Open
Conversation
…to feat/implement_gatk_mtdna_snv_calling
bartcharbon
reviewed
Mar 10, 2026
modules/fastq/minimap2.nf
Outdated
|
|
||
| stub: | ||
| cram="${meta.project.id}_${meta.sample.family_id}_${meta.sample.individual_id}.cram" | ||
| cram="${meta.project.id}_${meta.sample.family_id}_${meta.sample.individual_id}_unfiltered.cram" |
bartcharbon
reviewed
Mar 10, 2026
subworkflows/call_snv.nf
Outdated
| // mix outputs of all tools | ||
| //Channel.empty().mix(ch_snv_deepvariant, ch_snv_mtdna) | ||
| // | view | ||
| // | set { ch_snv_processed } |
Member
|
.def and changes to build.sh seem to be missing? |
bartcharbon
reviewed
Mar 10, 2026
config/nxf_cram.config
Outdated
|
|
||
| mitochondria { | ||
| GRCh38 { | ||
| chrm_bed = "${VIP_DIR_DATA}/resources/GRCh38/chrm.bed" |
Member
There was a problem hiding this comment.
chrm.bed should be added to the install_data.sh
dennishendriksen
requested changes
Mar 11, 2026
Contributor
dennishendriksen
left a comment
dennishendriksen
left a comment
There was a problem hiding this comment.
- update documentation e.g. workflow graph
- update test thresholds (should have improved)
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
3 participants
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Before submitting this PR, please make sure:
bash test/test.shand verified that all tests pass