Closed muffato closed 12 months ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit dfafb26
+| ✅ 131 tests passed |+
#| ❔ 18 tests were ignored |#
!| ❗ 15 tests had warnings |!
This code works fine for me in the local mode. The issue with LSF mode is still there, longranger doesn't run properly in LSF mode for me, but ignoring it for now.
Issue was resolved. Works fine in LSF mode with singularity 3.9.0.
Hi @ksenia-krasheninnikova and @priyanka-surana
I've run a few tests for lonranger and found some things that can be removed / tidied up, and also, as per Priyanka's comments, some things that could be improved to make the pipeline less Sanger-specific.
First of all, we should remember that the Longranger container cannot be made public. The modules
modules/local/longranger/*/main.nf
currently point at our GitLab and we make them use a private container on GitHub for GitHub CI (theif(System.getenv('GITHUB_ACTION') != null )
statements inconf/modules.config
). If anyone else wants to run Longranger, they will have to override the container definitions.Then, by default Longranger will run in "local" mode. To make it work over LSF, it needs some extra configuration. The
envWhitelist
andrunOptions
directives exist in the "singularity" scope and only the lines that were innextflow.config
could actually work. The lines inconf/modules.config
couldn't work because they were inside aprocess { ... }
block.I moved all the Sanger LSF config to a different profile in
conf/longranger_lsf_sanger.config
that has to be defined at the end ofconf/modules.config
so that it can override the non-LSF settings. To enable it, just addlongranger_lsf_sanger
to the list of profiles alongsidetest
andsingularity
.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).