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Add some Variant Calling #4

Merged
merged 39 commits into from
May 3, 2019
Merged

Add some Variant Calling #4

merged 39 commits into from
May 3, 2019

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maxulysse
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  • Update allelecount to 4.0.2
  • Update GATK to 4.1.2.0
  • Update docs
  • Add HaplotypeCaller
  • Add single Strelka and single Manta

PR checklist

  • This comment contains a description of changes (with reason)
  • If you've fixed a bug or added code that should be tested, add tests!
  • Ensure the test suite passes (nextflow run . -profile test,docker).

@maxulysse
update README
7b1833d
@maxulysse
update .travis.yml
961856c
@maxulysse
add Jenkinsfile
cefd329
@maxulysse
update conda environment file
1d3c120
@maxulysse
Merge remote-tracking branch 'upstream/dev' into dev
2cdbbda
@maxulysse
update software_version collect
95d5511
@maxulysse
trying to fix travis CI
e21ce88
@maxulysse
only one env
00c7704
@maxulysse
remove pip upgrade
3be2f63
@maxulysse
remove lint
3cd9748
@maxulysse
remove lib/SarekUtils.groovy
861577c
@maxulysse
add References to .gitignore
6cc6efe
@maxulysse
lower case
e2a44dd
@maxulysse
remove picard
1f0cce6
@maxulysse
improve software versions gathering
8627fc0
@maxulysse
fix docker owner
9bc65d1
@maxulysse
update tests
806cab5
@maxulysse
sort params
a58eaa2
@maxulysse
add preprocessing
b0fb4b9
@maxulysse
improve TSV localisation
ba09b0a
@maxulysse
improve multiple TSV
3d8208a
@maxulysse
add parrallelized BaseRecalibrator
0b777d4
@maxulysse
smaller test on travisCI
76bbfaf
@maxulysse
try to fix path to data
aa8d70f
@maxulysse
include building reference when testing...
af594ad
@maxulysse
reorganize tests
f58d255
@maxulysse
reduce memory and cpus
0678229
@maxulysse
add tests
23a8cb0
@maxulysse
add flowcellLaneFromFastq function
5be3163
@maxulysse
Merge remote-tracking branch 'upstream/dev' into nf-core
ac49c66
@maxulysse maxulysse merged commit c117cba into nf-core:dev May 3, 2019
@maxulysse maxulysse deleted the nf-core_VC branch May 3, 2019 11:07
maxulysse pushed a commit that referenced this pull request Mar 6, 2020
@ggabernet
Merge pull request #4 from nf-core/dev
c9db2c6 
update dev branch
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@maxulysse