Merge requests · biowdl / tasks

Set additional cpus for vardict

!101 · created Mar 21, 2019 by Ruben Vorderman develop
- MERGED
- 0
updated Mar 25, 2019
add bamFile input to scatterregions

!100 · created Mar 18, 2019 by Ruben Vorderman develop
- MERGED
- 0
updated Mar 19, 2019
Add copy

!99 · created Mar 12, 2019 by Ruben Vorderman develop
- MERGED
- 0
updated Mar 13, 2019
docker added for somatic variantcallers

!98 · created Mar 05, 2019 by Ruben Vorderman develop
- MERGED
- 0
updated Mar 05, 2019
Work with python slim containers to perform python script tasks.

!96 · created Feb 25, 2019 by Ruben Vorderman develop
- MERGED
- 0
updated Feb 25, 2019
Containerize tasks for RNA-seq

!97 · created Feb 25, 2019 by Ruben Vorderman develop
- MERGED
- 2
updated Feb 26, 2019
Containerize gffread and cpat

!94 · created Feb 22, 2019 by Ruben Vorderman develop
- MERGED
- 2
updated Feb 25, 2019
Dockerize GATK. Scattering now works with containers. Tabix another docker image.

!92 · created Feb 20, 2019 by Ruben Vorderman develop
- MERGED
- 9
updated Feb 21, 2019
add hisat2 task

!91 · created Feb 20, 2019 by Ruben Vorderman develop
- MERGED
- 0
updated Feb 20, 2019
some clean up

!95 · created Feb 22, 2019 by Ruben Vorderman develop
- MERGED
- 1
updated Feb 25, 2019
add docker for extract adapters, catadapt and fastqc

!88 · created Feb 08, 2019 by Ruben Vorderman develop
- MERGED
- 0
updated Feb 11, 2019
Move all picard tasks to containers.

!90 · created Feb 19, 2019 by Ruben Vorderman develop
- MERGED
- 0
updated Feb 19, 2019
allow for additional annotations to be added into mergecounts output

!89 · created Feb 14, 2019 by Ruben Vorderman develop
- MERGED
- 1
updated Feb 25, 2019
Saner input for cutadapt

!87 · created Feb 01, 2019 by Ruben Vorderman develop
- MERGED
- 0
updated Feb 04, 2019
Add docker for samtools and STAR

!86 · created Feb 01, 2019 by Ruben Vorderman develop
- MERGED
- 0
updated Feb 01, 2019
Make tasks suitable for running against relative paths.

!85 · created Jan 08, 2019 by Ruben Vorderman develop
- MERGED
- 0
updated Jan 08, 2019
add stringtie merge

!83 · created Dec 12, 2018 by Ruben Vorderman develop
- MERGED
- 0
updated Dec 12, 2018
Allow stringtie to skip novel transcripts

!84 · created Dec 13, 2018 by Ruben Vorderman develop
- MERGED
- 0
updated Dec 13, 2018
add outSAMunmapped to star

!81 · created Dec 06, 2018 by Ruben Vorderman develop
- MERGED
- 0
updated Feb 08, 2019
Adapt sane defaults for human analysis.

!82 · created Dec 06, 2018 by Ruben Vorderman develop
- MERGED
- 0
updated Dec 07, 2018