Hotfixes for production

muffato commented 1 year ago

Resolves #91

These changes are needed to make the pipeline behave more nicely in production:

maxRetries is already set to 5 on this branch, so no need to change that
The memory of sort is adjusted to account for some overheads and avoid the job to be killed
Temporary files for sort, FastK, and MerquryFK are created in the work directory rather than /tmp.

Note: the Markdown files are not up-to-date with dev, so will update them and include this PR's changes in #95

PR checklist

[x] 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
[x] Make sure your code lints (nf-core lint).
[x] 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).

github-actions[bot] commented 1 year ago

`nf-core lint` overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit 65133a6

+| ✅ 132 tests passed       |+
#| ❔  20 tests were ignored |#
!| ❗   1 tests had warnings |!

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muffato commented 1 year ago

@gq1 . Following your comments at the pipeline meeting last Tuesday, would I introduce a boolean parameter named something like use_work_dir_as_temp and only make sort, FastK and MerquryFK use . when it is set ? Your point was that it was a pretty Sanger-specific change that may not suit everyone

gq1 commented 1 year ago

Different temp dir may affect the performance?

muffato commented 1 year ago

Yes, that's the issue. /tmp (or whatever $TMPDIR defaults to) 1) is the place recommended by the HPC admins to make temporary files, 2) usually is local and has better performance than a network file-system. Here, we're trading off performance for convenience, but I feel we shouldn't force that to everyone

muffato commented 1 year ago

Oki. I just added the parameter. In production, we'll have to make sure we switch use_work_dir_as_temp on. I guess that'll be defined in the pipeline-orchestration repo, in genomenote.sh ?

cibinsb commented 1 year ago

Yes, for our production pipeline runs use_work_dir_as_temp parameter will be set to true.

sanger-tol / genomenote