Enable organelles subworkflow #27
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@gq1 The purpose of this PR is to try setting the borrowed NCBI API key to check if it solves request errors on tower. |
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I've done some digging. The environment variable See this part of the stack-trace The documentation https://biopython.org/docs/1.75/api/Bio.Entrez.html#module-Bio.Entrez says there is an MitoHifi itself (specifically the
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@muffato thank you very much for looking into it |
Change working server name to ubuntu-latest
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.github/workflows/ci.yml
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| @@ -49,6 +53,10 @@ jobs: | |||
| mkdir -p $NXF_SINGULARITY_CACHEDIR | |||
| mkdir -p $NXF_SINGULARITY_LIBRARYDIR | |||
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| - name: Fix Longranger repo | |||
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https://github.com/sanger-tol/genomeassembly/blob/fixes_before_release/conf/test_github.config
Maybe it is easier to change the image for the process in the profile config file.
This profile is only for Github, so you can change it here.
Pipeline logic slightly changed:
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.github/workflows/ci.yml
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| @@ -51,4 +61,4 @@ jobs: | |||
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| - name: Run pipeline with test data | |||
| run: | | |||
| nextflow run ${GITHUB_WORKSPACE} -profile test_github,singularity --outdir ./results | |||
| nextflow run ${GITHUB_WORKSPACE} -profile test_github,singularity -c conf/test_github_params.config --outdir ./results | |||
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Can we merge 2 test_github config files together?
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The function of having conf/test_github_params.config is to override HIFIASM and OATK settings from the ones set in the modules.conf file. It wouldn't work by setting them in the config corresponding to the test_github profile. Do you know how to force overriding the ext.args in the profile config?
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If it works in 2 config files, there is no reason for it not working in one file.
You can see the the extra setting for oatk in the one config being picked up.
Command executed:
oatk \
-k1001 -c90 -Ttmp \
-m insecta_mito.fam \
\
-t 2 \
-o baUndUnlc1 \
baUndUnlc1.fasta
The actual error message is
.command.run: line 24: /usr/bin/awk: No such file or directory
If you go to the container, you can see the awk being installed here: /usr/local/bin/oatk
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@gq1 It failed in the first place because it didn't pick up the right setting: it must have been -c5 from conf/test_github.config instead of -c 90 from conf/modules.config
[E::pathfinder] no organelle component found
[E::main] pathfinder program failed
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Sorry I didn't see the details.
I tried it on the farm and have the same problem. However, I didn't get this error: /usr/bin/awk: No such file or directory
Maybe @muffato knows, can we overwrite the process's ext.args in the profile config file, which is already defined in the modules.config?
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Yep ! I had to do that in the genome-note pipeline to add some BUSCO options in test mode:
https://github.com/sanger-tol/genomenote/blob/1.1.1/conf/modules.config#L52-L59
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modules.config is loaded after profile config file so it will overwrite the setting there.
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For genome-note I faced that same problem. My first solution was to define a profiles { test { ... } } block in conf/modules.config. It worked in some cases, but not always, but then I undid the change in sanger-tol/genomenote@f04a524 to what I posted in my comment above.
The solution I have now is that conf/modules.config is made aware of the profiles and changes ext.args depending on the profile. I leave the profile definition and conf/test.config unchanged.
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It seems working now.
conf/modules.config
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| container = "ghcr.io/sanger-tol/longranger:2.2.2-c4" | ||
| } | ||
| } | ||
| } |
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).