tasks merge requestshttps://git.lumc.nl/biowdl/tasks/-/merge_requests2018-05-17T12:23:28+02:00https://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/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/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/46fix outputs for metrics picard metrics2018-08-17T10:54:51+02:00Ruben Vordermanfix outputs for metrics picard metrics*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/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/99Add copy2019-03-13T09:27:52+01:00Ruben VordermanAdd copy*Created by: DavyCats*
*Created by: DavyCats*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/86Add docker for samtools and STAR2019-02-01T14:28:00+01:00Ruben VordermanAdd docker for samtools and STAR*Created by: DavyCats*
*Created by: DavyCats*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/98docker added for somatic variantcallers2019-03-05T15:31:23+01:00Ruben Vordermandocker added for somatic variantcallers*Created by: DavyCats*
*Created by: DavyCats*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/94Containerize gffread and cpat2019-02-25T12:47:09+01:00Ruben VordermanContainerize gffread and cpatDepends on https://github.com/BioContainers/containers/pull/310Depends on https://github.com/BioContainers/containers/pull/310https://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/95some clean up2019-02-25T10:05:22+01:00Ruben Vordermansome clean up*Created by: DavyCats*
*Created by: DavyCats*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/96Work with python slim containers to perform python script tasks.2019-02-25T13:09:05+01:00Ruben VordermanWork with python slim containers to perform python script tasks.https://git.lumc.nl/biowdl/tasks/-/merge_requests/87Saner input for cutadapt2019-02-04T09:06:55+01:00Ruben VordermanSaner input for cutadaptIt is ridiculous to use some sort of struct with md5 support where we instead can use a simple read1 and read2. Especially since we do not use the md5s here.
This removes an import from the task, so it can be used as a standalone file...It is ridiculous to use some sort of struct with md5 support where we instead can use a simple read1 and read2. Especially since we do not use the md5s here.
This removes an import from the task, so it can be used as a standalone file by other users.https://git.lumc.nl/biowdl/tasks/-/merge_requests/91add hisat2 task2019-02-20T16:12:17+01:00Ruben Vordermanadd hisat2 task*Created by: DavyCats*
*Created by: DavyCats*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/101Set additional cpus for vardict2019-03-25T08:36:45+01:00Ruben VordermanSet additional cpus for vardict*Created by: DavyCats*
Since there are some pipes in the vardict command, we should really be reserving additional cpus.*Created by: DavyCats*
Since there are some pipes in the vardict command, we should really be reserving additional cpus.https://git.lumc.nl/biowdl/tasks/-/merge_requests/88add docker for extract adapters, catadapt and fastqc2019-02-11T15:18:20+01:00Ruben Vordermanadd docker for extract adapters, catadapt and fastqc*Created by: DavyCats*
*Created by: DavyCats*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/97Containerize tasks for RNA-seq2019-02-26T15:17:23+01:00Ruben VordermanContainerize tasks for RNA-seqhttps://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*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/100add bamFile input to scatterregions2019-03-19T08:37:34+01:00Ruben Vordermanadd bamFile input to scatterregions*Created by: DavyCats*
*Created by: DavyCats*