tasks merge requestshttps://git.lumc.nl/biowdl/tasks/-/merge_requests2018-12-13T14:53:10+01:00https://git.lumc.nl/biowdl/tasks/-/merge_requests/84Allow stringtie to skip novel transcripts2018-12-13T14:53:10+01:00Ruben VordermanAllow stringtie to skip novel transcripts*Created by: DavyCats*
*Created by: DavyCats*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/85Make tasks suitable for running against relative paths.2019-01-08T13:55:27+01:00Ruben VordermanMake tasks suitable for running against relative paths.Many paths were using string instead of file.Many paths were using string instead of file.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/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/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/89allow for additional annotations to be added into mergecounts output2019-02-25T10:05:26+01:00Ruben Vordermanallow for additional annotations to be added into mergecounts output*Created by: DavyCats*
*Created by: DavyCats*
https://git.lumc.nl/biowdl/tasks/-/merge_requests/90Move all picard tasks to containers.2019-02-19T16:34:08+01:00Ruben VordermanMove all picard tasks to containers.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/92Dockerize GATK. Scattering now works with containers. Tabix another docker im...2019-02-21T13:25:46+01:00Ruben VordermanDockerize GATK. Scattering now works with containers. Tabix another docker image.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/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/97Containerize tasks for RNA-seq2019-02-26T15:17:23+01:00Ruben VordermanContainerize tasks for RNA-seqhttps://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/99Add copy2019-03-13T09:27:52+01:00Ruben VordermanAdd copy*Created by: DavyCats*
*Created by: DavyCats*
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*
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.