Fix comBGC: parsing multiple antiSMASH files #407
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
jfy133
approved these changes
Jul 24, 2024
|
The big Python block is really just indentation within a for loop 🙃 And yes, tested thoroughly! |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Symptoms before: Sometimes comBGC output contained correct BGC hits from antiSMASH, sometimes not.
2 reasons:
1. comBGC level: There was one indent level missing in a for loop, leading to only the last file of the supplied antiSMASH GBKs being parsed 🫠
2. pipeline level: The output channel of the
antismash/antismashlitemodule (which is input for comBGC) contains too many GBK files. We only want one file per sample (<samplename>.gbk), not all individual BGC-region GBKs (multiple files likek141_1214065.region001.gbk). This is fixed now by comBGC excluding files with theregion[0-9][0-9][0-9]pattern in their names.One could also fix 2. by applying a more specific glob pattern on module level, which I didn't get to work. For example,
!(*region[0-9][0-9][0-9]).gbkdoes the job if applied in bash terminal manually, but somehow not when applied via the module's main.nf liketuple val(meta), path("${prefix}/!(*region[0-9][0-9][0-9]).gbk") , emit: gbk_input🤷PR checklist
nf-core lint).nextflow run . -profile test,singularity --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).