Migrate Remapping nextflow pipeline to DSL2 #9
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
apriltuesday
approved these changes
Dec 20, 2023
| """ | ||
| } | ||
|
|
||
|
|
||
| process retrieve_target_genome { | ||
|
|
||
| input: | ||
| each target_assembly_accession |
There was a problem hiding this comment.
Should this be val instead of each? I'm not sure it makes a difference in practice, but semantically there should only ever be one target.
| update_source_genome(params.source_assembly_accession, retrieve_source_genome.out.source_fasta, | ||
| retrieve_source_genome.out.source_report, params.remapping_config) | ||
| update_target_genome(retrieve_target_genome.out.target_fasta, retrieve_target_genome.out.target_report, params.remapping_config) |
There was a problem hiding this comment.
I've realised we might be able to reduce some duplicated code between some of these processes now that we're passing in source & target assembly accessions... can happen later though.
There was a problem hiding this comment.
I agree. We also had a discussion about removing the custom assembly on the target and keeping it only in the source but I didn't want to drag this ticket out.
| process_remapped_variants.out.rs_report_filename | ||
| .concat(cluster_unclustered_variants.out.rs_report_filename) | ||
| .set{ rs_reports } |
There was a problem hiding this comment.
This is a good idea!
Co-authored-by: April Shen <[email protected]>
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Outdated suggestions cannot be applied.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.
Switch to DSL2