Code

Add workflow to merge VCFs#6

Code

Merged

amstilp merged 34 commits intomainUW-GAC/primed-file-conversion:mainfrom merge-vcf-workflowUW-GAC/primed-file-conversion:merge-vcf-workflowCopy head branch name to clipboardNov 20, 2024

+163-9

Commits

Commits on Nov 14, 2024

• Add beginning workflow to merge bcf files

  Show description for c9a1c38
  amstilp

  committed
  c9a1c38

• Allow merging to be done for separate sets of files in parallel

  Show description for 3cd7ebd
  amstilp

  committed
  3cd7ebd

Commits on Nov 15, 2024

• Switch to actually merging vcf files

  Show description for 6d35ef5
  amstilp

  committed
  6d35ef5

Commits on Nov 18, 2024

• Add disk size and memory inputs for merge_vcf task

  amstilp

  committed
  e372dad

• Register workflow in .dockstore file

  amstilp

  committed
  cb12b6f

• Try adding some debugging statements

  Show description for c55d930
  amstilp

  committed
  c55d930

• Try not creating index files

  Show description for 507e1f2
  amstilp

  committed
  507e1f2

• Create index files again

  Show description for c709537
  amstilp

  committed
  c709537

• Add debugging ls statement

  amstilp

  committed
  98821e8

• More detail in ls debugging statement

  amstilp

  committed
  30d7734

• Check username for debugging

  amstilp

  committed
  08022fc

• Specify the name of the output index file

  Show description for 6dd9bad
  amstilp

  committed
  6dd9bad

• Try specifying index file along with vcf in list of files to combine

  amstilp

  committed
  043123d

• Do not require indexes when merging

  Show description for 04ad109
  amstilp

  committed
  04ad109

• Actually switch the docker image...

  amstilp

  committed
  c8f3fb6

• Do not look for index file output

  Show description for 7fbdbab
  amstilp

  committed
  7fbdbab

• Add debugging ls and remove md5sum output

  amstilp

  committed
  7d67c71

• More debugging statements

  amstilp

  committed
  54f2423

• Remove output type argument from bcftools merge

  Show description for fd05a12
  amstilp

  committed
  fd05a12

• Fix how output prefix is specified in bcftools merge call

  Show description for 8dd1de4
  amstilp

  committed
  8dd1de4

Commits on Nov 19, 2024

• Add debugging print statement

  amstilp

  committed
  ddc8307

• Fix out_file to use tilde instead of dollar sign

  amstilp

  committed
  0298482

• Create and save index file for merged vcf also

  amstilp

  committed
  5d15f70

• Change argument for writing index

  amstilp

  committed
  b7bf31d

• Add argument to set missing genotypes to ref

  amstilp

  committed
  56951d9

• Create index files before merging

  amstilp

  committed
  3027ba2

• Create index file name from input, not vcf file path

  Show description for 87dadac
  amstilp

  committed
  87dadac

Commits on Nov 20, 2024

• Remove boolean create_index_files input

  Show description for 4d30f73
  amstilp

  committed
  4d30f73

• Add catch-all argument for users to specify merge options

  Show description for 371238a
  amstilp

  committed
  371238a

• Add WDL to womtool CI

  amstilp

  committed
  611ad3e

• Order WDLs in CI alphabetically

  amstilp

  committed
  d83a228

• Update README

  amstilp

  committed
  5d1a732

• Change input to vcf_files intsead of files_to_merge

  amstilp

  committed
  0bcd03f

• Specify optional input in create_index_file

  Show description for c423794
  amstilp

  committed
  c423794