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luslab-umitools | Added sample_id options in dedup

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Candice 2020-06-02 18:45:24 +02:00
parent 6970d25b59
commit 3aace7c0c2
1 changed files with 32 additions and 10 deletions
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40
tools/umi_tools/dedup/main.nf
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@ -20,12 +20,6 @@ nfUtils.check_internal_overrides(module_name, params)
/*-------------------------------------------------> DEDUP OPTIONS <-----------------------------------------------------*/ /*-------------------------------------------------> DEDUP OPTIONS <-----------------------------------------------------*/
/*-----------------------------------------------------------------------------------------------------------------------------
OUTPUT STATS OPTION -> --output-stats=[PREFIX]
-------------------------------------------------------------------------------------------------------------------------------*/
//Enter the prefix
params.internal_output_stats = 'sample'
/*----------------------------------------------------------------------------------------------------------------------------- /*-----------------------------------------------------------------------------------------------------------------------------
EXTRACT BARCODE OPTION -> --extract-umi-method EXTRACT BARCODE OPTION -> --extract-umi-method
-------------------------------------------------------------------------------------------------------------------------------*/ -------------------------------------------------------------------------------------------------------------------------------*/
@ -63,7 +57,18 @@ params.internal_cell_tag = ''
OUTPUT OPTION -> --stdout or -S OUTPUT OPTION -> --stdout or -S
-------------------------------------------------------------------------------------------------------------------------------*/ -------------------------------------------------------------------------------------------------------------------------------*/
//Insert output file name //Insert output file name
params.internal_output_file_name = "sample.dedup.bam" params.internal_output_file_name = ''
//Activate this option to use sample_id in the output file names -> e.g. sample1.dedup.bam
params.internal_output_sampleid = true
/*-----------------------------------------------------------------------------------------------------------------------------
OUTPUT STATS OPTION -> --output-stats=[PREFIX]
-------------------------------------------------------------------------------------------------------------------------------*/
//Enter the prefix
params.internal_output_stats = ''
//Activate this option to use sample_id as the prefix -> e.g. sample1_edit_distance
params.internal_output_stats_sampleid = true
/*-----------------------------------------------------------------------------------------------------------------------------*/
// dedup reusable component // dedup reusable component
process dedup { process dedup {
@ -91,15 +96,26 @@ process dedup {
dedup_pre_args += "-I " dedup_pre_args += "-I "
//Output_stats option //Output_stats option
if (params.internal_output_stats != null){ if (params.internal_output_stats_sampleid){
dedup_post_args += "--output-stats=$sample_id "
} else {
if (params.internal_output_stats != null){
dedup_post_args += "--output-stats=$params.internal_output_stats " dedup_post_args += "--output-stats=$params.internal_output_stats "
}
} }
//Output/ stdout option //Output/ stdout option
if (params.internal_output_file_name != null){ //TODO -> figure out how to get rid of the space between sample id and dedup.bam
if (params.internal_output_sampleid){
dedup_post_args += "-S $sample_id .dedup.bam "
}else {
if (params.internal_output_file_name != null){
dedup_post_args += "-S $params.internal_output_file_name " dedup_post_args += "-S $params.internal_output_file_name "
}
} }
// Displays the umi_tools command line to check for mistakes // Displays the umi_tools command line to check for mistakes
println dedup_pre_args println dedup_pre_args
println dedup_post_args println dedup_post_args
@ -113,3 +129,9 @@ process dedup {
//fileName=`basename $bam` //fileName=`basename $bam`
//sampleName="\${fileName%.Aligned.sortedByCoord.out.bam}" //sampleName="\${fileName%.Aligned.sortedByCoord.out.bam}"
//umi_tools dedup --umi-separator=":" -I $bam -S \${sampleName}.dedup.bam --output-stats=\${sampleName} //umi_tools dedup --umi-separator=":" -I $bam -S \${sampleName}.dedup.bam --output-stats=\${sampleName}
/*
Replace by:
//umi_tools dedup --umi-separator=":" -I $bam -S \${sample_id}.dedup.bam --output-stats=\${sample_id}
*/