tasks merge requestshttps://git.lumc.nl/biowdl/tasks/-/merge_requests2018-07-31T10:18:23+02:00https://git.lumc.nl/biowdl/tasks/-/merge_requests/40Add Various new tasks2018-07-31T10:18:23+02:00Ruben VordermanAdd Various new tasks*Created by: DavyCats*
- [x] vcfStats
- [x] MuTect2
- [x] Strelka
- [x] VarDict*Created by: DavyCats*
- [x] vcfStats
- [x] MuTect2
- [x] Strelka
- [x] VarDicthttps://git.lumc.nl/biowdl/tasks/-/merge_requests/39Macs22018-07-26T16:03:27+02:00Ruben VordermanMacs2*Created by: johnmous*
*Created by: johnmous*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/38Macs22018-07-26T15:36:38+02:00Ruben VordermanMacs2*Created by: johnmous*
*Created by: johnmous*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/37Add samplesheet structs2018-08-22T13:34:35+02:00Ruben VordermanAdd samplesheet structshttps://git.lumc.nl/biowdl/tasks/-/merge_requests/36Make optional values mandatory where appropriate2018-07-26T11:27:18+02:00Ruben VordermanMake optional values mandatory where appropriate*Created by: DavyCats*
Since we are moving to WDL 1.0, we can now define defaults for mandatory inputs. This is better for inputs which are required and have a default since optional inputs can still be set to `null` through an input JSON.*Created by: DavyCats*
Since we are moving to WDL 1.0, we can now define defaults for mandatory inputs. This is better for inputs which are required and have a default since optional inputs can still be set to `null` through an input JSON.https://git.lumc.nl/biowdl/tasks/-/merge_requests/35Add missing rquired inputs2018-07-24T09:05:04+02:00Ruben VordermanAdd missing rquired inputs*Created by: DavyCats*
*Created by: DavyCats*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/34Move all files to version 1.02018-07-23T15:38:24+02:00Ruben VordermanMove all files to version 1.0https://git.lumc.nl/biowdl/tasks/-/merge_requests/33fix missing space after toolcommand2018-07-23T14:34:08+02:00Ruben Vordermanfix missing space after toolcommand*Created by: DavyCats*
*Created by: DavyCats*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/32style changes and adds task to check file md52018-07-26T11:27:13+02:00Ruben Vordermanstyle changes and adds task to check file md5*Created by: DavyCats*
*Created by: DavyCats*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/31add validatevcf and validateannotation2018-07-19T09:23:32+02:00Ruben Vordermanadd validatevcf and validateannotation*Created by: DavyCats*
*Created by: DavyCats*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/30add picard metrics tools2018-07-19T09:23:20+02:00Ruben Vordermanadd picard metrics tools*Created by: DavyCats*
*Created by: DavyCats*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/29Macs22018-07-16T16:49:11+02:00Ruben VordermanMacs2*Created by: johnmous*
*Created by: johnmous*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/28Added precommand to ExtractAdaptersFastqc task2018-07-11T15:23:45+02:00Ruben VordermanAdded precommand to ExtractAdaptersFastqc task*Created by: papanikos*
*Created by: papanikos*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/27Fix typo in command2018-07-03T16:05:02+02:00Ruben VordermanFix typo in command*Created by: johnmous*
*Created by: johnmous*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/26Macs22018-07-02T16:40:49+02:00Ruben VordermanMacs2*Created by: johnmous*
*Created by: johnmous*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/25Added mkdir step2018-06-28T14:45:50+02:00Ruben VordermanAdded mkdir step*Created by: ffinfo*
*Created by: ffinfo*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/24Changes after testing2018-06-21T09:08:58+02:00Ruben VordermanChanges after testing*Created by: ffinfo*
*Created by: ffinfo*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/23Add memory runtime for validate fastq2018-06-20T13:52:43+02:00Ruben VordermanAdd memory runtime for validate fastqhttps://git.lumc.nl/biowdl/tasks/-/merge_requests/22Add validatefastq2018-06-19T16:53:21+02:00Ruben VordermanAdd validatefastqhttps://git.lumc.nl/biowdl/tasks/-/merge_requests/21Added seqstat, set minlength for cutadapt to 1.2018-06-19T10:39:24+02:00Ruben VordermanAdded seqstat, set minlength for cutadapt to 1.Also submitted issue upstream https://github.com/marcelm/cutadapt/pull/310
toolJars are now optional files as they should be.Also submitted issue upstream https://github.com/marcelm/cutadapt/pull/310
toolJars are now optional files as they should be.