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Patching samtools sort process behaviour when samtools sort resorts to using on-disk temporary files #1222
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Dev -> master for 3.14.0 release
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Hi @koustav-pal ! Thanks for the PR! Can you provide me an example of the stdout/ Nextflow log file when there is a failure here please? Is it a silent error? In any case, this PR should be made to nf-core/modules to update this module there. It can then be installed in pipelines from there. We also should be catching this exit status with the standard Line 17 in b89fac3
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Closing for now. Please feel free to re-open with a fix as suggested above. Be great to have a little more info on the failure and access to the logs generating it. |
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).nextflow run . -profile debug,test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).samtools sort resorts to using a combination of on-disk and in-memory
temporary files when it is unable to sort using memory only. In such cases,
samtools issues an exit code of
140
and provides a suitable error messagestating that it is using in-memory and on-disk temporary files.
This patch modulates samtools sort
errorStrategy
when such a scenario isobserved.