Skip to content

Remove option to run bwamem as fallback aligner #763

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
ramprasadn merged 3 commits into from
Dec 19, 2025
Merged

Remove option to run bwamem as fallback aligner #763

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
1cdddde
remove option to bwamem as fallback aligner
ramprasadn Dec 18, 2025
27396e9
update changelog
ramprasadn Dec 18, 2025
d708ee8
Update main.nf
ramprasadn Dec 19, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 5 additions & 3 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Don't call mobile elements in mitochondrial DNA. [#741](https://github.com/nf-core/raredisease/pull/741)
- Call SVs in mitochondria using mitochondrial alignments in the genome alignment files instead of from BAM files generated by the mitochondrial subworkflow. [#742](https://github.com/nf-core/raredisease/pull/742)
- Update gens-preproc script [#747](https://github.com/nf-core/raredisease/pull/747)
- Removed parameter `bwa_as_fallback` [#763](https://github.com/nf-core/raredisease/pull/763)

### `Fixed`

Expand All @@ -31,9 +32,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Parameters

| Old parameter | New parameter |
| ------------- | ---------------- |
| | sambamba_regions |
| Old parameter | New parameter |
| --------------- | ---------------- |
| | sambamba_regions |
| bwa_as_fallback | |

### Tool updates

Expand Down
1 change: 0 additions & 1 deletion nextflow.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,6 @@ params {

// Main options
analysis_type = 'wgs'
bwa_as_fallback = false
bait_padding = 100
concatenate_snv_calls = false
extract_alignments = false
Expand Down
6 changes: 0 additions & 6 deletions nextflow_schema.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -531,12 +531,6 @@
"fa_icon": "fas fa-align-center",
"enum": ["wgs", "wes", "mito"]
},
"bwa_as_fallback": {
"type": "boolean",
"description": "Specifies whether or not to use bwa as a fallback aligner in case bwamem2 throws an error.",
"help_text": "errorStrategy needs to be set to ignore for the bwamem2 process for the fallback to work. Turned off by default.",
"fa_icon": "fas fa-toggle-on"
},
"concatenate_snv_calls": {
"type": "boolean",
"description": "Specifies whether to generate a concatenated VCF file containing both nuclear & mitochondrial snv calls",
Expand Down
17 changes: 0 additions & 17 deletions subworkflows/local/align_bwa_bwamem2_bwameme/main.nf
View file
Open in desktop
Copy link
Contributor

@fellen31 fellen31 Dec 19, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

remove line 6.

Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,6 @@
//

include { BWA_MEM as BWA } from '../../../modules/nf-core/bwa/mem/main'
include { BWA_MEM as BWAMEM_FALLBACK } from '../../../modules/nf-core/bwa/mem/main'
include { BWAMEM2_MEM } from '../../../modules/nf-core/bwamem2/mem/main'
include { BWAMEME_MEM } from '../../../modules/nf-core/bwameme/mem/main'
include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_ALIGN } from '../../../modules/nf-core/samtools/index/main'
Expand Down Expand Up @@ -45,22 +44,6 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME {
BWAMEM2_MEM ( ch_reads_input, ch_bwamem2_index, ch_genome_fasta, true )
ch_align = BWAMEM2_MEM.out.bam
ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions.first())

if (params.bwa_as_fallback) {
ch_reads_input
.join(BWAMEM2_MEM.out.bam, remainder: true)
.branch { meta, reads, bam ->
ERROR: bam.equals(null)
return [meta, reads] // return reads
SUCCESS: !bam.equals(null)
return [meta, bam] // return bam
}
.set { ch_fallback }

BWAMEM_FALLBACK ( ch_fallback.ERROR, ch_bwa_index, ch_genome_fasta, true )
ch_align = ch_fallback.SUCCESS.mix(BWAMEM_FALLBACK.out.bam)
ch_versions = ch_versions.mix(BWAMEM_FALLBACK.out.versions.first())
}
}

SAMTOOLS_INDEX_ALIGN ( ch_align )
Expand Down
Loading