp test to fail...

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only now?

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yes because it wasn't working, it should have been:
docker.fixOwnership = true
But when I do that, then the test fails.
So as it wasn't really working to start with, decide to remove it instead of fixing it

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ok

docker.enabled = true
docker.userEmulation = { params.use_gatk_spark ? false : true }.call()
charliecloud.enabled = false
podman.enabled = false
shifter.enabled = false
singularity.enabled = false
} else if ("$PROFILE" == "singularity") {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
params.singularity_pull_docker_container = false
singularity.autoMounts = true
singularity.enabled = true
charliecloud.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
}
}
31 changes: 15 additions & 16 deletions nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -143,63 +143,62 @@ profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
conda {
params.enable_conda = true
charliecloud.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
singularity.enabled = false
}
mamba {
params.enable_conda = true
conda.useMamba = true
params.enable_conda = true
charliecloud.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
singularity.enabled = false
}
docker {
docker.enabled = true
docker.userEmulation = { params.use_gatk_spark ? false : true }.call()
singularity.enabled = false
charliecloud.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
fixOwnership = true
singularity.enabled = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
singularity.enabled = true
charliecloud.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
podman {
podman.enabled = true
charliecloud.enabled = false
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
singularity.enabled = false
}
shifter {
shifter.enabled = true
charliecloud.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
singularity.enabled = false
}
charliecloud {
charliecloud.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
singularity.enabled = false
}
gitpod {
executor.name = 'local'
executor.cpus = 16
executor.memory = 60.GB
executor.name = 'local'
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
Expand Down
63 changes: 3 additions & 60 deletions tests/test_default.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@
- path: results/preprocessing/recalibrated/test/test.recal.cram.crai
# binary changes md5sums on reruns.
- path: results/reports/bcftools/strelka/test/test.strelka.variants.bcftools_stats.txt
md5sum: 28d99fd4fa63e24e6805f1d12c3b71d3
# conda changes md5sums for test.
- path: results/reports/fastqc/test-test_L1
- path: results/reports/markduplicates/test/test.md.metrics
contains: ["test 8547 767 84 523391 3882 0 0 0.385081", "1.0 767 767"]
Expand All @@ -49,9 +49,9 @@
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
md5sum: b1c2a861f64e20a94108a6de3b76c582
- path: results/reports/samtools/test/test.md.cram.stats
md5sum: 52411f93d9b5382342b40a351c2e313c
# conda changes md5sums for test.
- path: results/reports/samtools/test/test.recal.cram.stats
md5sum: 811d834ff8849e69e7c5925dc2a34257
# conda changes md5sums for test.
- path: results/reports/vcftools/strelka/test/test.strelka.variants.FILTER.summary
md5sum: dd87f507da7de20d5318841af312493b
- path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.count
Expand All @@ -67,60 +67,3 @@
- path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi
- path: results/strelka
should_exist: false
- name: Run default pipeline without intervals
command: nextflow run main.nf -profile test,no_intervals
tags:
- default
- no_intervals
- preprocessing
files:
- path: results/csv/markduplicates.csv
md5sum: 0d6120bb99e92f6810343270711ca53e
- path: results/csv/markduplicates_no_table.csv
md5sum: 2a2d3d4842befd4def39156463859ee3
- path: results/csv/recalibrated.csv
md5sum: 42628ec994c16f565e5407b40a9c1ac3
- path: results/multiqc
- path: results/no_intervals.bed
md5sum: f3dac01ea66b95fe477446fde2d31489
- path: results/no_intervals.bed.gz
md5sum: f3dac01ea66b95fe477446fde2d31489
- path: results/no_intervals.bed.gz.tbi
md5sum: f3dac01ea66b95fe477446fde2d31489
- path: results/preprocessing/markduplicates/test/test.md.cram
# binary changes md5sums on reruns.
- path: results/preprocessing/markduplicates/test/test.md.cram.crai
# binary changes md5sums on reruns.
- path: results/preprocessing/recal_table/test/test.recal.table
md5sum: 4ac774bf5f1157e77426fd82f5ac0fbe
- path: results/preprocessing/recalibrated/test/test.recal.cram
# binary changes md5sums on reruns.
- path: results/preprocessing/recalibrated/test/test.recal.cram.crai
# binary changes md5sums on reruns.
- path: results/reports/fastqc/test-test_L1
- path: results/reports/markduplicates/test/test.md.metrics
contains: ["test 8547 767 84 523391 3882 0 0 0.385081", "1.0 767 767"]
- path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
md5sum: 76fa71922a3f748e507c2364c531dfcb
- path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
md5sum: abc5df85e302b79985627888870882da
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
md5sum: d536456436eb275159b8c6af83213d80
- path: results/reports/mosdepth/test/test.md.regions.bed.gz
md5sum: 38fe39894abe62e38f8ac214cba64f2b
- path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
md5sum: b1c2a861f64e20a94108a6de3b76c582
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
md5sum: 76fa71922a3f748e507c2364c531dfcb
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
md5sum: abc5df85e302b79985627888870882da
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
md5sum: d536456436eb275159b8c6af83213d80
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
md5sum: 38fe39894abe62e38f8ac214cba64f2b
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
md5sum: b1c2a861f64e20a94108a6de3b76c582
- path: results/reports/samtools/test/test.md.cram.stats
md5sum: 52411f93d9b5382342b40a351c2e313c
- path: results/reports/samtools/test/test.recal.cram.stats
md5sum: d80ad11b8e308a3d5b1fb6f8e13cef38
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