Re-structure pipeline #134
Merged
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
Adjustment of the voting scheme and updated viral taxonomy and bugfixes for new release
Fix Chromomap container
Merge small set of fixes for new release #123
mberacochea
reviewed
Oct 4, 2024
subworkflows/local/annotate.nf
Outdated
| viphos_annotations = ANNOTATION.out.map { _, __, annotations -> annotations }.collect() | ||
| taxonomy_annotations = ASSIGN.out.map { _, __, taxonomy -> taxonomy }.collect() | ||
| checkv_results = CHECKV.out.map { _, __, quality_summary, ___ -> quality_summary }.collect() | ||
| viphos_annotations = ANNOTATION.out.annotations.groupTuple().map{ |
There was a problem hiding this comment.
Is this groupTuple required becase ANNOTATION return a list of files? I'm not sure I follow
There was a problem hiding this comment.
it is in development stage yet, I'm not sure what it returns either :D
|
So far.. it look goods to me :) Thank you @KateSakharova |
KateSakharova
force-pushed
the
feature/re-structure-pipeline
branch
from
cd0039a to
74d296b
Compare
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Outdated suggestions cannot be applied.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.
Restructured pipeline to nf-core view
Now virify supports samplesheet (fq1 and fq2 are optional)
id,assembly,fq1,fq2
For assembly as input:
If you have assembly as input you can use old argument --fasta - that will run pipieline for 1 assembly.
If you have more than 1 assembly - use samplesheet.
For raw_reads as input:
You need to use ONLY samplesheet (even for 1 run). I replaced --illumina option with --assemble (boolean). User should specify that flag to force assembly process (that flag will help user to understand what he is doing). Hopefully, nobody uses it because it is experimental feature.