luslab-umitools | Added basic options to dedup tool in umi_tools

This commit is contained in:
Candice 2020-06-02 17:23:54 +02:00
parent 4656667374
commit 6970d25b59

View file

@ -1,5 +1,8 @@
#!/usr/bin/env nextflow
// Specify DSL2
nextflow.preview.dsl = 2
// Include NfUtils
params.classpath = "umi_tools/groovy/NfUtils.groovy"
Class groovyClass = new GroovyClassLoader(getClass().getClassLoader()).parseClass(new File(params.classpath));
@ -8,9 +11,6 @@ GroovyObject nfUtils = (GroovyObject) groovyClass.newInstance();
// Define internal params
module_name = 'dedup'
// Specify DSL2
nextflow.preview.dsl = 2
// Local default params
params.internal_outdir = 'results'
params.internal_process_name = 'dedup'
@ -18,6 +18,53 @@ params.internal_process_name = 'dedup'
// Check for internal parameter overrides
nfUtils.check_internal_overrides(module_name, params)
/*-------------------------------------------------> DEDUP OPTIONS <-----------------------------------------------------*/
/*-----------------------------------------------------------------------------------------------------------------------------
OUTPUT STATS OPTION -> --output-stats=[PREFIX]
-------------------------------------------------------------------------------------------------------------------------------*/
//Enter the prefix
params.internal_output_stats = 'sample'
/*-----------------------------------------------------------------------------------------------------------------------------
EXTRACT BARCODE OPTION -> --extract-umi-method
-------------------------------------------------------------------------------------------------------------------------------*/
//Default extract barcode -> Barcodes are contained at the end of the read separated as specified with --umi-separator option
//Enter the character that corresponds to the UMI separator
params.internal_umi_separator = ':'
/*-----------------------------------------------------------------------------------------------------------------------------*/
//Barcodes contained in a tag(s) -> --extract-umi-method=tag
params.internal_extract_method_tag = false
// IF params.internal_extract_method_tag = true -> choose between the 6 options below
//Umi tag options
//--umi-tag=[TAG], --umi-tag-split=[SPLIT], --umi-tag-delimiter=[DELIMITER]
//Select tag, split ot delimiter
params.internal_umi_tag_active = false
params.internal_umi_tag_split_active = false
params.internal_umi_tag_delim_active = false
//If one set to true, insert tag, split or delimiter in the param below
params.internal_umi_tag = ''
//Cell tag options
//--umi-tag=[TAG], --umi-tag-split=[SPLIT], --umi-tag-delimiter=[DELIMITER]
//Select tag, split ot delimiter
params.internal_cell_tag_active = false
params.internal_cell_tag_split_active = false
params.internal_cell_tag_delim_active = false
//If one set to true, insert tag, split or delimiter in the param below
params.internal_cell_tag = ''
/*-----------------------------------------------------------------------------------------------------------------------------
OUTPUT OPTION -> --stdout or -S
-------------------------------------------------------------------------------------------------------------------------------*/
//Insert output file name
params.internal_output_file_name = "sample.dedup.bam"
// dedup reusable component
process dedup {
publishDir "umi_tools/dedup/${params.internal_outdir}/${params.internal_process_name}",
@ -30,9 +77,39 @@ process dedup {
tuple val(sample_id), path(bam), emit: dedupBam
script:
//Initializing dedup arguments
dedup_pre_args = "umi_tools dedup "
dedup_post_args = ''
//Method used to extract barcodes
if (params.internal_umi_separator != null){
dedup_pre_args += "--umi-separator=\"$params.internal_umi_separator\" "
}
//Input args
dedup_pre_args += "-I "
//Output_stats option
if (params.internal_output_stats != null){
dedup_post_args += "--output-stats=$params.internal_output_stats "
}
//Output/ stdout option
if (params.internal_output_file_name != null){
dedup_post_args += "-S $params.internal_output_file_name "
}
// Displays the umi_tools command line to check for mistakes
println dedup_pre_args
println dedup_post_args
"""
fileName=`basename $bam`
sampleName="\${fileName%.Aligned.sortedByCoord.out.bam}"
umi_tools dedup --umi-separator=":" -I $bam -S \${sampleName}.dedup.bam --output-stats=\${sampleName}
$dedup_pre_args $bam $dedup_post_args
"""
}
//fileName=`basename $bam`
//sampleName="\${fileName%.Aligned.sortedByCoord.out.bam}"
//umi_tools dedup --umi-separator=":" -I $bam -S \${sampleName}.dedup.bam --output-stats=\${sampleName}