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enable pytest with conda and singularity #691

Merged
merged 6 commits into from
Jul 26, 2022
Merged

enable pytest with conda and singularity #691

merged 6 commits into from
Jul 26, 2022

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maxulysse
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PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
    • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
    • If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Jul 26, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2fb8c01

+| ✅ 145 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-07-26 12:11:41

@asp8200
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asp8200 commented Jul 26, 2022 •
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So I tried running the tests for cnvkit (randomly chosen) on a linux-server on commit 2fb8c01 like this:

$ PROFILE=singularity pytest --tag cnvkit --symlink --kwdof --git-aware --color=yes

but it failed. I guess it is just a problem with my setup, while this PR is probably fine. Here is the error-log from the test:

================================================================================================ test session starts ================================================================================================
platform linux -- Python 3.10.5, pytest-7.1.2, pluggy-1.0.0
rootdir: /home/aspe/dev/maxulysse_sarek
plugins: workflow-1.6.0
collecting ...
collected 69 items

Run variant calling on somatic samples with cnvkit and skip variant calling on matched normal:
	command:   nextflow run main.nf -profile test,tools_somatic --tools cnvkit --only_paired_variant_calling
	directory: /tmp/pytest_workflow_cavfgx0b/Run_variant_calling_on_somatic_samples_with_cnvkit_and_skip_variant_calling_on_matched_normal
	stdout:    /tmp/pytest_workflow_cavfgx0b/Run_variant_calling_on_somatic_samples_with_cnvkit_and_skip_variant_calling_on_matched_normal/log.out
	stderr:    /tmp/pytest_workflow_cavfgx0b/Run_variant_calling_on_somatic_samples_with_cnvkit_and_skip_variant_calling_on_matched_normal/log.err
'Run variant calling on somatic samples with cnvkit and skip variant calling on matched normal' done.

...

Run variant calling on germline sample with cnvkit:
	command:   nextflow run main.nf -profile test,tools_germline --tools cnvkit
	directory: /tmp/pytest_workflow_cavfgx0b/Run_variant_calling_on_germline_sample_with_cnvkit
	stdout:    /tmp/pytest_workflow_cavfgx0b/Run_variant_calling_on_germline_sample_with_cnvkit/log.out
	stderr:    /tmp/pytest_workflow_cavfgx0b/Run_variant_calling_on_germline_sample_with_cnvkit/log.err
'Run variant calling on germline sample with cnvkit' done.

tests/test_only_paired_VC.yml FFFFFFFFFFFFFFF                                                                                                                                                                 [ 21%]
tests/test_tools.yml FFFFFFFFFFFFFFFFFFFFFFFFF.FFFFFFFFFFFF.FFFFFFFFFFFFF.F                                                                                                                                   [100%]One or more tests failed. Keeping temporary directories and logs. Use '--kwd' or '--keep-workflow-wd' to disable this behaviour.


===================================================================================================== FAILURES ======================================================================================================
___________________________________________________________________________________________________ test session ____________________________________________________________________________________________________
'/tmp/pytest_workflow_cavfgx0b/Run_variant_calling_on_somatic_samples_with_cnvkit_and_skip_variant_calling_on_matched_normal/results/multiqc' does not exist while it should
___________________________________________________________________________________________________ test session ____________________________________________________________________________________________________
'/tmp/pytest_workflow_cavfgx0b/Run_variant_calling_on_somatic_samples_with_cnvkit_and_skip_variant_calling_on_matched_normal/results/variant_calling/cnvkit/sample4_vs_sample3/multi_intervals.antitarget.bed' does not exist while it should

...

___________________________________________________________________________________________________ test session ____________________________________________________________________________________________________
'/tmp/pytest_workflow_cavfgx0b/Run_variant_calling_on_germline_sample_with_cnvkit/results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted.cns' does not exist while it should
___________________________________________________________________________________________________ test session ____________________________________________________________________________________________________
'/tmp/pytest_workflow_cavfgx0b/Run_variant_calling_on_germline_sample_with_cnvkit/results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted.targetcoverage.cnn' does not exist while it should
___________________________________________________________________________________________________ test session ____________________________________________________________________________________________________
'Run variant calling on germline sample with cnvkit' exited with exit code '1' instead of '0'.
================================================================================================= warnings summary ==================================================================================================
../../anaconda3/envs/nextflow/lib/python3.10/site-packages/pytest_workflow/plugin.py:122: 20 warnings
  /home/aspe/anaconda3/envs/nextflow/lib/python3.10/site-packages/pytest_workflow/plugin.py:122: PytestRemovedIn8Warning: The (fspath: py.path.local) argument to YamlFile is deprecated. Please use the (path: pathlib.Path) argument instead.
  See https://docs.pytest.org/en/latest/deprecations.html#fspath-argument-for-node-constructors-replaced-with-pathlib-path
    return YamlFile.from_parent(parent, fspath=path)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
============================================================================================== short test summary info ==============================================================================================
FAILED tests/test_only_paired_VC.yml::Run variant calling on somatic samples with cnvkit and skip variant calling on matched normal::results/multiqc::should exist
FAILED tests/test_only_paired_VC.yml::Run variant calling on somatic samples with cnvkit and skip variant calling on matched normal::results/variant_calling/cnvkit/sample4_vs_sample3/multi_intervals.antitarget.bed::should exist
FAILED tests/test_only_paired_VC.yml::Run variant calling on somatic samples with cnvkit and skip variant calling on matched normal::results/variant_calling/cnvkit/sample4_vs_sample3/multi_intervals.target.bed::should exist

...
I used
pytest 7.1.2
singularity 3.7.1-1.el7
nextflow 22.04.0
python 3.10.5

I tried running one of the failing tests, "Run variant calling on somatic samples with cnvkit", manually like this:

PROFILE=singularity nextflow run main.nf -profile test,tools_somatic --tools cnvkit --only_paired_variant_calling

and all the expected output-files are generated.

@maxulysse
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Having mount issue with pytest:

  WARNING: Skipping mount /usr/local/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
  FATAL:   container creation failed: mount /tmp/pytest_workflow_fd40z6lq/Run_default_pipeline/work->/tmp/pytest_workflow_fd40z6lq/Run_default_pipeline/work error: while mounting /tmp/pytest_workflow_fd40z6lq/Run_default_pipeline/work: destination /tmp/pytest_workflow_fd40z6lq/Run_default_pipeline/work doesn't exist in container

I'm assuming your issue might be the same.
I'll try to fix that

@maxulysse
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Had to add TMPDIR=~ to my command line to make the singularity pytest tests work:

TMPDIR=~ PROFILE=singularity pytest --tag default --symlink --kwdof --git-aware --color=yes

@maxulysse
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Had to add TMPDIR=~ to my command line to make the singularity pytest tests work:

I'm assuming any other TMPDIR should actually do the trick

@maxulysse
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maxulysse commented Jul 26, 2022 •
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Couldn't get TMP=/tmp on my computer, so used TMP=~/tmp that way easier to clean up

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asp8200 commented Jul 26, 2022 •
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Well done, @maxulysse. I can confirm that I am now able to run the tests locally with the command:

TMPDIR=~ PROFILE=singularity pytest --tag cnvkit --symlink --kwdof --git-aware --color=yes

after first having run

python -m pip install --upgrade pip pytest-workflow

@maxulysse maxulysse requested a review from asp8200 July 26, 2022 15:57
asp8200
asp8200 reviewed Jul 26, 2022
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CHANGELOG.md
### Changed

- [#679](https://github.com/nf-core/sarek/pull/679) - Back to `dev`
- [#691](https://github.com/nf-core/sarek/pull/691) - To run the same pytest as before locally, use `PROFILE=docker`
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Suggested change
- [#691](https://github.com/nf-core/sarek/pull/691) - To run the same pytest as before locally, use `PROFILE=docker`
- [#691](https://github.com/nf-core/sarek/pull/691) - To run the same pytest as before locally, use TMPDIR=~/tmp, and `PROFILE=conda`, `PROFILE=docker` or `PROFILE=singularity`.

or something like that.

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Before we had just docker, all the rest is new, let's not document that too much for now, as we're still figuring it out ;-)

asp8200
asp8200 approved these changes Jul 26, 2022
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LGTM

@maxulysse maxulysse merged commit a40a304 into nf-core:dev Jul 26, 2022
@maxulysse maxulysse deleted the dev_pytest_singularity branch July 26, 2022 16:09
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