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add contig ignore to beintervals #143

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Jun 10, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#136](https://github.com/nf-core/rnavar/pull/136) - Replaced unzip module with gunzip, removed unzip module
- [#138](https://github.com/nf-core/rnavar/pull/138) - Proper usage of GVCF
- [#142](https://github.com/nf-core/rnavar/pull/142) - Fix dbsnp channels
- [#143](https://github.com/nf-core/rnavar/pull/143) - Use `DROP_MISSING_CONTIGS` by default in `GATK4_BEDTOINTERVALLIST`

### Dependencies

Expand Down
26 changes: 15 additions & 11 deletions conf/modules.config
Original file line number Diff line number Diff line change
Expand Up @@ -3,10 +3,10 @@
Config file for defining DSL2 per module options and publishing paths
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Available keys to override module options:
ext.args = Additional arguments appended to command in module.
ext.args2 = Second set of arguments appended to command in module (multi-tool modules).
ext.args3 = Third set of arguments appended to command in module (multi-tool modules).
ext.prefix = File name prefix for output files.
ext.args = Additional arguments appended to command in module.
ext.args2 = Second set of arguments appended to command in module (multi-tool modules).
ext.args3 = Third set of arguments appended to command in module (multi-tool modules).
ext.prefix = File name prefix for output files.
----------------------------------------------------------------------------------------
*/

Expand Down Expand Up @@ -150,7 +150,7 @@ process {
process {

withName: '.*:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT' {
ext.prefix = {"${meta.id}.aligned"}
ext.prefix = {"${meta.id}.aligned"}
publishDir = [
path: { "${params.outdir}/preprocessing/${meta.id}" },
mode: params.publish_dir_mode,
Expand All @@ -161,7 +161,7 @@ process {

withName: '.*:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX' {
ext.args = params.bam_csi_index ? '-c' : ''
ext.prefix = {"${meta.id}.aligned"}
ext.prefix = {"${meta.id}.aligned"}
publishDir = [
path: { "${params.outdir}/preprocessing/${meta.id}" },
mode: params.publish_dir_mode,
Expand Down Expand Up @@ -190,7 +190,7 @@ process {
'--VALIDATION_STRINGENCY LENIENT',
params.remove_duplicates ? '--REMOVE_DUPLICATES true' : ''
].join(' ').trim()
ext.prefix = {"${meta.id}.md"}
ext.prefix = {"${meta.id}.md"}
publishDir = [
[
path: { "${params.outdir}/preprocessing/${meta.id}" },
Expand Down Expand Up @@ -255,7 +255,7 @@ if(!params.skip_baserecalibration) {
'--use-original-qualities',
'--add-output-sam-program-record'
].join(' ').trim()
ext.prefix = {"${meta.id}.recal"}
ext.prefix = {"${meta.id}.recal"}
publishDir = [
path: { "${params.outdir}/preprocessing/${meta.id}" },
mode: params.publish_dir_mode,
Expand All @@ -266,7 +266,7 @@ if(!params.skip_baserecalibration) {

withName: '.*:RECALIBRATE:SAMTOOLS_INDEX' {
ext.args = params.bam_csi_index ? '-c' : ''
ext.prefix = {"${meta.id}.recal"}
ext.prefix = {"${meta.id}.recal"}
publishDir = [
path: { "${params.outdir}/preprocessing/${meta.id}" },
mode: params.publish_dir_mode,
Expand Down Expand Up @@ -310,7 +310,7 @@ process {

withName: TABIX_TABIX {
ext.args = params.bam_csi_index ? '--csi' : ''
ext.prefix = {"${meta.id}.haplotypecaller"}
ext.prefix = {"${meta.id}.haplotypecaller"}
publishDir = [
path: { "${params.outdir}/variant_calling/${meta.id}" },
mode: params.publish_dir_mode,
Expand All @@ -319,7 +319,7 @@ process {
}

withName: GATK4_VARIANTFILTRATION {
ext.prefix = {"${meta.id}.haplotypecaller.filtered"}
ext.prefix = {"${meta.id}.haplotypecaller.filtered"}
ext.args = [
params.gatk_vf_window_size ? "--window $params.gatk_vf_window_size" : '',
params.gatk_vf_cluster_size ? "--cluster $params.gatk_vf_cluster_size" : '',
Expand All @@ -332,4 +332,8 @@ process {
pattern: "*.{vcf.gz,vcf.gz.tbi}"
]
}

withName: 'NFCORE_RNAVAR:RNAVAR:GATK4_BEDTOINTERVALLIST' {
ext.args = '--DROP_MISSING_CONTIGS TRUE'
}
}
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