WGS-processing/yml/helper/bwamem-gatk-report-wf.yml

   1 sample: ERR1726424
   2
   3 reference:
   4   class: File
   5   format: edam:format_1929
   6   location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
   7
   8 fullintervallist:
   9   class: File
  10   location: /data-sdd/pgp/testdata/full-noalt-scattered.interval_list
  11
  12 fastq1:
  13   class: File
  14   format: edam:format_1930
  15   location: keep:c96565a96cd428fe92bf70e97488bd80+21857/ERR1726424_1.fastq/ERR1726424_1.fastq.gz
  16
  17 fastq2:
  18   class: File
  19   format: edam:format_1930
  20   location: keep:0ea6e3aaa6ead18a2cc4ba67a22939e9+25007/ERR1726424_2.fastq/ERR1726424_2.fastq.gz
  21
  22 clinvarvcf:
  23   class: File
  24   format: edam:format_3016
  25   location: keep:242ba3b9049aee86ab2c72db4f3b2822+223/38/clinvar.vcf.gz
  26
  27 reportfunc:
  28   class: File
  29   location: ../src/annotation/generatereport.py
  30
  31 headhtml:
  32   class: File
  33   format: edam:format_1964
  34   location: /data-sdd/pgp/arvados-tutorial/src/annotation/head.html
  35
  36 tailhtml:
  37   class: File
  38   format: edam:format_1964
  39   location: /data-sdd/pgp/arvados-tutorial/src/annotation/tail.html
  40
  41 scattercount: '32'
  42
  43 knownsites:
  44   class: File
  45   format: edam:format_3016
  46   location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz