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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

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f3312d9
add sention for bwa mem
maxulysse Nov 5, 2019
9f08533
disable docker and singularity
maxulysse Nov 5, 2019
477a99f
disable container
maxulysse Nov 5, 2019
0cf67ca
add fastaFai for bwamem
maxulysse Nov 5, 2019
c55c19f
remove module samtools from label sentieon
maxulysse Nov 5, 2019
6a06f02
fix output from bwa mem
maxulysse Nov 5, 2019
aea3512
fix output channel BamMapped from MapReads
maxulysse Nov 5, 2019
b93b1f2
set params.sentieon to null by default
maxulysse Nov 5, 2019
313fda0
add SentieonDedup process
maxulysse Nov 5, 2019
152016e
fix typo
maxulysse Nov 5, 2019
962600e
add fastaFai to SentieonDedup process
maxulysse Nov 5, 2019
22f545c
fix bam indexing
maxulysse Nov 5, 2019
ea839de
fix bam indexing
maxulysse Nov 5, 2019
3419fd9
fix bam indexing
maxulysse Nov 5, 2019
4f6154e
add SentieonBQSR
maxulysse Nov 5, 2019
7e00bb2
add label sentieon to SentieonBQSR
maxulysse Nov 5, 2019
04395c7
fix metrics output for SentieonBQSR
maxulysse Nov 5, 2019
c31bf4e
increase cpus for Sentieon BQSR
maxulysse Nov 8, 2019
2d5f759
remove indexing
maxulysse Nov 8, 2019
23a88b3
add index for dedup
maxulysse Nov 11, 2019
bc55997
bwa mem sentieon specific process
maxulysse Nov 12, 2019
d874bd6
TSV file for sentieon Dedup
maxulysse Nov 12, 2019
2ce9735
TSV for every step for Sentieon
maxulysse Nov 12, 2019
babb391
recal -> deduped
maxulysse Nov 12, 2019
bea7238
fix input for TSV recalibrate
maxulysse Nov 12, 2019
efaec9f
enable restart from recalibrate with TSV with Sentieon
maxulysse Nov 12, 2019
f5744e4
fix sention variant calling from mapping and recalibrate
maxulysse Nov 12, 2019
ee5beaf
code polishing
maxulysse Nov 12, 2019
88f4af3
add dump tag for imput sample
maxulysse Nov 12, 2019
2b6842f
add dump tag for bamDedupedSentieon
maxulysse Nov 12, 2019
1b979e5
code polishing
maxulysse Nov 12, 2019
60a9fb3
code polishing
maxulysse Nov 12, 2019
dc25d27
code polishing
maxulysse Nov 12, 2019
fba89d0
code polishing
maxulysse Nov 12, 2019
6f73d83
remove when statement
maxulysse Nov 12, 2019
b0f091e
fix typo
maxulysse Nov 12, 2019
1aa82a9
remove tsv for recalibrate with sentieon
maxulysse Nov 12, 2019
bbe01fb
add dnascope dnaseq
maxulysse Nov 12, 2019
2d980d8
fix dnascope
maxulysse Nov 12, 2019
f67f8f3
add TNscope process
maxulysse Nov 13, 2019
9d6c76e
fix TNscope output
maxulysse Nov 13, 2019
0aa8ebe
add pon for TNscope
maxulysse Nov 13, 2019
10ad687
add params.pon_index
maxulysse Nov 13, 2019
03332fc
add annotation for sention DNAseq, DNAscope, TNscope
maxulysse Nov 13, 2019
afc5046
add default pon_index
maxulysse Nov 13, 2019
dd7c1f8
typo
maxulysse Nov 13, 2019
0c29e69
fix typo
maxulysse Nov 13, 2019
2fe67d5
improve automatic annotation
maxulysse Nov 13, 2019
2bbc127
typo
maxulysse Nov 13, 2019
66276c3
typo
maxulysse Nov 13, 2019
fc27dd0
add condition on when statement on TNscope
maxulysse Nov 13, 2019
6d91247
clean up
maxulysse Nov 14, 2019
c23306b
code polish
maxulysse Nov 14, 2019
a85b9be
add when statement on all sentieon processes with params.sentieon
maxulysse Nov 18, 2019
b84cbc4
remove munin sentieon specific configs from config
maxulysse Nov 20, 2019
38d113e
load sarek specific config
maxulysse Nov 20, 2019
daaf48f
update path to specific config
maxulysse Nov 20, 2019
4ce48d5
Merge remote-tracking branch 'upstream/dev' into sentieon
maxulysse Dec 9, 2019
dc043d0
better comments
maxulysse Dec 9, 2019
68571f4
fix error on channel name
maxulysse Dec 9, 2019
4286ef3
fix output for MergeBamRecal
maxulysse Dec 9, 2019
77de228
fix MergeBamRecal output
maxulysse Dec 10, 2019
72fb602
fix TSV file
maxulysse Dec 10, 2019
d896596
update comments and docs
maxulysse Dec 10, 2019
c75a95b
add warning for sentieon only processes
maxulysse Dec 10, 2019
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