Helper script for downstream analysis #51
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maxulysse
reviewed
Oct 21, 2019
maxulysse
reviewed
Oct 21, 2019
maxulysse
reviewed
Oct 21, 2019
maxulysse
reviewed
Oct 21, 2019
maxulysse
reviewed
Oct 21, 2019
maxulysse
reviewed
Oct 21, 2019
maxulysse
reviewed
Oct 21, 2019
maxulysse
reviewed
Oct 21, 2019
maxulysse
reviewed
Oct 21, 2019
maxulysse
reviewed
Oct 21, 2019
maxulysse
reviewed
Oct 21, 2019
maxulysse
reviewed
Oct 21, 2019
maxulysse
reviewed
Oct 21, 2019
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Looks good, just need to fix the Markdown linting ;-) |
Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>
Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>
Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>
Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>
Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>
Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>
Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>
maxulysse
reviewed
Dec 18, 2019
szilvajuhos
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Apr 24, 2020
maxulysse
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May 15, 2020
Removing nf-core#51 and moving downstream to szilvajuhos/btb-scripts
maxulysse
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May 18, 2020
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
maxulysse
pushed a commit
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May 18, 2020
Removing nf-core#51 and moving downstream to szilvajuhos/btb-scripts
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So what's your plan with this PR now? |
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Moved already to btb-scripts: szilvajuhos/btb-scripts@89f4a66 . The only thing in the diff we can consider to keep is the CPU requirement for pilepu merge https://github.com/nf-core/sarek/pull/51/files#diff-28b7bea57b04f15beeb4c1de0ee78382R2910 |
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I see, do you want to keep that, I'm making a PR now to add some tests, I can easily squeeze that in |
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Not at all, we can keep it independent of Sarek, get rid of it. |
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I meant squeezing in the 1 cpu requirement for the pileupmerge process |
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Oh, that one, yes please, squeeze in. |
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This script (and docs) helps to add RankScore annotation to VCFs, so we can load them into Scout.
PR checklist
nextflow run . -profile test,docker).nextflow run . -profile test,singularityis working, dunno what is wrong with docker (left for @maxulysse )nf-core lint .). - lint needs some config variables alsodocsis updatedCHANGELOG.mdis updatedREADME.mdis updatedLearn more about contributing: guidelines