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Fix bakta running only for one sample #178
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I don't see how it was running for 1 sample only before 🤔 The ch_fasta
channel contains meta and fasta, so it should run for all samples, no? And the inputs to BAKTA_BAKTA
have the same structure as before if I read the mapping correctly. Can you explain what changed exactly?
I ran a few tests and found that when providing a local path to the Bakta database, the workflow processes only a single sample. However, when I set the workflow to download the database ( Do you think I should try to find a more suitable fix? |
Co-authored-by: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com>
Wait, I've just found the issue 😅 . |
ch_versions = ch_versions.mix(UNTAR.out.versions) | ||
} else { | ||
ch_baktadb = Channel.from(ch_path_baktadb).map{ db -> db } |
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ch_path_baktadb
is already a channel. Re-creating it to assign ch_bakta
caused the unusual behavior of processing only a single sample.
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I see! I don't have to check how we did it in funcscan then, you already found the culprit ;)
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LGTM now 🚀
ch_versions = ch_versions.mix(UNTAR.out.versions) | ||
} else { | ||
ch_baktadb = Channel.from(ch_path_baktadb).map{ db -> db } |
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I see! I don't have to check how we did it in funcscan then, you already found the culprit ;)
Thanks @jasmezz :) |
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).PR Description
Fixed bakta that was running for one sample only.
Closes #171