bird-workflow/sample_bird_workflow.yml at main · ReddyLab/bird-workflow · GitHub

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replicate_names:
  - Input1
  - Input2
  - Output1
  - Output2
alignment_sets:
  - { class: File, path: "/data/reddylab/gjohnson/scz/ORI_library_files_and_data/alignment_and_processing/alignments/Input1/Input1_lengthFiltered.bam" }
  - { class: File, path: "/data/reddylab/gjohnson/scz/ORI_library_files_and_data/alignment_and_processing/alignments/Input2/Input2_lengthFiltered.bam" }
  - { class: File, path: "/data/reddylab/gjohnson/scz/ORI_library_files_and_data/alignment_and_processing/alignments/Output1/Output1.bam" }
  - { class: File, path: "/data/reddylab/gjohnson/scz/ORI_library_files_and_data/alignment_and_processing/alignments/Output2/Output2.bam" }
mpileup_depth: 0
genome_file:
  class: File
  path: "/data/reddylab/Reference_Data/Genomes/hg38/hg38.fa"
locations:
  class: File
  path: "01_mpileups/samtools_mpileup/sample_positions.txt"
bird_output_prefix: sczps_no_peaks
min_effect: 1.25
bird_output_file: "ignore this value"
mcmc_sample_count: 10
bird_range: "ignore this value"