Bump rseqc #4601
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Bump rseqc #4601
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This reverts commit d350b3b.
robsyme
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Dec 14, 2023
Do you have a reason for that? Just curious.
I agreed initially, and was taking those out, but there are good reasons for not doing that- see discussion here: https://nfcore.slack.com/archives/C049MBCEW06/p1702571330445939
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lrauschning
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Dec 21, 2023
* Bump rseqc * snapshot updates for junc sat * Update timestamp here- it's just a non-lethal warning about missing index files * Bump a couple of versions * Bump the read distribution versions * Bump some more vesions in the snapshots * Bump tin snapshot * Hide pysam warning that causes mismatch with docker * Revert "Hide pysam warning that causes mismatch with docker" This reverts commit d350b3b. * Remove index warning from conda logs * Fix snap * Revert md5 fix no longer needed --------- Co-authored-by: Matthias Hörtenhuber <[email protected]>
lrauschning
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Jan 17, 2024
* Bump rseqc * snapshot updates for junc sat * Update timestamp here- it's just a non-lethal warning about missing index files * Bump a couple of versions * Bump the read distribution versions * Bump some more vesions in the snapshots * Bump tin snapshot * Hide pysam warning that causes mismatch with docker * Revert "Hide pysam warning that causes mismatch with docker" This reverts commit d350b3b. * Remove index warning from conda logs * Fix snap * Revert md5 fix no longer needed --------- Co-authored-by: Matthias Hörtenhuber <[email protected]>
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In this PR I'm bumping all the RSeQC modules. This is mostly straightforward, the snapshot updates are pretty much just versions.
The unusual thing is:
This is necessitated by this issue, whereby pysam prints a particular warning to logs. It only does so with Conda, so I've just grep'd out the warning so that the Docker and Conda versions behave the same.
See nf-core/rnaseq#1140 for motivation.
PR checklist
Closes #XXX
versions.ymlfile.labelPROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-awarePROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-awarePROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware