Fix fastq_create_umi_consensus_fgbio and swap to nf-test #7718
+872
−345
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
|
no duplex? |
No duplex 😕 ? Do you mean no stub (as I have totally forgotten to put that in?) |
|
Sorry, I get you, I've updated the PR description to explain. |
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Outdated suggestions cannot be applied.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.
The
fastq_create_umi_consensus_fgbiosubworkflow was broken last summer when the fgbio modules were updated in #5624, but the pytest didn't trigger at that point.This PR:
samtools viewto filter the bam files with -f 1, but I don't think that the nf-core/fastquorum pipeline does this, so I suspect this is not required (pending confirmation from @nh13 or someone else from Fulcrum Genomics).dumpcommands