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luslab-umitools | Renamed params and changed relative paths
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parent
ff0265fda4
commit
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2 changed files with 10 additions and 9 deletions
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@ -1,25 +1,26 @@
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#!/usr/bin/env nextflow
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#!/usr/bin/env nextflow
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// Include NfUtils
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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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Class groovyClass = new GroovyClassLoader(getClass().getClassLoader()).parseClass(new File(params.classpath));
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GroovyObject nfUtils = (GroovyObject) groovyClass.newInstance();
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GroovyObject nfUtils = (GroovyObject) groovyClass.newInstance();
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// Define internal params
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// Define internal params
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module_name = 'umitools'
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module_name = 'dedup'
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// Specify DSL2
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// Specify DSL2
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nextflow.preview.dsl = 2
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nextflow.preview.dsl = 2
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// Local default params
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// Local default params
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params.internal_outdir = params.outdir
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params.internal_outdir = 'results'
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params.internal_process_name = 'umitools'
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params.internal_process_name = 'dedup'
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// Check for internal parameter overrides
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// Check for internal parameter overrides
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nfUtils.check_internal_overrides(module_name, params)
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nfUtils.check_internal_overrides(module_name, params)
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// dedup reusable component
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// dedup reusable component
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process umi_tools {
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process dedup {
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publishDir "${params.internal_outdir}/${params.internal_process_name}",
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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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mode: "copy", overwrite: true
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input:
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input:
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@ -4,12 +4,12 @@
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nextflow.preview.dsl=2
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nextflow.preview.dsl=2
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// Log
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// Log
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log.info ("Starting test pipeline for BAM deduplication")
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log.info ("Starting test for BAM deduplication")
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/* Module inclusions
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/* Module inclusions
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--------------------------------------------------------------------------------------*/
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--------------------------------------------------------------------------------------*/
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include umi_tools from './umi-tools.nf'
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include dedup from '../main.nf'
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/*------------------------------------------------------------------------------------*/
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/*------------------------------------------------------------------------------------*/
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/* Define input channels
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/* Define input channels
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@ -52,8 +52,8 @@ Channel
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workflow {
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workflow {
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// Run dedup
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// Run dedup
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umi_tools( ch_test_meta_bambai )
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dedup ( ch_test_meta_bambai )
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// Collect file names and view output
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// Collect file names and view output
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umi_tools.out.dedupBam | view
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dedup.out.dedupBam | view
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}
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}
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