merge_samplesheets.yaml

#parent folder of both sample sheets and merge script
prefix: /nfs/jbailey5/baileyweb/bailey_share
output_folder: 230101_merging/ #where output data will go
merge_script: bin/mipscripts_v0dev2.py #subfolder and file of Jeff's merging script
output_sheet: mikalayi_merged_sample_sheet.tsv #output merged sample sheet name
sample_set: JJJ #sample sets to pull from the sample sheets
probe: IBC #probes to pull from the sample sheets
samples: #samples to use - includes subfolders of the prefix folder
  - raw_data/210403_nextseq/210403_samples.tsv
  - raw_data/210422_nextseq/210422_samples.tsv
  - raw_data/210528_nextseq/210528_samples.tsv
  - raw_data/210625_nextseq/210625_samples.tsv
  - raw_data/210707_nextseq/210707_samples.tsv
  - raw_data/211108_nextseq/211108_samples.tsv
  - raw_data/211223_nextseq/211223_samples.tsv
add_columns: #additional columns to include in the final sample sheet
  - X384.Column
  - Capture.Plate.Name
  - Capture.Plate.Location
exclude_columns: #samples to exclude from the final sample sheet
  - HC
  - 3D7
  - 7G8
  - LC
  - NTC
  - '"HB3"'
  - DD2
  - V1S
  - G8
  - PMP
  - NTP
  - empty