Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

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

Conversation

maxulysse
Copy link
Member

  • 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
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
1 participant
@maxulysse