hutspot merge requestshttps://git.lumc.nl/klinische-genetica/capture-lumc/hutspot/-/merge_requests2021-03-04T16:05:29+01:00https://git.lumc.nl/klinische-genetica/capture-lumc/hutspot/-/merge_requests/18Update pytest workflow code2021-03-04T16:05:29+01:00van den BergUpdate pytest workflow code* Fix deprecated pytest-workflow marks
* Increase memory for covstats task* Fix deprecated pytest-workflow marks
* Increase memory for covstats taskvan den Bergvan den Berghttps://git.lumc.nl/klinische-genetica/capture-lumc/hutspot/-/merge_requests/17Revert "Remove explicit tmp folder"2020-07-24T16:19:24+02:00van den BergRevert "Remove explicit tmp folder"This reverts commit 1b7d807f1fc7160783d10af84d50a18e9104d5acThis reverts commit 1b7d807f1fc7160783d10af84d50a18e9104d5achttps://git.lumc.nl/klinische-genetica/capture-lumc/hutspot/-/merge_requests/16Add optional bed coverage output files2020-06-26T09:02:16+02:00van den BergAdd optional bed coverage output filesvan den Bergvan den Berghttps://git.lumc.nl/klinische-genetica/capture-lumc/hutspot/-/merge_requests/15No longer merge fastq files from different read groups together2020-04-23T13:22:10+02:00van den BergNo longer merge fastq files from different read groups togetherNo longer merge the raw fastq files, but trim and map them per readgroup. The different read groups are merged in the MarkDuplicates step, which accepts multiple bam files.
This is faster because it prevents an additional read/write o...No longer merge the raw fastq files, but trim and map them per readgroup. The different read groups are merged in the MarkDuplicates step, which accepts multiple bam files.
This is faster because it prevents an additional read/write of all the raw fastq data, and because more of the pipeline can be run in parallel when there are multiple readgroups.
[] Try to fix gitlab-ci in this branchRuben VordermanRuben Vordermanhttps://git.lumc.nl/klinische-genetica/capture-lumc/hutspot/-/merge_requests/14Try to fix CI2020-04-29T07:10:37+02:00Ruben VordermanTry to fix CIhttps://git.lumc.nl/klinische-genetica/capture-lumc/hutspot/-/merge_requests/13Deprecate conda, make pipeline more general2020-01-10T11:51:11+01:00van den BergDeprecate conda, make pipeline more general1. Deprecate conda in favour of singularity
2. Convert all test cases to use conda
3. Fix a bug in the coverage calculation that was caused by singularity
4. Remove the external gatk.jar file as a dependency
5. Specify 1 or more...1. Deprecate conda in favour of singularity
2. Convert all test cases to use conda
3. Fix a bug in the coverage calculation that was caused by singularity
4. Remove the external gatk.jar file as a dependency
5. Specify 1 or more vcf files for base recalibration, instead of `ONETHOUSAND`, `HAPMAP`, `ONETHOUSAND`Ruben VordermanRuben Vordermanhttps://git.lumc.nl/klinische-genetica/capture-lumc/hutspot/-/merge_requests/12Fix typo in resource requirement.2019-12-20T09:02:52+01:00Ruben VordermanFix typo in resource requirement.https://git.lumc.nl/klinische-genetica/capture-lumc/hutspot/-/merge_requests/11Fix picard heapspace error in align rule2019-07-29T08:50:25+02:00van den BergFix picard heapspace error in align ruleIn the Singularity image for picard, the default heapsize is too small,
leading to crashes in the pipeline when the rule 'align' runs out of
heap space. The solution is to explicitly specify the heap space that
picard can use, thereby ov...In the Singularity image for picard, the default heapsize is too small,
leading to crashes in the pipeline when the rule 'align' runs out of
heap space. The solution is to explicitly specify the heap space that
picard can use, thereby overriding the default value that is set in the
Singularity image.
This issue was reported on capture-lumc-wrapper, see
https://git.lumc.nl/klinische-genetica/capture-lumc/capture-lumc-wrapper/issues/26
for details.
This change was first implemented locally for 20190715W19_11131serie114WESbatch46,
since that contained several 'SPOED' samples. This analysis ran successfully.Ruben VordermanRuben Vordermanhttps://git.lumc.nl/klinische-genetica/capture-lumc/hutspot/-/merge_requests/10Licensing2019-03-12T13:28:16+01:00Sander BollenLicensinghttps://git.lumc.nl/klinische-genetica/capture-lumc/hutspot/-/merge_requests/9Pytest workflow testing2019-02-19T17:07:49+01:00Sander BollenPytest workflow testinghttps://git.lumc.nl/klinische-genetica/capture-lumc/hutspot/-/merge_requests/8fix vcfstats conda env2019-01-21T16:07:29+01:00Sander Bollenfix vcfstats conda envhttps://git.lumc.nl/klinische-genetica/capture-lumc/hutspot/-/merge_requests/7explicitly put output of bc -l in variable.2018-09-17T17:01:55+02:00Sander Bollenexplicitly put output of bc -l in variable.Fixes check of fraction. Fixes #29Fixes check of fraction. Fixes #29https://git.lumc.nl/klinische-genetica/capture-lumc/hutspot/-/merge_requests/6Fastq data in stats2018-03-27T16:07:41+02:00Sander BollenFastq data in statsAdd fastqc reports to the stats.jsonAdd fastqc reports to the stats.jsonbowbowhttps://git.lumc.nl/klinische-genetica/capture-lumc/hutspot/-/merge_requests/5Handle cases where no regions of interest are defined (e.g. WGS)2018-03-08T10:57:22+01:00Sander BollenHandle cases where no regions of interest are defined (e.g. WGS)Addresses #10Addresses #10Colibri on API Infrabowbowhttps://git.lumc.nl/klinische-genetica/capture-lumc/hutspot/-/merge_requests/4Copy bai to bam.bai2018-03-07T15:54:41+01:00Sander BollenCopy bai to bam.baiAddresses #3 and fixes a wildcard issue in refflats.Addresses #3 and fixes a wildcard issue in refflats.Colibri on API Infrabowbowhttps://git.lumc.nl/klinische-genetica/capture-lumc/hutspot/-/merge_requests/3Vtoolscoverage2018-03-06T10:13:31+01:00Sander BollenVtoolscoverageAddresses #8Addresses #8bowbowhttps://git.lumc.nl/klinische-genetica/capture-lumc/hutspot/-/merge_requests/2Review comments2018-03-02T12:25:47+01:00Sander BollenReview commentshttps://git.lumc.nl/klinische-genetica/capture-lumc/hutspot/-/merge_requests/1WIP: Review2018-03-02T12:42:33+01:00bowWIP: ReviewAs done in [hutspot-lovd](https://git.lumc.nl/klinische-genetica/capture-lumc/hutspot-lovd), this is the review branch for the pipeline. It's *NOT* meant for merging, since all the files are gone (this is a hackish way to get line-by-lin...As done in [hutspot-lovd](https://git.lumc.nl/klinische-genetica/capture-lumc/hutspot-lovd), this is the review branch for the pipeline. It's *NOT* meant for merging, since all the files are gone (this is a hackish way to get line-by-line comments on the entire code base).Colibri on API InfraSander BollenSander Bollen