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input bam file has always the same name #665

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Oct 16, 2018
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input bam file has always the same name #665

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b94bd78
input bam file has always the same name
maxulysse Oct 15, 2018
d3889c3
update CHANGELOG [skip ci]
maxulysse Oct 16, 2018
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -11,6 +11,10 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.

- [#663](https://github.com/SciLifeLab/Sarek/pull/663) - Update `do_release.sh` script

### `Fixed`

- [#665](https://github.com/SciLifeLab/Sarek/pull/665) - Input bam file now has always the same name (whether it is from a single fastq pair or multiple) in the MarkDuplicates process, so metrics too

## [2.2.1] - 2018-10-04

### `Changed`
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8 changes: 4 additions & 4 deletions main.nf
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Expand Up @@ -233,12 +233,12 @@ process MarkDuplicates {
}

input:
set idPatient, status, idSample, file(bam) from mergedBam
set idPatient, status, idSample, file("${idSample}.bam") from mergedBam

output:
set idPatient, file("${idSample}_${status}.md.bam"), file("${idSample}_${status}.md.bai") into duplicateMarkedBams
set idPatient, status, idSample, val("${idSample}_${status}.md.bam"), val("${idSample}_${status}.md.bai") into markDuplicatesTSV
file ("${bam}.metrics") into markDuplicatesReport
file ("${idSample}.bam.metrics") into markDuplicatesReport

when: step == 'mapping' && !params.onlyQC

Expand All @@ -247,8 +247,8 @@ process MarkDuplicates {
gatk --java-options -Xmx${task.memory.toGiga()}g \
MarkDuplicates \
--MAX_RECORDS_IN_RAM 50000 \
--INPUT ${bam} \
--METRICS_FILE ${bam}.metrics \
--INPUT ${idSample}.bam \
--METRICS_FILE ${idSample}.bam.metrics \
--TMP_DIR . \
--ASSUME_SORT_ORDER coordinate \
--CREATE_INDEX true \
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