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Control-FREEC improvements #204

Merged
merged 34 commits into from
May 18, 2020
Merged

Control-FREEC improvements #204

merged 34 commits into from
May 18, 2020

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maxulysse
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nf-core/sarek pull request

Replace #196

Many thanks for contributing to nf-core/sarek!

Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).

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!
  • If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repo
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • Make sure your code lints (nf-core lint .).
  • Documentation in docs is updated
  • CHANGELOG.md is updated
  • README.md is updated

Learn more about contributing: CONTRIBUTING.md

@maxulysse maxulysse added the enhancement New feature or request label May 8, 2020
@maxulysse maxulysse added this to the 2.6 milestone May 8, 2020
@maxulysse maxulysse requested a review from szilvajuhos May 8, 2020 14:54
@maxulysse maxulysse marked this pull request as draft May 8, 2020 15:08
szilvajuhos
szilvajuhos reviewed May 12, 2020
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Looks perfect for me, thank you for cleaning up my clutter. Will start tests today so we can be sure it works as expected.

maxulysse
maxulysse commented May 12, 2020
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Just need to add some docs

@maxulysse maxulysse marked this pull request as ready for review May 12, 2020 07:28
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Lots of changes because I reorder and updated params in all files and docs.

maxulysse
maxulysse commented May 12, 2020
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docs/input.md Outdated Show resolved Hide resolved
maxulysse
maxulysse commented May 12, 2020
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Szilveszter Juhos and others added 18 commits May 15, 2020 10:44
@maxulysse
added script to help downstream analysis, adding RankScore for Scout
cb13187
@maxulysse
nf-core bump-version . 2.5.1
8551b2f 
fix script name in docs

fix markdownlint

fix autoMounts in singularity profile, closes nf-core#48

build 2.5.1 version of annotation containers

update CHANGELOG

Typo

Update .github/workflows/branch.yml

Update .github/workflows/branch.yml

Update README.md
@maxulysse
reducing CPU usage for Mpileup
fc1dd2f 
cleanup with meld

some docs additions

Update docs/downstream.md

Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>

Update docs/downstream.md

Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>

added extra space

Update docs/downstream.md

Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>

Update docs/downstream.md

Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>

Update docs/downstream.md

Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>

Update docs/downstream.md

Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>

Update docs/downstream.md

Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>

Update docs/downstream.md

Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>
@maxulysse
First time CF is working with extra pileups
3b11389
@maxulysse
yet an other version that somehow worked
203b756
@maxulysse
remove --normal_pileup and --tumor_pileup params
fd80e8c
@ggabernet @maxulysse
update freebayes germline command
fad7a6a
@ggabernet @maxulysse
update changelog
3929a67
@maxulysse
fix --save_bam_mapped + small typos
5a62d50
@maxulysse
update CHANGELOG
455fd06
@maxulysse
add step controlfreec
815c36e
@maxulysse
use nf-core header
fa09b3d
@maxulysse
update config
b46f4e2
@maxulysse
cleanup
5f6eabc
@maxulysse
add mappability files to igenomes
04cb2cd
@maxulysse
better name for tsv file
e5a27b4
@maxulysse
fix output directory
c514c3f
@maxulysse
enable usage of - in names of tools or steps
50a584c
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did some small rebasing to clean up the mess that was the commit history

szilvajuhos
szilvajuhos approved these changes May 18, 2020
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Looks both tests went smoothly.

@maxulysse maxulysse merged commit fdbdaac into nf-core:dev May 18, 2020
@maxulysse maxulysse deleted the ControlFREEC branch May 18, 2020 11:22
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@szilvajuhos szilvajuhos szilvajuhos approved these changes

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@maxulysse @szilvajuhos @ggabernet