Closed muffato closed 1 year ago
@muffato Try adding --jobmode=lsf
to LONGRANGER_ALIGN
ext.args
and running it.
In an interactive session with 12 cores:
--jobmode=lsf
: 4m 59sAt the last dev day, I did the same on a 16-core interactive session:
--jobmode=lsf
: 4m 42swhich shows how variable the runtime can be.
Overall, I'm not too troubled by the difference on this test dataset. I'm reinsured that I can see the jobs filling up bjobs
when run in LSF jobmode.
This PR is to make longranger work in LSF mode in the pipeline. I haven't had any issue with my tests so far (the
test
profile of this pipeline). The only change I had to make was adding this template, which I guess you had uncommitted in your checkoutI'll leave this as a draft PR until we've confirmed it works for everyone
PR checklist
nf-core lint
).nextflow run . -profile 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).