Collect intervallist channel output and propagate to genotyping step #1872
Conversation
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
|
Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.0.2. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
| @@ -16,7 +16,7 @@ process GATK4_GENOMICSDBIMPORT { | |||
| output: | |||
| tuple val(meta), path("$prefix") , optional:true, emit: genomicsdb | |||
| tuple val(meta), path("$updated_db") , optional:true, emit: updatedb | |||
| tuple val(meta), path("*.interval_list"), optional:true, emit: intervallist | |||
| tuple val(meta), path("$interval_list"), optional:true, emit: intervallist | |||
There was a problem hiding this comment.
heads up: these changes should be made in nf-core/modules and then imported here so others benefit from the work too :)
There was a problem hiding this comment.
I have opened an issue (nf-core/modules#8393) and PR to nf-core modules (nf-core/modules#8394).
|
hey! Do you need to update the module, aka run nf-core modules update for the genotypegvcf module? |
|
Not sure I follow. As in for this PR? |
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Outdated suggestions cannot be applied.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.
Addresses #1870
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).