Conversation
Contributor
There was a problem hiding this comment.
Pull request overview
Updates the trimming step so that UMI information stored in the BAM RX tag can be carried through BAM→FASTQ conversion (and then through fastp) by explicitly copying RX into FASTQ output.
Changes:
- Bump
fastpconda dependency from1.0.1to1.1.0. - Remove the
fastp_pathoverride and invokefastpdirectly from the environment. - Update
samtools fastqinvocation to attempt to copyRXtags into FASTQ (-T RX).
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.
| File | Description |
|---|---|
| modules/fastp.nf | Update fastp/samtools invocation to preserve RX tag during BAM→FASTQ→fastp trimming. |
| conf/test.config | Remove unused fastp_path param from the test profile. |
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
|
|
||
| samtools fastq -n ${bam} | \\ | ||
| ${fastp_path}fastp --stdin \\ | ||
| samtools fastq -T RX -n ${bam} | \\ |
Comment on lines
+26
to
+27
| samtools fastq -T RX -n ${bam} | \\ | ||
| fastp --stdin \\ |
This file contains hidden or 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
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
relies on this change to bwameth, so will need to wait for bioconda release or use another installation.
brentp/bwa-meth@2bf5ae3