mirror of
https://github.com/MillironX/nf-core_modules.git
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137 lines
No EOL
5 KiB
Text
137 lines
No EOL
5 KiB
Text
#!/usr/bin/env nextflow
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// Specify DSL2
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nextflow.preview.dsl = 2
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// Include NfUtils
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params.classpath = "umi_tools/groovy/NfUtils.groovy"
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Class groovyClass = new GroovyClassLoader(getClass().getClassLoader()).parseClass(new File(params.classpath));
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GroovyObject nfUtils = (GroovyObject) groovyClass.newInstance();
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// Define internal params
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module_name = 'dedup'
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// Local default params
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params.internal_outdir = 'results'
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params.internal_process_name = 'dedup'
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// Check for internal parameter overrides
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nfUtils.check_internal_overrides(module_name, params)
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/*-------------------------------------------------> DEDUP OPTIONS <-----------------------------------------------------*/
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/*-----------------------------------------------------------------------------------------------------------------------------
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EXTRACT BARCODE OPTION -> --extract-umi-method
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-------------------------------------------------------------------------------------------------------------------------------*/
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//Default extract barcode -> Barcodes are contained at the end of the read separated as specified with --umi-separator option
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//Enter the character that corresponds to the UMI separator
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params.internal_umi_separator = ':'
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/*-----------------------------------------------------------------------------------------------------------------------------*/
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//Barcodes contained in a tag(s) -> --extract-umi-method=tag
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params.internal_extract_method_tag = false
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// IF params.internal_extract_method_tag = true -> choose between the 6 options below
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//Umi tag options
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//--umi-tag=[TAG], --umi-tag-split=[SPLIT], --umi-tag-delimiter=[DELIMITER]
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//Select tag, split ot delimiter
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params.internal_umi_tag_active = false
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params.internal_umi_tag_split_active = false
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params.internal_umi_tag_delim_active = false
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//If one set to true, insert tag, split or delimiter in the param below
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params.internal_umi_tag = ''
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//Cell tag options
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//--umi-tag=[TAG], --umi-tag-split=[SPLIT], --umi-tag-delimiter=[DELIMITER]
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//Select tag, split ot delimiter
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params.internal_cell_tag_active = false
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params.internal_cell_tag_split_active = false
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params.internal_cell_tag_delim_active = false
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//If one set to true, insert tag, split or delimiter in the param below
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params.internal_cell_tag = ''
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/*-----------------------------------------------------------------------------------------------------------------------------
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OUTPUT OPTION -> --stdout or -S
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-------------------------------------------------------------------------------------------------------------------------------*/
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//Insert output file name
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params.internal_output_file_name = ''
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//Activate this option to use sample_id in the output file names -> e.g. sample1.dedup.bam
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params.internal_output_sampleid = true
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/*-----------------------------------------------------------------------------------------------------------------------------
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OUTPUT STATS OPTION -> --output-stats=[PREFIX]
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-------------------------------------------------------------------------------------------------------------------------------*/
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//Enter the prefix
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params.internal_output_stats = ''
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//Activate this option to use sample_id as the prefix -> e.g. sample1_edit_distance
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params.internal_output_stats_sampleid = true
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/*-----------------------------------------------------------------------------------------------------------------------------*/
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// dedup reusable component
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process dedup {
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publishDir "umi_tools/dedup/${params.internal_outdir}/${params.internal_process_name}",
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mode: "copy", overwrite: true
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input:
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tuple val(sample_id), path(bai), path(bam)
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output:
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tuple val(sample_id), path(bam), emit: dedupBam
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script:
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//Initializing dedup arguments
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dedup_pre_args = "umi_tools dedup "
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dedup_post_args = ''
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//Method used to extract barcodes
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if (params.internal_umi_separator != null){
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dedup_pre_args += "--umi-separator=\"$params.internal_umi_separator\" "
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}
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//Input args
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dedup_pre_args += "-I "
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//Output_stats option
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if (params.internal_output_stats_sampleid){
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dedup_post_args += "--output-stats=$sample_id "
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} else {
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if (params.internal_output_stats != null){
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dedup_post_args += "--output-stats=$params.internal_output_stats "
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}
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}
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//Output/ stdout option
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//TODO -> figure out how to get rid of the space between sample id and dedup.bam
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if (params.internal_output_sampleid){
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dedup_post_args += "-S $sample_id .dedup.bam "
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}else {
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if (params.internal_output_file_name != null){
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dedup_post_args += "-S $params.internal_output_file_name "
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}
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}
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// Displays the umi_tools command line to check for mistakes
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println dedup_pre_args
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println dedup_post_args
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"""
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$dedup_pre_args $bam $dedup_post_args
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"""
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}
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//fileName=`basename $bam`
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//sampleName="\${fileName%.Aligned.sortedByCoord.out.bam}"
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//umi_tools dedup --umi-separator=":" -I $bam -S \${sampleName}.dedup.bam --output-stats=\${sampleName}
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/*
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Replace by:
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//umi_tools dedup --umi-separator=":" -I $bam -S \${sample_id}.dedup.bam --output-stats=\${sample_id}
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*/ |