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Add more time for DamageProfiler on large ref genomes #176

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Merged
apeltzer merged 5 commits into from
Apr 10, 2019
Merged

Add more time for DamageProfiler on large ref genomes #176

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670fd3a
Add better base config for large ref data (DMGProfiler)
apeltzer Mar 13, 2019
da0b5c2
Bump Changelog [skip ci]
apeltzer Mar 13, 2019
93fdf72
Add extra time for bwa index
apeltzer Mar 19, 2019
0b7f779
Add task defaults for large reference genomes to base config
apeltzer Apr 4, 2019
416d0fe
Merge branch 'dev' into damageprofiler-more
apeltzer Apr 10, 2019
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4 changes: 3 additions & 1 deletion CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -14,12 +14,14 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
* Merged in [nf-core/tools](https://github.com/nf-core/tools) release V1.6 template changes

### `Fixed`
* [#152](https://github.com/nf-core/eager/pull/152) - DamageProfiler errors [won't crash entire pipeline anymore](https://github.com/nf-core/eager/issues/171)
* [#176](https://github.com/nf-core/eager/pull/176) - Increase runtime for DamageProfiler on [large reference genomes](https://github.com/nf-core/eager/issues/173)
* [#172](https://github.com/nf-core/eager/pull/152) - DamageProfiler errors [won't crash entire pipeline anymore](https://github.com/nf-core/eager/issues/171)
* [#174](https://github.com/nf-core/eager/pull/190) - Publish DeDup files [properly](https://github.com/nf-core/eager/issues/183)

### `Dependencies`

* Added DeDup v0.12.4 (json support)
* Added DeDup v0.12.5 (json support)
* Added mtnucratio v0.5 (json support)
* Updated Picard 2.18.27 -> 2.19.0
* Updated GATK 4.1.0.0 -> 4.1.1.1
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6 changes: 4 additions & 2 deletions conf/base.config
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Expand Up @@ -23,14 +23,15 @@ process {
memory = { check_max( 2.GB, 'memory' ) }
cache = false
}

withName:convertBam {
cpus = { check_max(8 * task.attempt, 'cpus') }
}
withName:makeSeqDict {
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
}

withname:makeBWAIndex {
time = params.large_ref ? '12.h' : { check_max(8.h * task.attempt, 'time') }
}
withName:bwa {
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
cpus = { check_max(8 * task.attempt, 'cpus') }
Expand Down Expand Up @@ -63,6 +64,7 @@ process {

withName: damageprofiler {
errorStrategy = 'ignore'
params.large_ref ? "time = { check_max(8.h * task.attempt, 'time') }" : "time = { check_max(2.h * task.attempt, 'time') }"
}

withName: extract_unmapped_reads {
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