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Dsl2 variant#285

Merged
maxulysse merged 76 commits intonf-core:dsl2from
maxulysse:dsl2_variant
Oct 20, 2020
Merged

Dsl2 variant#285
maxulysse merged 76 commits intonf-core:dsl2from
maxulysse:dsl2_variant

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@maxulysse maxulysse commented Sep 29, 2020

  • Trying to get CI to work again
  • Trying to get nf-core lint . to work again
  • Getting conda to work
  • Simplifying the main container

nf-core/sarek pull request

Many thanks for contributing to nf-core/sarek!

Please fill in the appropriate checklist below (delete whatever is not relevant).
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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 .).
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  • CHANGELOG.md is updated
  • README.md is updated

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FriederikeHanssen
FriederikeHanssen reviewed Sep 29, 2020
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Comment thread environment.yml Outdated
Comment thread environment.yml Outdated
Comment thread modules/local/functions.nf
@maxulysse
MAPPING as a separate workflow
b7d3f9e
@maxulysse
MARKDUPLICATES as a module
b675300
@maxulysse
fix: process without container
3149c4c
@maxulysse
fix: --step prepare_recalibration
384c9b6
@maxulysse
fix: --skip_markduplicates
7c38825
@maxulysse
fix: typo
93a15ec
@maxulysse
add: PREPARE_RECALIBRATION as a module
6d1f534
@maxulysse
fix: test_annotation profile fix from dev
9c563c0
@maxulysse
minor code polish
334ce4a
@maxulysse
fix: restore --step variantcalling ci test
4bbc401
@maxulysse
update modules.config
b9f4d08
@maxulysse
use modules.config
5605fa8
@maxulysse
add comments on take inputs
aec9bc5
@maxulysse
improve mapping subworkflow
8bd3179
@maxulysse
improve markduplicates subworkflow
1d3ef0f
@maxulysse
improve prepare_recalibration subworkflow
cb1041c
@maxulysse
use container and conda directive
298a499
@maxulysse
improve reusability of module
ecc0912
@maxulysse
add: RECALIBRATE as a module
224c911
@maxulysse
add: RECALIBRATE as a module + code improvment
55eaf76
@maxulysse
fix: correct usage of --save_bam_mapped
271b8dd
@maxulysse maxulysse marked this pull request as draft October 8, 2020 08:12
FriederikeHanssen
FriederikeHanssen reviewed Oct 20, 2020
View reviewed changes
Comment thread modules/local/process/bwamem2_mem.nf
params.options = [:]
def options = initOptions(params.options)

environment = params.enable_conda ? "bioconda::bwa-mem2=2.0 bioconda::samtools=1.10" : null
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@FriederikeHanssen FriederikeHanssen Oct 20, 2020

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FYI: BWA-Mem2 was updated a couple of days ago to a new release 2.1. It is in conda already, but as far as I saw the biocontainers are not updated yet. Apparently, the new release reduces index size quiet a bit :)

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@maxulysse maxulysse Oct 20, 2020

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Good to know, I'll keep a look at the containers.

@maxulysse maxulysse marked this pull request as ready for review October 20, 2020 15:21
@maxulysse maxulysse merged commit 5b2935c into nf-core:dsl2 Oct 20, 2020
@maxulysse maxulysse deleted the dsl2_variant branch October 20, 2020 15:25
chelauk added a commit that referenced this pull request Jan 16, 2021
@chelauk
still reverting
d88a533 
Revert "Merge pull request #285 from MaxUlysse/dsl2_variant"

This reverts commit 5b2935c, reversing
changes made to 7f6a57e.
chelauk added a commit that referenced this pull request Jan 16, 2021
@chelauk
reverting
dd852ae 
Revert "Merge pull request #285 from MaxUlysse/dsl2_variant"

This reverts commit 5b2935c, reversing
changes made to 7f6a57e.
@maxulysse maxulysse added the DSL2 label Jan 19, 2021
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maxulysse commented Jan 26, 2021

@chelauk what happened here? I'm a bit confused

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chelauk commented Jan 26, 2021 •
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Hi @maxulysse
I am really sorry, I was playing with DSL2, and I didn't realise that I could alter the nf-core/sarek.git branch, but I could and I did I have attempted to restore it to the point where I first messed with it.
Again, my apologies.

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maxulysse commented Jan 26, 2021

@chelauk no problem at all, I made a copy of the branch in case, but I assume you have one too.

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chelauk commented Jan 26, 2021

phew! I'll make sure I don't push directly here, and do the usual pull requests if necessary. Yes I have a local copy.
thanks

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maxulysse commented Jan 26, 2021

OK, then I'll delete the copy I made, and don't worry, from my point of view, mistake is mine, that should not have been possible.

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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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@maxulysse @chelauk @FriederikeHanssen
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