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Release 2.5 pulls dev SNPEff Containers #49

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apeltzer opened this issue Oct 15, 2019 · 1 comment
Closed

Release 2.5 pulls dev SNPEff Containers #49

apeltzer opened this issue Oct 15, 2019 · 1 comment
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@maxulysse
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bug Something isn't working
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2.5.1

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@apeltzer
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https://github.com/nf-core/sarek/blob/2.5/conf/base.config
@apeltzer
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More specifically this here:

sarek/conf/base.config

Line 71 in c5fc547

container = {(params.annotation_cache && params.snpEff_cache) ? 'nfcore/sarek:dev' : "nfcore/sareksnpeff:dev.${params.genome}"}

@apeltzer apeltzer added this to the 2.5.1 milestone Oct 15, 2019
@maxulysse maxulysse self-assigned this Oct 21, 2019
@maxulysse maxulysse added the bug Something isn't working label Oct 21, 2019
@maxulysse maxulysse mentioned this issue Oct 21, 2019
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maxulysse pushed a commit to maxulysse/nf-core_sarek that referenced this issue May 18, 2020
@maxulysse
added script to help downstream analysis, adding RankScore for Scout
7acb297 
nf-core bump-version . 2.5.1

fix script name in docs

fix markdownlint

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

add patch to branch protection

use correct tag for containers close nf-core#49

update CHANGELOG

Try to fix branch protection

Update README.md

reducing CPU usage for Mpileup

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>

First time CF is working with extra pileups

First working version

Removing nf-core#51 and moving downstream to szilvajuhos/btb-scripts

Fixing some null parameters and C&P typos

yet an other version that somehow worked

remove --normal_pileup and --tumor_pileup params

update freebayes germline command

update changelog

fix --save_bam_mapped + small typos

update CHANGELOG

add step controlfreec

use nf-core header

update config

cleanup

add mappability files to igenomes

better name for tsv file

fix output directory

enable usage of - in names of tools or steps

better default for coefficientofvariation

improve help

update and reorder params

reorder and update params

update and reorder params

update docs

fix prepare_recalibration step

update CHANGELOG

Apply suggestions from code review
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