WGS-processing/yml/wgs-processing-wf-chr19.yml

   1 reference:
   2   class: File
   3   format: edam:format_1929
   4   location: keep:18657d75efb4afd31a14bb204d073239+13611/GRCh38_no_alt_plus_hs38d1_analysis_set.fna
   5
   6 #the difference between this and the whole genome version is that this interval list is restricted to chr19
   7 fullintervallist:
   8   class: File
   9   location: keep:380552882945f62850d298f8e86e5039+75/chr19-scattered.interval_list
  10
  11 fastqdir:
  12   class: Directory
  13   location: keep:35d4f4c5720a1e1c7b5c583cc901c3e0+3765
  14
  15 clinvarvcf:
  16   class: File
  17   format: edam:format_3016
  18   location: keep:18657d75efb4afd31a14bb204d073239+13611/clinvar.vcf.gz
  19
  20 reportfunc:
  21   class: File
  22   location: ../src/annotation/generatereport.py
  23
  24 headhtml:
  25   class: File
  26   format: edam:format_2331
  27   location: ../src/annotation/head.html
  28
  29 tailhtml:
  30   class: File
  31   format: edam:format_2331
  32   location: ../src/annotation/tail.html
  33
  34 scattercount: '20'
  35
  36 knownsites1:
  37   class: File
  38   format: edam:format_3016
  39   location: keep:18657d75efb4afd31a14bb204d073239+13611/Homo_sapiens_assembly38.dbsnp138.vcf
  40
  41 knownsites2:
  42   class: File
  43   format: edam:format_3016
  44   location: keep:18657d75efb4afd31a14bb204d073239+13611/Homo_sapiens_assembly38.known_indels.vcf.gz