tasks merge requestshttps://git.lumc.nl/biowdl/tasks/-/merge_requests2018-06-12T12:22:21+02:00https://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/22Add validatefastq2018-06-19T16:53:21+02:00Ruben VordermanAdd validatefastqhttps://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/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/18Changes for QC pipeline2018-06-12T11:57:30+02:00Ruben VordermanChanges for QC pipelinehttps://git.lumc.nl/biowdl/tasks/-/merge_requests/2Star2018-03-15T16:04:47+01:00Ruben VordermanStar*Created by: DavyCats*
*Created by: DavyCats*
https://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/9Changes for virus assembly pipeline2018-05-07T12:00:05+02:00Ruben VordermanChanges for virus assembly pipelinehttps://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/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/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/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/5add SplitNCigarReads2018-03-20T16:04:34+01:00Ruben Vordermanadd SplitNCigarReads*Created by: DavyCats*
*Created by: DavyCats*
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/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/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/13Centrifuge classify and kreport tasks2018-06-20T21:19:36+02:00Ruben VordermanCentrifuge classify and kreport tasks*Created by: papanikos*
One point to consider is handling the output of the `classify` task.
For now I opted for explicitly specifying if this should be compressed or not and handle the redirection accordingly. It works for both cases,...*Created by: papanikos*
One point to consider is handling the output of the `classify` task.
For now I opted for explicitly specifying if this should be compressed or not and handle the redirection accordingly. It works for both cases, but I am open to other suggestions if this won't do.https://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/1Add task for bowtie aligner2018-03-14T17:33:45+01:00Ruben VordermanAdd task for bowtie aligner*Created by: johnmous*
*Created by: johnmous*