sequencing/config.yml at master · ccls/sequencing · GitHub

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###########################################################################
#
# Configuration file for RINS command line run
#
# Please give the Whole Path of a file, and do not include space in file names
#
# example as follows
#
# Please fill all the required parameters
#
###########################################################################
#
#
#				THIS IS FOR THE RUBY VERSION ONLY
#
#
###########################################################################


# file format can be either "fasta" or "fastq"
#
#	This will soon be replaced by a file_format_detector
#
:file_format: fasta

#	files is a hash
#		the keys should either be left and right or just single
:files:
  :left:  /Users/jakewendt/rins_test/rins/test_sample/testset_forkun_1.fa
  :right: /Users/jakewendt/rins_test/rins/test_sample/testset_forkun_2.fa
#  :left:  /Users/jakewendt/rins_test/rins/test_sample/testset_forkun_1_head.fa
#  :right: /Users/jakewendt/rins_test/rins/test_sample/testset_forkun_2_head.fa

#	if the raw files are fasta, link them instead of copying them in
:link_sample_fa_files: true

#
#	If pre_chopped, the chopped filename must be the same as the raw
#	file name with "_chopped_#{chop_read_length}" at end before extension.
#
#	testset_forkun_1.fa -> testset_forkun_1_chopped_25.fa
#
:pre_chopped: true

# reference files
#
#	Blat requires the file suffix.
#	The other references do not.
#	There is a 4GB file size limit in blat.
#	all_bacterial.fna is 4GB.
#	virus_all.fasta is just a few hundred meg.
#	Combining the 2 will raises errors.
#	So, the blat_reference can be an array.
#	blat will be run on each and the results combined.
#
:blat_reference:
  - /Volumes/cube/working/indexes/virus_all.fasta
#  - /Volumes/cube/working/indexes/all_bacterial.fna

:bowtie_index_human: /Volumes/cube/working/indexes/hg18

#	for dark
:bowtie_human_indexes:
  - /Volumes/cube/working/indexes/hg18
  - /Volumes/cube/working/indexes/hg19
  - /Volumes/cube/working/indexes/Blast1
  - /Volumes/cube/working/indexes/Blast2

:blastn_index_human:     /Volumes/cube/working/indexes/hg18
#:blastn_index_non_human: /Users/jakewendt/rins/indexes/virus
#:blastn_index_non_human: /Volumes/cube/working/indexes/all_bacterial_and_viral
:blastn_index_non_human: /Volumes/cube/working/indexes/nt


#
#	Additional options with their defaults include ...
#
#	The results output filename
#	(can be specified on the command line or in the config file)
#		:output_filename: results.txt
#
#	Size of the chopped reads for the initial blat call
#		:chop_read_length: 25
#
#	MinIdentity match for the initial blat call
#		:minIdentity: 80
#
#
#		:compress_ratio_thrd: 0.5
#
#	The number of trinity iterations that are run
#		:iteration: 2
#
#
#		:bowtie_threads: 6
#
#
#		:bowtie_mismatch: 3
#
#
#		:paired_fragment_length: 300
#
#
#		:min_contig_length: 300
#
#
#		:trinity_threads: 6
#
#
#		:blastn_evalue_thrd: 0.05
#
#
#		:similarity_thrd: 0.8
#
#	Exit if an expected file is empty or missing
#		:die_on_failed_file_check: false
#