Commit dfb2162d authored by lrodrig1's avatar lrodrig1
Browse files

minor changes in picard markduplicates in Nextflow

parent c455a945
process PICARD_MARKDUPLICATES {
tag "picard markduplicates"
tag { "picard MarkDuplicates "}
container 'quay.io/biocontainers/picard:2.10.6--py35_0'
input:
path input
......@@ -20,4 +20,4 @@ process PICARD_MARKDUPLICATES {
METRICS_FILE=\$outputName.dedup.metrics.txt \\
ASSUME_SORTED=TRUE
"""
}
\ No newline at end of file
}
......@@ -4,10 +4,6 @@
include {
PICARD_MARKDUPLICATES
} from "../modules/picard_markduplicates"
/*
* Include for samtools_index
*/
include {
SAMTOOLS_INDEX
} from "../modules/samtools_index"
......@@ -18,12 +14,12 @@ include {
workflow SUB_PICARD_MARKDUPLICATES {
take:
input
main:
PICARD_MARKDUPLICATES(input)
SAMTOOLS_INDEX(PICARD_MARKDUPLICATES.out.alignments)
emit:
alignments = SAMTOOLS_INDEX.out
metrics = PICARD_MARKDUPLICATES.out.metrics
}
\ No newline at end of file
}
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