# the paths below assume youre are running the test
# from withing Baltica directory

path:
  /home/tbrittoborges/sirv_test/

# full path to the alignment files
sample_path:
  /home/tbrittoborges/Baltica/data/


samples:
  mix1_1: mix1_1.bam
  mix2_1: mix2_1.bam
  mix3_1: mix3_1.bam
  mix1_2: mix1_2.bam
  mix2_2: mix2_2.bam
  mix3_2: mix3_2.bam
  mix1_3: mix1_3.bam
  mix2_3: mix2_3.bam
  mix3_3: mix3_3.bam
  mix1_4: mix1_4.bam
  mix2_4: mix2_4.bam
  mix3_4: mix3_4.bam
  mix1_5: mix1_5.bam
  mix2_5: mix2_5.bam
  mix3_5: mix3_5.bam

# which comparison should we make?
# in the format case-vs-control
# conditions groups are extracted from '{group}_{replicate}'
contrasts:
  mix2-vs-mix1:
    - mix2
    - mix1
  mix3-vs-mix1:
    - mix3
    - mix1
  mix3-vs-mix2:
    - mix3
    - mix2

assembly:
  GRCh38_90
# In case of doubt, please RSeQC infer_experiment result
strandness:
  fr-firststrand
# If the read length is variable, use the maximum value
read_len:
  101
# full path to the reference transcriptome model
ref:
  /home/tbrittoborges/Baltica/data/SIRV.gtf
# full path to the reference sequence
ref_fa:
  /home/tbrittoborges/Baltica/data/SIRV.fa

# Leafcutter-specific parameters
leafcutter_min_samples_per_group:
  3
leafcutter_min_samples_per_intron:
  5
leafcutter_min_coverage:
  20
leafcutter_min_cluster_reads:
  30
leafcutter_max_intron_length:
  500000

# Majiq-specific parametes
majiq_non_changing_threshold:
  0.05
majiq_threshold:
  0.2
majiq_minreads:
  5
# adjusted p-value threshold for LeafCutter and JunctionSeq
fdr:
  0.05