filter BAM for popscle, zip Souporcell intermediate files, updated or specificy libraries/software #10

royoelen · 2023-07-13T10:36:11Z

updated or specificied some libraries and software, so that the image builds again
using specific fork of Souporcell that zips the alignment files during the realignment step, greatly reducing the filesystem usage
filter the BAM files used for popscle, to only contain variants that are present in the genotype data, greatly reducing memory usage and runtime for the popscle pileup step

- updated CMAKE using the source - using the other Souporcell repo

…f the container

…in the VCF before progressing to the popscle steps

… filter

royoelen and others added 13 commits January 25, 2023 11:31

- using souporcell that we modified, and checking out correct branch

0456df4

- allow name change for some repo using allow-releaseinfo-change

7b5e29c

- updated CMAKE using the source - using the other Souporcell repo

- using correct synthax for git checkout/switch for the git version o…

c22347c

…f the container

- specifiying the DoubletDetection version

0325856

- installing openJDK 17 for Picard

24d86f9

- fixed installing jdk17

8db0d1b

- fixed early termination of script

ce89d24

- added functionality for filtering the bam file on variants present …

ae5018b

…in the VCF before progressing to the popscle steps

- fixed output directory so that it is picked up in popscle after bam…

1c1312e

… filter

- additionally creating directory to place filtered BAM file in

292199c

- add double 'and'

769fd63

- excluding all sif files

bdf0f16

- fix wildcard for popscle input

e05f545

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