New module: Ultra
#871
New module: Ultra
#871
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- Update to last versions.yml file - Update meta.yml - Correct typos
| \$(pwd)/$genome \\ | ||
| \$(pwd)/$gtf \\ | ||
| \$(pwd)/$reads \\ |
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Why do we need ${pwd} here? The tool requires the full path?
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Actually yes. The tool do not resolve the file path properly yet, so full path to files is needed.
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I re-tested this with variations, but I could also only get it to work with $(pwd) (no ./$gtf, no $gtf)
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I submitted a new issue at the ULTRA-repo, with a fix-suggestion. Could be quick, but as I said on the mergathon call, I don't think it's a blocker for merging in - everything else looks good,
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Thanks for the issue 👍
I also think it could be merge in this temporary state.
In any case, I will update the module as soon as the patch is applied.
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Looks like you have added quite a bit of non-conventional code to get this module working @sguizard . Be great if we can try and make things simpler. Not entirely sure why the tool has been written this way but maybe we can discuss on the PR.
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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The conda test failed because it couldn't download the fastq.gz file. |
Those data might be useful in a debugging purpose.
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Looks awesome! Thanks @sguizard ! |
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@sguizard there's actually a new release now, that's supposed to avoid the $pwd problem. But I guess that can wait for next release. |
New module for uLTRA: An efficient alignment method for spliced long reads
PR checklist
versions.ymlfile.labelPROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wdPROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wdPROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd