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more docs #9

Merged
merged 38 commits into from
May 21, 2019
Merged

more docs #9

merged 38 commits into from
May 21, 2019

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maxulysse
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  • improve tests
  • code polishing
  • more docs

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).
  • Documentation in docs is updated
  • CHANGELOG.md is updated
  • README.md is updated

@maxulysse
more time for no_output_timeout
b0acaa1
@maxulysse
https for links
1e43ca4
@maxulysse
update usage.md + change --strelkaBP to -noStrelkaBP
f4e1f46
@maxulysse
switch for ensemblvep 96
8140a38
@maxulysse
update docs
366e72f
@maxulysse
add docs about annotation
eee21fc
@maxulysse
add docs about containers
ab14770
@maxulysse
add information about input
b2cd43d
@maxulysse
improve tests
70b784f
@maxulysse
clean up tests
3166c7e
@maxulysse
update docs on usage
dad929f
@maxulysse
add ASCAT
3862d27
@maxulysse
improve QC reports
7a66c0c
@maxulysse
update docs
ca2d4dc
@maxulysse
update process names
cc1246e
@maxulysse
switch back to vep version 95
5a30948
@maxulysse
use https file for multiple
30f75a1
@maxulysse
fix tests
c29ef66
@maxulysse
update README
3478c7a
@maxulysse
improve docs
dc3541e
@maxulysse
improve Jenkins tests
13d232f
@maxulysse
refactoring + parallelisation of ApplyBQSR
6c86ec8
@maxulysse
extend no_output_timeout
efee7d7
@maxulysse
specify tag 1.6 for nfcore/base
f053341
@maxulysse
add docs about monochrome_logs
cc4121a
@maxulysse
update script
113ca64
@maxulysse
update tests
e0a64b0
@maxulysse
add --monochrome logs for tests
64c8d45
@maxulysse
fix snpEff output
74ee480
@maxulysse
code polishing - lowercase
be2f03b
apeltzer
apeltzer approved these changes May 21, 2019
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maxulysse and others added 2 commits May 21, 2019 10:22
@maxulysse @apeltzer
Update docs/usage.md
7f4ea8f 
Co-Authored-By: Alexander Peltzer <apeltzer@users.noreply.github.com>
@maxulysse @apeltzer
Update docs/usage.md
1057b63 
Co-Authored-By: Alexander Peltzer <apeltzer@users.noreply.github.com>
@maxulysse maxulysse merged commit 77b98d3 into nf-core:dev May 21, 2019
@maxulysse maxulysse deleted the nf-core-docs branch May 21, 2019 09:34
FriederikeHanssen pushed a commit that referenced this pull request Jul 21, 2022
@nickhsmith
Merge pull request #9 from GCJMackenzie/add_vqsr_subworkflow
03909c9 
Add vqsr subworkflow
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@apeltzer apeltzer apeltzer approved these changes

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2 participants
@maxulysse @apeltzer