template.yml

########################################################
## assembly and reference files of GENOME.
########################################################
gtf_path : test/GRCh38v110_snippet.gtf
fa_path : test/GRCh38v110_snippet.fa
########################################################
## reads mapped to TRANSCRIPTOME (*.bam/*.sam)
## format: 'id : ribosome profiling paths'
## DO NOT change id after data is parsed to h5 file
########################################################
ribo_paths :
  sample_1 : test/SRR000001.sam
  sample_2 : test/SRR000002.sam
  sample_3 : test/SRR000003.sam
########################################################
## path to hdf5 database created to store data.
########################################################
h5_path : GRCh38v110_snippet.h5
########################################################
## Out prefix for predictions, defaults to hdf5 path
########################################################
out_prefix : test_out/
#
####################
## ADVANCED SETUP ##
####################
#
########################################################
## A custom set of riboseq data selected for training.
## Use ids applied in ribo_paths, leave commented if NA.
## Replicates can be merged where the number of mapped 
## reads are summed for multiple experiments. 
########################################################
## example: only use sample_1 and sample_3
samples:
  - sample_1
  - sample_3
#
## example: sample_1 and sample_2 are merged (replicates)
#samples:
#  - - sample_1
#    - sample_2
#
########################################################
## Training times can be sped up by removing transcripts
## with few reads from the training step. 
## This does not affect samples within the test set. 
## Filtering is performed based on the number of reads 
## mapped to the transcript.
########################################################
## example: ommit transcripts with less than 6 reads during 
## training/validation
cond :
  ribo:
    num_reads : x > 6
#
## example: custom rules per data set
#cond :
#  ribo:
#    num_reads : 
#      sample_1 : "x > 10"
#      sample_2 : "x > 0"
#      sample_3 : "x > 0"