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

tools/umi_tools/dedup/main.nf

@@ -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}