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Update config files and other minor code polishing #1325

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merged 27 commits into from
Nov 10, 2023
Merged

Update config files and other minor code polishing #1325

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0080ffd
code polish
maxulysse Nov 9, 2023
77f45b4
Merge branch 'dev' into config_update
maxulysse Nov 9, 2023
43388e2
move sentieon model to igenomes
maxulysse Nov 9, 2023
c5a34bf
Merge branch 'config_update' of github.com:nf-core/sarek into config_…
maxulysse Nov 9, 2023
a49ba51
update CHANGELOG
maxulysse Nov 9, 2023
dd4d590
code polish
maxulysse Nov 9, 2023
47b3b9b
align
maxulysse Nov 9, 2023
2bc2bda
closure in modules config files
maxulysse Nov 9, 2023
13ff7f1
not an nf-core subworkflow
maxulysse Nov 9, 2023
9a919b2
update ngscheckmate ncm module
maxulysse Nov 9, 2023
30c499b
single over double quotes
maxulysse Nov 9, 2023
a637854
use config file from subworkflows
maxulysse Nov 9, 2023
73f601c
update tags
maxulysse Nov 9, 2023
36e13bf
code polish
maxulysse Nov 9, 2023
1bdaba3
Apply suggestions from code review
maxulysse Nov 9, 2023
94d4f4c
closure here too
maxulysse Nov 9, 2023
e04257c
Merge branch 'config_update' of github.com:nf-core/sarek into config_…
maxulysse Nov 9, 2023
7f8765c
code polishing
maxulysse Nov 9, 2023
74be4e5
typo
maxulysse Nov 9, 2023
3636510
exclude don't work in glob pattern
maxulysse Nov 9, 2023
1b91848
fix save output as bam
maxulysse Nov 9, 2023
5bb015c
Apply suggestions from code review
maxulysse Nov 9, 2023
e18d84b
Update conf/modules/msisensorpro.config
maxulysse Nov 9, 2023
8822d44
remove duplicate tags + md5sum
maxulysse Nov 10, 2023
fcb3258
Merge branch 'config_update' of github.com:nf-core/sarek into config_…
maxulysse Nov 10, 2023
43ad1dd
add sentieon model file in tests
maxulysse Nov 10, 2023
055818f
Update conf/modules/markduplicates.config
maxulysse Nov 10, 2023
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -26,6 +26,8 @@ Pårtetjåkko is a mountain in the south of the park.
- [#1304](https://github.com/nf-core/sarek/pull/1304) - Update modules
- [#1311](https://github.com/nf-core/sarek/pull/1311) - Update local modules with an `environment.yml` file
- [#1317](https://github.com/nf-core/sarek/pull/1317) - Add new tools to subway map
- [#1325](https://github.com/nf-core/sarek/pull/1325) - Move `sentieon_dnascope_model` params into `igenomes.config`
- [#1325](https://github.com/nf-core/sarek/pull/1325) - Refactor config files

### Fixed

Expand All @@ -36,6 +38,7 @@ Pårtetjåkko is a mountain in the south of the park.
- [#1315](https://github.com/nf-core/sarek/pull/1315) - Avoid clash of configs of `FILTERVARIANTTRANCHES` in the Sentieon-Haplotyper and GATK-Haplotypecaller subworkflows
- [#1318](https://github.com/nf-core/sarek/pull/1218) - Fix writing of params.json on S3
- [#1324](https://github.com/nf-core/sarek/pull/1324) - Fix various typos & code formatting
- [#1325](https://github.com/nf-core/sarek/pull/1325) - Update bcfannotate tests and related config files

### Removed

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88 changes: 44 additions & 44 deletions conf/base.config
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Expand Up @@ -21,84 +21,84 @@ process {

// Process-specific resource requirements
// See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
withLabel:error_ignore {
errorStrategy = 'ignore'
}
withLabel:error_retry {
errorStrategy = 'retry'
maxRetries = 2
}
withLabel:process_single {
cpus = { check_max( 1 , 'cpus' ) }
memory = { check_max( 6.GB * task.attempt, 'memory' ) }
time = { check_max( 4.h * task.attempt, 'time' ) }
cpus = { check_max( 1 , 'cpus' ) }
memory = { check_max( 6.GB * task.attempt, 'memory' ) }
time = { check_max( 4.h * task.attempt, 'time' ) }
}
withLabel:process_low {
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 12.GB * task.attempt, 'memory' ) }
time = { check_max( 4.h * task.attempt, 'time' ) }
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 12.GB * task.attempt, 'memory' ) }
time = { check_max( 4.h * task.attempt, 'time' ) }
}
withLabel:process_medium {
cpus = { check_max( 6 * task.attempt, 'cpus' ) }
memory = { check_max( 36.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
cpus = { check_max( 6 * task.attempt, 'cpus' ) }
memory = { check_max( 36.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
}
withLabel:process_high {
cpus = { check_max( 12 * task.attempt, 'cpus' ) }
memory = { check_max( 72.GB * task.attempt, 'memory' ) }
time = { check_max( 16.h * task.attempt, 'time' ) }
cpus = { check_max( 12 * task.attempt, 'cpus' ) }
memory = { check_max( 72.GB * task.attempt, 'memory' ) }
time = { check_max( 16.h * task.attempt, 'time' ) }
}
withLabel:process_long {
time = { check_max( 20.h * task.attempt, 'time' ) }
time = { check_max( 20.h * task.attempt, 'time' ) }
}
withLabel:process_high_memory {
memory = { check_max( 200.GB * task.attempt, 'memory' ) }
}
withLabel:error_ignore {
errorStrategy = 'ignore'
}
withLabel:error_retry {
errorStrategy = 'retry'
maxRetries = 2
memory = { check_max( 200.GB * task.attempt, 'memory' ) }
}
withName: 'UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX' {
cpus = { check_max( 1 * task.attempt, 'cpus' ) }
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
cpus = { check_max( 1 * task.attempt, 'cpus' ) }
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
}
withName: 'FASTQC'{
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
}
withName: 'FASTP'{
cpus = { check_max( 12 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
cpus = { check_max( 12 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
}
withName: 'BWAMEM1_MEM|BWAMEM2_MEM' {
cpus = { check_max( 24 * task.attempt, 'cpus' ) }
memory = { check_max( 30.GB * task.attempt, 'memory' ) }
cpus = { check_max( 24 * task.attempt, 'cpus' ) }
memory = { check_max( 30.GB * task.attempt, 'memory' ) }
}
withName:'CNVKIT_BATCH' {
label = "process_high"
memory = { check_max( 36.GB * task.attempt, 'memory' ) }
label = "process_high"
memory = { check_max( 36.GB * task.attempt, 'memory' ) }
}
withName: 'GATK4_MARKDUPLICATES|GATK4SPARK_MARKDUPLICATES' {
cpus = { check_max( 6 * task.attempt, 'cpus' ) }
memory = { check_max( 30.GB * task.attempt, 'memory' ) }
cpus = { check_max( 6 * task.attempt, 'cpus' ) }
memory = { check_max( 30.GB * task.attempt, 'memory' ) }
}
withName:'GATK4_APPLYBQSR|GATK4SPARK_APPLYBQSR|GATK4_BASERECALIBRATOR|GATK4SPARK_BASERECALIBRATOR|GATK4_GATHERBQSRREPORTS'{
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
}
withName:'MOSDEPTH'{
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
}
withName:'STRELKA.*|MANTA.*' {
cpus = { check_max( 10 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
cpus = { check_max( 10 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
}
withName:'SAMTOOLS_CONVERT'{
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
}
withName:'GATK4_MERGEVCFS'{
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
}
withName: 'MULTIQC' {
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 12.GB * task.attempt, 'memory' ) }
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 12.GB * task.attempt, 'memory' ) }
}
}
69 changes: 35 additions & 34 deletions conf/igenomes.config
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Expand Up @@ -43,40 +43,41 @@ params {
vep_species = 'homo_sapiens'
}
'GATK.GRCh38' {
ascat_alleles = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_alleles_hg38.zip"
ascat_genome = 'hg38'
ascat_loci = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_loci_hg38.zip"
ascat_loci_gc = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/GC_G1000_hg38.zip"
ascat_loci_rt = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/RT_G1000_hg38.zip"
bwa = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/"
bwamem2 = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/BWAmem2Index/"
dragmap = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/dragmap/"
chr_dir = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/Chromosomes"
cf_chrom_len = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/Length/Homo_sapiens_assembly38.len"
dbsnp = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz"
dbsnp_tbi = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi"
dbsnp_vqsr = '--resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz'
dict = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict"
fasta = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta"
fasta_fai = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai"
germline_resource = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz"
germline_resource_tbi = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz.tbi"
intervals = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/intervals/wgs_calling_regions_noseconds.hg38.bed"
known_snps = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz"
known_snps_tbi = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz.tbi"
known_snps_vqsr = '--resource:1000G,known=false,training=true,truth=true,prior=10.0 1000G_omni2.5.hg38.vcf.gz'
known_indels = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz"
known_indels_tbi = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"
known_indels_vqsr = '--resource:gatk,known=false,training=true,truth=true,prior=10.0 Homo_sapiens_assembly38.known_indels.vcf.gz --resource:mills,known=false,training=true,truth=true,prior=10.0 Mills_and_1000G_gold_standard.indels.hg38.vcf.gz'
mappability = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/Control-FREEC/out100m2_hg38.gem"
ngscheckmate_bed = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/NGSCheckMate/SNP_GRCh38_hg38_wChr.bed"
pon = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz"
pon_tbi = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz.tbi"
snpeff_db = 105
snpeff_genome = 'GRCh38'
vep_cache_version = 110
vep_genome = 'GRCh38'
vep_species = 'homo_sapiens'
ascat_alleles = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_alleles_hg38.zip"
ascat_genome = 'hg38'
ascat_loci = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_loci_hg38.zip"
ascat_loci_gc = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/GC_G1000_hg38.zip"
ascat_loci_rt = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/RT_G1000_hg38.zip"
bwa = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/"
bwamem2 = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/BWAmem2Index/"
cf_chrom_len = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/Length/Homo_sapiens_assembly38.len"
chr_dir = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/Chromosomes"
dbsnp = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz"
dbsnp_tbi = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi"
dbsnp_vqsr = '--resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz'
dict = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict"
dragmap = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/dragmap/"
fasta = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta"
fasta_fai = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai"
germline_resource = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz"
germline_resource_tbi = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz.tbi"
intervals = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/intervals/wgs_calling_regions_noseconds.hg38.bed"
known_indels = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz"
known_indels_tbi = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"
known_indels_vqsr = '--resource:gatk,known=false,training=true,truth=true,prior=10.0 Homo_sapiens_assembly38.known_indels.vcf.gz --resource:mills,known=false,training=true,truth=true,prior=10.0 Mills_and_1000G_gold_standard.indels.hg38.vcf.gz'
known_snps = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz"
known_snps_tbi = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz.tbi"
known_snps_vqsr = '--resource:1000G,known=false,training=true,truth=true,prior=10.0 1000G_omni2.5.hg38.vcf.gz'
mappability = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/Control-FREEC/out100m2_hg38.gem"
ngscheckmate_bed = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/NGSCheckMate/SNP_GRCh38_hg38_wChr.bed"
pon = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz"
pon_tbi = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz.tbi"
sentieon_dnascope_model = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model"
snpeff_db = 105
snpeff_genome = 'GRCh38'
vep_cache_version = 110
vep_genome = 'GRCh38'
vep_species = 'homo_sapiens'
}
'Ensembl.GRCh37' {
bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/"
Expand Down
26 changes: 13 additions & 13 deletions conf/modules/aligner.config
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Expand Up @@ -16,24 +16,24 @@
process {

if (params.step == 'mapping') {
withName: "BWAMEM1_MEM" {
ext.when = { params.aligner == "bwa-mem" }
withName: 'BWAMEM1_MEM' {
ext.when = { params.aligner == 'bwa-mem' }
}

withName: "BWAMEM2_MEM" {
ext.when = { params.aligner == "bwa-mem2" }
withName: 'BWAMEM2_MEM' {
ext.when = { params.aligner == 'bwa-mem2' }
}

withName: "DRAGMAP_ALIGN" {
ext.when = { params.aligner == "dragmap" }
withName: 'DRAGMAP_ALIGN' {
ext.when = { params.aligner == 'dragmap' }
ext.args = { "--RGSM ${meta.patient}_${meta.sample} --RGID ${meta.read_group}" }
}

withName: "SENTIEON_BWAMEM" {
ext.when = { params.aligner == "sentieon-bwamem" }
withName: 'SENTIEON_BWAMEM' {
ext.when = { params.aligner == 'sentieon-bwamem' }
}

withName: "(BWAMEM.*_MEM|DRAGMAP_ALIGN|SENTIEON_BWAMEM)" {
withName: 'BWAMEM.*_MEM|DRAGMAP_ALIGN|SENTIEON_BWAMEM' {
ext.prefix = { params.split_fastq > 1 ? "${meta.id}".concat('.').concat(reads.get(0).name.tokenize('.')[0]) : "${meta.id}.sorted" }
publishDir = [
mode: params.publish_dir_mode,
Expand All @@ -55,22 +55,22 @@ process {
]
}

withName: "(BWAMEM.*_MEM|DRAGMAP_ALIGN)" {
withName: 'BWAMEM.*_MEM|DRAGMAP_ALIGN' {
// Markduplicates Spark NEEDS name-sorted reads or runtime goes through the roof
// However if it's skipped, reads need to be coordinate-sorted
// Only name sort if Spark for Markduplicates + duplicate marking is not skipped
// Currently SENTIEON_BWAMEM only supports coordinate sorting the reads.
ext.args2 = { params.use_gatk_spark && params.use_gatk_spark.contains('markduplicates') && (!params.skip_tools || (params.skip_tools && !params.skip_tools.split(',').contains('markduplicates'))) ? '-n' : '' }
}

withName: "BWAMEM.*_MEM|SENTIEON_BWAMEM" {
withName: 'BWAMEM.*_MEM|SENTIEON_BWAMEM' {
// Using -B 3 for tumor samples
ext.args = { meta.status == 1 ? "-K 100000000 -Y -B 3 -R ${meta.read_group}" : "-K 100000000 -Y -R ${meta.read_group}" }
}
}

withName: 'MERGE_BAM|INDEX_MERGE_BAM' {
publishDir = [
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/preprocessing/" },
pattern: "*{bam,bai}",
Expand All @@ -80,6 +80,6 @@ process {
}

withName: 'MERGE_BAM' {
ext.prefix = { "${meta.id}.sorted" }
ext.prefix = { "${meta.id}.sorted" }
}
}
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