luslab-umitools | Renamed umi-tools.nf to dedup.nf

tools/umi_tools/dedup/dedup.nf

@@ -0,0 +1,37 @@
+#!/usr/bin/env nextflow
+
+// Include NfUtils
+Class groovyClass = new GroovyClassLoader(getClass().getClassLoader()).parseClass(new File(params.classpath));
+GroovyObject nfUtils = (GroovyObject) groovyClass.newInstance();
+
+// Define internal params
+module_name = 'umitools'
+
+// Specify DSL2
+nextflow.preview.dsl = 2
+
+// Local default params
+params.internal_outdir = params.outdir
+params.internal_process_name = 'umitools'
+
+// Check for internal parameter overrides
+nfUtils.check_internal_overrides(module_name, params)
+
+// dedup reusable component
+process umi_tools {
+    publishDir "${params.internal_outdir}/${params.internal_process_name}",
+        mode: "copy", overwrite: true
+
+    input:
+      tuple val(sample_id), path(bai), path(bam)
+       
+    output:
+      tuple val(sample_id), path(bam), emit: dedupBam
+
+    script:
+    """
+    fileName=`basename $bam`
+    sampleName="\${fileName%.Aligned.sortedByCoord.out.bam}"
+    umi_tools dedup --umi-separator=":" -I $bam -S \${sampleName}.dedup.bam --output-stats=\${sampleName}
+    """
+}