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Add Sentieon possibilities to Sarek #66

Merged
merged 65 commits into from
Dec 10, 2019
Merged

Add Sentieon possibilities to Sarek #66

merged 65 commits into from
Dec 10, 2019

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maxulysse
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@maxulysse maxulysse commented Nov 14, 2019 •
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  • Add sentieon possibilities to Sarek
    • preprocessing
    • variant calling with DNAseq, DNAscope and TNscope

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: guidelines

@maxulysse
add sention for bwa mem
f3312d9
@maxulysse
disable docker and singularity
9f08533
@maxulysse
disable container
477a99f
@maxulysse
add fastaFai for bwamem
0cf67ca
@maxulysse
remove module samtools from label sentieon
c55c19f
@maxulysse
fix output from bwa mem
6a06f02
@maxulysse
fix output channel BamMapped from MapReads
aea3512
@maxulysse
set params.sentieon to null by default
b93b1f2
@maxulysse
add SentieonDedup process
313fda0
@maxulysse
fix typo
152016e
@maxulysse
add fastaFai to SentieonDedup process
962600e
@maxulysse
fix bam indexing
22f545c
@maxulysse
fix bam indexing
ea839de
@maxulysse
fix bam indexing
3419fd9
@maxulysse
add SentieonBQSR
4f6154e
@maxulysse
add label sentieon to SentieonBQSR
7e00bb2
@maxulysse
fix metrics output for SentieonBQSR
04395c7
@maxulysse
increase cpus for Sentieon BQSR
c31bf4e
@maxulysse
remove indexing
2d5f759
@maxulysse
add index for dedup
23a88b3
@maxulysse
bwa mem sentieon specific process
bc55997
@maxulysse
TSV file for sentieon Dedup
d874bd6
@maxulysse
TSV for every step for Sentieon
2ce9735
@maxulysse
recal -> deduped
babb391
@maxulysse
fix input for TSV recalibrate
bea7238
@maxulysse
enable restart from recalibrate with TSV with Sentieon
efaec9f
@maxulysse
fix sention variant calling from mapping and recalibrate
f5744e4
@maxulysse
code polishing
ee5beaf
@maxulysse
add dump tag for imput sample
88f4af3
@maxulysse
add dump tag for bamDedupedSentieon
2b6842f
@maxulysse maxulysse self-assigned this Nov 14, 2019
maxulysse
maxulysse commented Nov 14, 2019
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@maxulysse maxulysse added the enhancement New feature or request label Nov 14, 2019
@maxulysse maxulysse mentioned this pull request Nov 20, 2019
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@maxulysse
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Needs docs

@apeltzer
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Ping once you need a review!

@maxulysse
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Just one last commits with the docs and I'm ok

@maxulysse maxulysse requested a review from a team December 10, 2019 10:38
apeltzer
apeltzer approved these changes Dec 10, 2019
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Docs are getting better with each release update :-)

docs/output.md
@@ -1,72 +1,97 @@
# nf-core/sarek: Output
# nf-core/sarek: Output <!-- omit in toc -->
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Uuh! Nice :-)

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I did just read the docs of the tool you advised to try ;-)

@maxulysse maxulysse merged commit af57a10 into nf-core:dev Dec 10, 2019
@maxulysse maxulysse deleted the sentieon branch December 10, 2019 14:14
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@apeltzer apeltzer apeltzer approved these changes

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