tasks merge requestshttps://git.lumc.nl/biowdl/tasks/-/merge_requests2018-12-03T15:35:36+01:00https://git.lumc.nl/biowdl/tasks/-/merge_requests/78Macs2 biocontainer2018-12-03T15:35:36+01:00Ruben VordermanMacs2 biocontainer*Created by: johnmous*
*Created by: johnmous*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/79Update stringtie.wdl2018-12-06T10:05:59+01:00Ruben VordermanUpdate stringtie.wdl*Created by: DavyCats*
*Created by: DavyCats*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/80Add argument for filtering on MAPQ (alignment quality) for View task2018-12-05T09:07:04+01:00Ruben VordermanAdd argument for filtering on MAPQ (alignment quality) for View task*Created by: johnmous*
*Created by: johnmous*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/77Add yamltojson task.2018-11-27T16:38:07+01:00Ruben VordermanAdd yamltojson task.https://git.lumc.nl/biowdl/tasks/-/merge_requests/75Add multiqc2018-11-23T10:59:40+01:00Ruben VordermanAdd multiqchttps://git.lumc.nl/biowdl/tasks/-/merge_requests/76update docs to V0.12018-11-26T14:54:35+01:00Ruben Vordermanupdate docs to V0.1*Created by: DavyCats*
*Created by: DavyCats*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/73Add gffread task2018-11-15T16:09:07+01:00Ruben VordermanAdd gffread taskhttps://git.lumc.nl/biowdl/tasks/-/merge_requests/74add SomaticSeq2018-11-26T09:50:27+01:00Ruben Vordermanadd SomaticSeq*Created by: DavyCats*
*Created by: DavyCats*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/72Add CPAT2018-11-13T16:28:54+01:00Ruben VordermanAdd CPAThttps://git.lumc.nl/biowdl/tasks/-/merge_requests/69increase memory on bamstats2018-10-25T09:31:00+02:00Ruben Vordermanincrease memory on bamstatshttps://git.lumc.nl/biowdl/tasks/-/merge_requests/68fixed fastqc call-caching2018-10-22T12:54:05+02:00Ruben Vordermanfixed fastqc call-cachingThe variable name differed between runs, because it contained some execution folder specific stuff. This let the call-caching to fail every time.
I fixed it with a comment telling why the fix was made.
The change was tested and confi...The variable name differed between runs, because it contained some execution folder specific stuff. This let the call-caching to fail every time.
I fixed it with a comment telling why the fix was made.
The change was tested and confirmed to fix the problem.https://git.lumc.nl/biowdl/tasks/-/merge_requests/71Add gffcompare2018-11-12T15:15:56+01:00Ruben VordermanAdd gffcomparehttps://git.lumc.nl/biowdl/tasks/-/merge_requests/70Some new tasks and memory setting changes2018-11-07T09:42:49+01:00Ruben VordermanSome new tasks and memory setting changes*Created by: DavyCats*
*Created by: DavyCats*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/63remove link creation from CombineGVCFs2018-09-24T16:58:40+02:00Ruben Vordermanremove link creation from CombineGVCFs*Created by: DavyCats*
*Created by: DavyCats*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/67fix CaseControl and macs2 tasks2018-10-16T10:32:19+02:00Ruben Vordermanfix CaseControl and macs2 tasks*Created by: DavyCats*
*Created by: DavyCats*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/64Added CaseControl tool2018-09-27T11:53:13+02:00Ruben VordermanAdded CaseControl tool*Created by: ffinfo*
*Created by: ffinfo*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/65Added struct2018-10-09T09:12:12+02:00Ruben VordermanAdded struct*Created by: ffinfo*
*Created by: ffinfo*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/66Fixing names2018-10-09T10:09:03+02:00Ruben VordermanFixing names*Created by: ffinfo*
*Created by: ffinfo*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/62Add bamstats2018-09-12T12:29:13+02:00Ruben VordermanAdd bamstatshttps://git.lumc.nl/biowdl/tasks/-/merge_requests/59Fixed -U arg2018-09-03T13:54:13+02:00Ruben VordermanFixed -U arg*Created by: papanikos*
This handles the absence of unpaired reads better, so the task command is properly constructed in gams where unpairedReads might not be defined (or defined as an empty array).*Created by: papanikos*
This handles the absence of unpaired reads better, so the task command is properly constructed in gams where unpairedReads might not be defined (or defined as an empty array).