tasks merge requestshttps://git.lumc.nl/biowdl/tasks/-/merge_requests2018-06-13T10:11:03+02:00https://git.lumc.nl/biowdl/tasks/-/merge_requests/20fix conda command SampleConfig2018-06-13T10:11:03+02:00Ruben Vordermanfix conda command SampleConfig*Created by: DavyCats*
*Created by: DavyCats*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/17Caching related changes2018-06-12T13:04:51+02:00Ruben VordermanCaching related changes*Created by: DavyCats*
*Created by: DavyCats*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/19Switched executable2018-06-12T12:22:21+02:00Ruben VordermanSwitched executable*Created by: ffinfo*
*Created by: ffinfo*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/18Changes for QC pipeline2018-06-12T11:57:30+02:00Ruben VordermanChanges for QC pipelinehttps://git.lumc.nl/biowdl/tasks/-/merge_requests/16Centrifuge related changes2018-06-12T11:54:32+02:00Ruben VordermanCentrifuge related changes*Created by: papanikos*
Centrifuge can accept lists of files as input and this mainly addresses that.
In a workflow context this deals with the issue of merging input files (e.g. with multiple `common.concatenateTextFiles` tasks)*Created by: papanikos*
Centrifuge can accept lists of files as input and this mainly addresses that.
In a workflow context this deals with the issue of merging input files (e.g. with multiple `common.concatenateTextFiles` tasks)https://git.lumc.nl/biowdl/tasks/-/merge_requests/14add limitBAMsortRAM to STAR and make sampleConfig write to file2018-06-01T09:58:11+02:00Ruben Vordermanadd limitBAMsortRAM to STAR and make sampleConfig write to file*Created by: DavyCats*
*Created by: DavyCats*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/15Biowdl 252018-05-30T13:35:26+02:00Ruben VordermanBiowdl 25*Created by: DavyCats*
*Created by: DavyCats*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/11Changes needed for the iterative assembly pipeline2018-05-21T16:06:59+02:00Ruben VordermanChanges needed for the iterative assembly pipelinehttps://git.lumc.nl/biowdl/tasks/-/merge_requests/12Adding flash task for combining overlapping reads2018-05-17T12:23:28+02:00Ruben VordermanAdding flash task for combining overlapping reads*Created by: papanikos*
*Created by: papanikos*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/10Extra tasks required for assembly.2018-05-07T13:29:33+02:00Ruben VordermanExtra tasks required for assembly.https://git.lumc.nl/biowdl/tasks/-/merge_requests/8Run time settings and additional adjustments2018-04-17T17:47:20+02:00Ruben VordermanRun time settings and additional adjustments*Created by: DavyCats*
- add runtime settings
- don't make a new BAM file if only one is given (samtools merge), instead link
- rename gff to gtf*Created by: DavyCats*
- add runtime settings
- don't make a new BAM file if only one is given (samtools merge), instead link
- rename gff to gtfhttps://git.lumc.nl/biowdl/tasks/-/merge_requests/7add intervals option to SplitNCigarReads2018-03-29T19:44:00+02:00Ruben Vordermanadd intervals option to SplitNCigarReads*Created by: DavyCats*
*Created by: DavyCats*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/6add merge counts2018-03-29T19:42:26+02:00Ruben Vordermanadd merge counts*Created by: DavyCats*
I'm not sure if the R script is in the right place here.*Created by: DavyCats*
I'm not sure if the R script is in the right place here.https://git.lumc.nl/biowdl/tasks/-/merge_requests/4Add quantification tools2018-03-29T19:37:55+02:00Ruben VordermanAdd quantification tools*Created by: DavyCats*
*Created by: DavyCats*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/5add SplitNCigarReads2018-03-20T16:04:34+01:00Ruben Vordermanadd SplitNCigarReads*Created by: DavyCats*
*Created by: DavyCats*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/3modify definition of defaults in star.wdl2018-03-16T13:22:38+01:00Ruben Vordermanmodify definition of defaults in star.wdl*Created by: DavyCats*
*Created by: DavyCats*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/2Star2018-03-15T16:04:47+01:00Ruben VordermanStar*Created by: DavyCats*
*Created by: DavyCats*