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replace --TMP_DIR by --tmp-dir in BaseRecalibrator to close #704 #705

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2 changes: 2 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- [#693](https://github.com/SciLifeLab/Sarek/pull/693) - Qualimap bamQC is now ran after mapping and after recalibration for better QC
- [#700](https://github.com/SciLifeLab/Sarek/pull/700) - Update GATK to `4.0.9.0`
- [#702](https://github.com/SciLifeLab/Sarek/pull/702) - update FastQC to `0.11.8`
- [#705](https://github.com/SciLifeLab/Sarek/pull/705) - Change `--TMP_DIR` by `--tmp-dir` for GATK `4.0.9.0` BaseRecalibrator

### `Fixed`

Expand All @@ -34,6 +35,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- [#679](https://github.com/SciLifeLab/Sarek/pull/679) - Add publishDirMode for `germlineVC.nf`
- [#700](https://github.com/SciLifeLab/Sarek/pull/700) - Fix [#699](https://github.com/SciLifeLab/Sarek/issues/699) missing DP in the FORMAT column VCFs for MuTect2
- [#702](https://github.com/SciLifeLab/Sarek/pull/702) - Fix [#701](https://github.com/SciLifeLab/Sarek/issues/701)
- [#705](https://github.com/SciLifeLab/Sarek/pull/705) - Fix [#704](https://github.com/SciLifeLab/Sarek/issues/704)

## [2.2.1] - 2018-10-04

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6 changes: 3 additions & 3 deletions main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -352,7 +352,7 @@ process CreateRecalibrationTable {
BaseRecalibrator \
--input ${bam} \
--output ${idSample}.recal.table \
--TMP_DIR /tmp \
--tmp-dir /tmp \
-R ${genomeFile} \
-L ${intervals} \
--known-sites ${dbsnp} \
Expand Down Expand Up @@ -418,8 +418,8 @@ process RecalibrateBam {
--input ${bam} \
--output ${idSample}.recal.bam \
-L ${intervals} \
--create-output-bam-index true \
--bqsr-recal-file ${recalibrationReport}
--create-output-bam-index true \
--bqsr-recal-file ${recalibrationReport}
"""
}
// Creating a TSV file to restart from this step
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