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change prefix

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This commit is contained in:
SusiJo 2022-06-03 12:45:52 +02:00
parent 1db7771ea9
commit 230224700e
3 changed files with 23 additions and 1 deletions
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2
modules/gatk4/markduplicatesspark/main.nf
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@ -23,7 +23,7 @@ process GATK4_MARKDUPLICATES_SPARK {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}.bam" def prefix = task.ext.prefix ?: "${meta.id}"
def input_list = bam.collect{"--input $it"}.join(' ') def input_list = bam.collect{"--input $it"}.join(' ')

14
tests/modules/gatk4/markduplicatesspark/main.nf
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@ -3,6 +3,7 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { GATK4_MARKDUPLICATES_SPARK } from '../../../../modules/gatk4/markduplicatesspark/main.nf' include { GATK4_MARKDUPLICATES_SPARK } from '../../../../modules/gatk4/markduplicatesspark/main.nf'
include { GATK4_MARKDUPLICATES_SPARK as GATK4_MARKDUPLICATES_SPARK_CRAM } from '../../../../modules/gatk4/markduplicatesspark/main.nf'
include { GATK4_MARKDUPLICATES_SPARK as GATK4_MARKDUPLICATES_SPARK_METRICS } from '../../../../modules/gatk4/markduplicatesspark/main.nf' include { GATK4_MARKDUPLICATES_SPARK as GATK4_MARKDUPLICATES_SPARK_METRICS } from '../../../../modules/gatk4/markduplicatesspark/main.nf'
workflow test_gatk4_markduplicates_spark { workflow test_gatk4_markduplicates_spark {
@ -29,6 +30,19 @@ workflow test_gatk4_markduplicates_spark_multiple_bams {
GATK4_MARKDUPLICATES_SPARK ( input, fasta, fai, dict ) GATK4_MARKDUPLICATES_SPARK ( input, fasta, fai, dict )
} }
// chr 22
workflow test_gatk4_markduplicates_spark_multiple_bams_cram_out {
input = [ [ id:'test', single_end:false ], // meta map
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true)
] ]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
GATK4_MARKDUPLICATES_SPARK_CRAM ( input, fasta, fai, dict )
}
// chr 22 // chr 22
workflow test_gatk4_markduplicates_spark_multiple_bams_metrics { workflow test_gatk4_markduplicates_spark_multiple_bams_metrics {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map

8
tests/modules/gatk4/markduplicatesspark/nextflow.config
View file

@ -2,9 +2,17 @@ process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: GATK4_MARKDUPLICATES_SPARK {
ext.prefix = { "${meta.id}.bam" }
}
withName: GATK4_MARKDUPLICATES_SPARK_CRAM {
ext.prefix = { "${meta.id}.cram" }
}
withName: GATK4_MARKDUPLICATES_SPARK_METRICS { withName: GATK4_MARKDUPLICATES_SPARK_METRICS {
ext.prefix = { "${meta.id}.bam" }
ext.args = '--metrics-file test.metrics' ext.args = '--metrics-file test.metrics'
} }
} }
// override tests/config/nextflow.config // override tests/config/nextflow.config
docker.userEmulation = false docker.userEmulation = false