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Cnv for real now#513

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FriederikeHanssen merged 47 commits intonf-core:devfrom
FriederikeHanssen:cnv_for_real_now
Apr 14, 2022
Merged

Cnv for real now#513
FriederikeHanssen merged 47 commits intonf-core:devfrom
FriederikeHanssen:cnv_for_real_now

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@FriederikeHanssen FriederikeHanssen commented Mar 25, 2022

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 you've added a new tool - add to the software_versions process and a regex to scrape_software_versions.py
    • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
    • If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint .).
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@FriederikeHanssen
Add in controlfreec sw
c894353
@FriederikeHanssen
nf-core update mpileup
3358c23
@FriederikeHanssen
first controlfreec version
98c0ddc
@FriederikeHanssen
install controlfreec again with significance script
2f51ecc
@FriederikeHanssen
add controlfreec plotting modules
5f070bf
@FriederikeHanssen
Install freec2circos
44a1a37
@FriederikeHanssen
Work on pari contronlfreec implementation to get tests to pass
c0473a9
@FriederikeHanssen
First running version of ControlFreec
ffe76cd
@FriederikeHanssen
nf-core modules update freec to fix typo
245c1d9
@FriederikeHanssen
fix manta-strelka combination output channel name
be78070
@FriederikeHanssen
add nextflow config with test args for freec
241ef86
@FriederikeHanssen
Fix StrelkaBP input mapping
577cff8
@FriederikeHanssen
Add StrelkaBP tests
a36a986
@FriederikeHanssen
Add controlfreec paired conf
20667a7
@FriederikeHanssen
Copy controlfreec map :crying:
0a33326
@FriederikeHanssen
same quotes, same spaces
afda89c
@FriederikeHanssen
Add tumor only controlfreec (can't test, as test data won't pass)
a7ce499
@FriederikeHanssen
Make controlfreec workflow agnostic to paired or single input
6ab729e
@FriederikeHanssen
add required cf input to tumor vc workflow
47e0497
@FriederikeHanssen
Adapt fodler structure to use controlfreec subworkflow
163c154
@FriederikeHanssen
nf-core modules update -all
6390a5d
@FriederikeHanssen
nf-core modules update -all
fa6de98
@FriederikeHanssen
prettier
817d718
@FriederikeHanssen
tests pass
50b1dda
FriederikeHanssen
FriederikeHanssen commented Apr 11, 2022
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Comment thread subworkflows/nf-core/variantcalling/controlfreec/main.nf Outdated
@FriederikeHanssen FriederikeHanssen marked this pull request as ready for review April 14, 2022 06:58
@FriederikeHanssen
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FriederikeHanssen commented Apr 14, 2022

Just fixing the CF test now.

maxulysse
maxulysse reviewed Apr 14, 2022
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Comment thread .github/workflows/ci.yml
maxulysse
maxulysse reviewed Apr 14, 2022
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Comment thread conf/modules.config Outdated
maxulysse
maxulysse reviewed Apr 14, 2022
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Comment thread conf/modules.config
maxulysse
maxulysse reviewed Apr 14, 2022
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Comment thread nextflow.config
FriederikeHanssen and others added 2 commits April 14, 2022 10:02
@FriederikeHanssen
Fix output paths
3351d2a
@FriederikeHanssen @maxulysse
Update conf/modules.config
97b0999 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
maxulysse
maxulysse reviewed Apr 14, 2022
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Comment thread subworkflows/local/prepare_genome.nf Outdated
maxulysse
maxulysse approved these changes Apr 14, 2022
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Love it <3

maxulysse
maxulysse reviewed Apr 14, 2022
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Comment thread nextflow_schema.json Outdated
maxulysse
maxulysse reviewed Apr 14, 2022
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Comment thread nextflow_schema.json
@FriederikeHanssen
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FriederikeHanssen commented Apr 14, 2022

Still trying to track down the problems Nick had with strelka

@FriederikeHanssen
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FriederikeHanssen commented Apr 14, 2022

nf-core lint fails on ascat module lcoally, I started adapting it for the upstream fix so i would like to leave it as is

@FriederikeHanssen FriederikeHanssen merged commit 5000c94 into nf-core:dev Apr 14, 2022
@FriederikeHanssen FriederikeHanssen deleted the cnv_for_real_now branch July 10, 2023 19:00
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@FriederikeHanssen @maxulysse
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