Skip to content
This repository was archived by the owner on May 7, 2019. It is now read-only.

Add Travis CI Testing to ExoSeq#34

Open
apeltzer wants to merge 59 commits intodevfrom
addTestingFinally
Open

Add Travis CI Testing to ExoSeq#34
apeltzer wants to merge 59 commits intodevfrom
addTestingFinally

Conversation

@apeltzer
Copy link
Copy Markdown
Member

@apeltzer apeltzer commented Aug 9, 2018

Starting to work on adding proper testcases for ExoSeq now.

@apeltzer apeltzer added the WIP Work in progress label Aug 9, 2018
@apeltzer apeltzer self-assigned this Aug 9, 2018
@apeltzer apeltzer changed the base branch from master to dev August 14, 2018 11:29
@apeltzer apeltzer removed the WIP Work in progress label Aug 15, 2018
Alexander Peltzer and others added 27 commits August 15, 2018 10:03
Figuring out what is wrong with Travis
d47b620
Old is the new new!
695aca5
Use channels for gfasta
2a6874e
gatk-launch -> gatk
3e34dca
Handle dbsnp files as channels
5ed3471
Correct small files
ba340b9
Add Kit files to summary
5f97f6d
Add test kit
a5157d8
Add kit specific files in channels
6334d65
Add faidx to ApplyBQSR
73c78d5
Use target from ch_kit_target_for_bqsr
6337684
Add channels for target_bed
b5d1fae
Add changes to use picard metrics for everything
4dd85bb
Remove qualimap from dependencies
c5bd11a
Add HSMetrics to MultiQC report
ca17fc0
Connect hsmetrics channels properly
b9c16d5
--Qualimap
b097d7c
Not really picard anymore ;-)
16efba1
remove qualimap from base.config
d2dc21d
Metrics fixing
b061d99
Fixing CollectMultipleMetrics GATK4.X
cfd5826
Add vcf indexing
eb05b7c
Add igvtools / indexing for vcf files
ce88bf0
Fixing HSmetrics issues
3be293d
GATK4 requires r-base
9dd07d1
This works - but the plotting of MultiMetrics doesn't work due to too
ffe74ef 
small input size.
@apeltzer
Merge branch 'dev' into addTestingFinally
7655b9b
@apeltzer
Copy link
Copy Markdown
Member Author

apeltzer commented Aug 17, 2018

Couple of comments:

  • Testing Exome Kits works, but if there is no data hit you end up having a problem with Picards HSMetrics module that runs some R code on the results obtained (which you can't skip unfortunately)
  • I'm actually quite happy to switch back to QualiMap instead, after my PR in bioconda is through (require BED 3-column support in QualiMap, which was just introduced in August 2017 and therefore requiring an update of QualiMap to at least this version

Sign up for free to subscribe to this conversation on GitHub. Already have an account? Sign in.

Reviewers

No reviews

Assignees

@apeltzer apeltzer

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

1 participant

@apeltzer
⚡