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luslab-umitools | Renamed params and changed relative paths

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Candice 2020-06-01 16:41:47 +02:00
parent ff0265fda4
commit 4656667374
2 changed files with 10 additions and 9 deletions
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11
tools/umi_tools/dedup/main.nf
View file

@ -1,25 +1,26 @@
#!/usr/bin/env nextflow #!/usr/bin/env nextflow
// Include NfUtils // Include NfUtils
params.classpath = "umi_tools/groovy/NfUtils.groovy"
Class groovyClass = new GroovyClassLoader(getClass().getClassLoader()).parseClass(new File(params.classpath)); Class groovyClass = new GroovyClassLoader(getClass().getClassLoader()).parseClass(new File(params.classpath));
GroovyObject nfUtils = (GroovyObject) groovyClass.newInstance(); GroovyObject nfUtils = (GroovyObject) groovyClass.newInstance();
// Define internal params // Define internal params
module_name = 'umitools' module_name = 'dedup'
// Specify DSL2 // Specify DSL2
nextflow.preview.dsl = 2 nextflow.preview.dsl = 2
// Local default params // Local default params
params.internal_outdir = params.outdir params.internal_outdir = 'results'
params.internal_process_name = 'umitools' params.internal_process_name = 'dedup'
// Check for internal parameter overrides // Check for internal parameter overrides
nfUtils.check_internal_overrides(module_name, params) nfUtils.check_internal_overrides(module_name, params)
// dedup reusable component // dedup reusable component
process umi_tools { process dedup {
publishDir "${params.internal_outdir}/${params.internal_process_name}", publishDir "umi_tools/dedup/${params.internal_outdir}/${params.internal_process_name}",
mode: "copy", overwrite: true mode: "copy", overwrite: true
input: input:

8
tools/umi_tools/dedup/test/test.nf
View file

@ -4,12 +4,12 @@
nextflow.preview.dsl=2 nextflow.preview.dsl=2
// Log // Log
log.info ("Starting test pipeline for BAM deduplication") log.info ("Starting test for BAM deduplication")
/* Module inclusions /* Module inclusions
--------------------------------------------------------------------------------------*/ --------------------------------------------------------------------------------------*/
include umi_tools from './umi-tools.nf' include dedup from '../main.nf'
/*------------------------------------------------------------------------------------*/ /*------------------------------------------------------------------------------------*/
/* Define input channels /* Define input channels
@ -52,8 +52,8 @@ Channel
workflow { workflow {
// Run dedup // Run dedup
umi_tools( ch_test_meta_bambai ) dedup ( ch_test_meta_bambai )
// Collect file names and view output // Collect file names and view output
umi_tools.out.dedupBam | view dedup.out.dedupBam | view
} }