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v0.2.0#42

Merged
rernst merged 131 commits intomasterfrom
develop
Jul 10, 2020
Merged

v0.2.0#42
rernst merged 131 commits intomasterfrom
develop

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@rernst rernst commented Jul 8, 2020 •
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  • Refactor code layout / style
  • New modules
    • ControlFREEC 11.5
    • GATK 3.8.1 - BaseRecalibrator, CatVariantsGVCF, CombineVariantsGVCF, GenotypeGVCFs, HaplotypeCallerGVCF
    • Manta 1.6.0
    • MultiQC 1.9
    • Picard 2.22.0 - CollectWgsMetrics
    • STARFusion 1.8.1
    • Sambamba 0.7.0 - Index
    • UCSC 377 - GenePredToBed
    • Utils - MergeFastqLanes
  • Renamed modules
    • Preseq/2.0.3/Lc_extrap.nf -> Preseq/2.0.3/LCExtrap.nf
    • Utils/mergeFastqLanes.nf -> Utils/MergeFastqLanes.nf
    • ucsc/377/genePredToBed/GenePredToBed.nf -> UCSC/377/GenePredToBed.nf
    • ucsc/377/gtfToGenePred/GtfToGenePred.nf -> UCSC/377/GtfToGenePred.nf
  • Removed modules
    • STAR-Fusion 1.8.1
    • STAR 2.6.0c
    • fgbio 1.1.0 DemuxFastqs.nf

rernst and others added 25 commits June 10, 2020 16:52
@rernst
Update Freec
05ed063
@rernst
Update freec
6744482
@rernst
Create config in process
d9678ef
refactored
19c1e25
@rernst
Fix config def
ab68a08
@rernst
Add CollectWgsMetrics
c782c51
@rernst
Multiqc compatibility
7735672
@rernst
Add MultiQC 1.9
c2af633
@rernst
Update to .gz files
1d22468
@rernst
Rename output.
fe1a616
Added controlfreec & manta
5733f26
@sawibo
Merge pull request #39 from UMCUGenetics/dev-dx
4310fbc 
Dev dx
refactor
468123f
moved -p to optionals
0843a75
refactor
5240070
refactor
d2d204f
refactor
683f2ac
refactor
7287113
refactor
fd6f74e
refactor
856727c
@rernst
Add optional_pr
75592c8
Merged Robert's ControlFREEC modules, deleted old ones.
1a3439a 
Added Manta.
Added containers for both manta & freec.
@sawibo
Merge pull request #38 from UMCUGenetics/mqc_input_fix
e45df6c 
small_fixes
@sawibo
Merge pull request #40 from UMCUGenetics/dev-manta
a9eff08 
Dev manta
@sawibo
Merge pull request #41 from UMCUGenetics/dev-dx
8be1a77 
Merge dev-dx with develop
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rernst commented Jul 8, 2020

@tilschaef
Can you move the following files / modules:
UCSC/377/GenePredToBed/GenePredToBed.nf -> UCSC/377/GenePredToBed.nf
UCSC/377/GtfToGenePred.nf -> UCSC/377/GtfToGenePred.nf

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tilschaef commented Jul 8, 2020

Yes, I will include that in my upcoming pull-request.

Dev ubec (#44)
6e9a802 
* mv files
@rernst rernst merged commit 3890843 into master Jul 10, 2020
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