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Add Travis CI Testing to ExoSeq #34

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Add Travis CI Testing to ExoSeq #34

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@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
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Correct small files
ba340b9
Add Kit files to summary
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Add test kit
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Add kit specific files in channels
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Add faidx to ApplyBQSR
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Use target from ch_kit_target_for_bqsr
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Add channels for target_bed
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Add changes to use picard metrics for everything
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Remove qualimap from dependencies
c5bd11a
Add HSMetrics to MultiQC report
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Connect hsmetrics channels properly
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--Qualimap
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Not really picard anymore ;-)
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remove qualimap from base.config
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Metrics fixing
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Fixing CollectMultipleMetrics GATK4.X
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Add vcf indexing
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Add igvtools / indexing for vcf files
ce88bf0
Fixing HSmetrics issues
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GATK4 requires r-base
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This works - but the plotting of MultiMetrics doesn't work due to too
ffe74ef 
small input size.
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Merge branch 'dev' into addTestingFinally
7655b9b
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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

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