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luslab-umitools | Minor corrections to main.nf in umi_tools/dedup

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Candice 2020-06-02 19:05:08 +02:00
parent 08d26794b5
commit 07b485eeec
1 changed files with 6 additions and 7 deletions
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13
tools/umi_tools/dedup/main.nf
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@ -4,8 +4,8 @@
nextflow.preview.dsl = 2 nextflow.preview.dsl = 2
// Include NfUtils // Include NfUtils
params.classpath = "umi_tools/groovy/NfUtils.groovy" params.internal_classpath = "umi_tools/groovy/NfUtils.groovy"
Class groovyClass = new GroovyClassLoader(getClass().getClassLoader()).parseClass(new File(params.classpath)); Class groovyClass = new GroovyClassLoader(getClass().getClassLoader()).parseClass(new File(params.internal_classpath));
GroovyObject nfUtils = (GroovyObject) groovyClass.newInstance(); GroovyObject nfUtils = (GroovyObject) groovyClass.newInstance();
// Define internal params // Define internal params
@ -88,7 +88,7 @@ process dedup {
dedup_post_args = '' dedup_post_args = ''
//Method used to extract barcodes //Method used to extract barcodes
if (params.internal_umi_separator != null){ if (params.internal_umi_separator != ''){
dedup_pre_args += "--umi-separator=\"$params.internal_umi_separator\" " dedup_pre_args += "--umi-separator=\"$params.internal_umi_separator\" "
} }
@ -99,18 +99,17 @@ process dedup {
if (params.internal_output_stats_sampleid){ if (params.internal_output_stats_sampleid){
dedup_post_args += "--output-stats=$sample_id " dedup_post_args += "--output-stats=$sample_id "
} else { } else {
if (params.internal_output_stats != null){ if (params.internal_output_stats != ''){
dedup_post_args += "--output-stats=$params.internal_output_stats " dedup_post_args += "--output-stats=$params.internal_output_stats "
} }
} }
//Output/ stdout option //Output/ stdout option
//TODO -> figure out how to get rid of the space between sample id and dedup.bam
if (params.internal_output_sampleid){ if (params.internal_output_sampleid){
dedup_post_args += "-S $sample_id .dedup.bam " dedup_post_args += "-S ${sample_id}.dedup.bam "
}else { }else {
if (params.internal_output_file_name != null){ if (params.internal_output_file_name != ''){
dedup_post_args += "-S $params.internal_output_file_name " dedup_post_args += "-S $params.internal_output_file_name "
} }
} }