Add sampleNames_file option for QUILT and STITCH
#186
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
atrigila
reviewed
Feb 20, 2025
There was a problem hiding this comment.
We should make these changes in nf-core modules because it is starting to differ quite a bit from the original module.
There was a problem hiding this comment.
The update is here
nf-core/modules#7508
There was a problem hiding this comment.
I will do the same for stitch and then update the pipeline.
| @@ -62,22 +62,22 @@ | |||
| "id": "NA12878", | |||
| "panel": "1000GP", | |||
| "chr": "22", | |||
| "chunk": "16570065-16597215", | |||
| "chunk": "22:16570065-16597215", | |||
There was a problem hiding this comment.
Why do chunks add the chromosome now?
There was a problem hiding this comment.
It's an old update to standardize with the other subworkflow that use in the meta map the region (chr:start-end) convention.
There was a problem hiding this comment.
The snapshot hasn't been updated when the change was made.
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Outdated suggestions cannot be applied.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.
This PR solve #178
Stitch and Quilt subworkflow now expect two files
bampath(list of bam path) andbamname(list of sample names in the same order asbampath).PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,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).