config.yaml

##-------------------------------------##
## Working directory
##-------------------------------------##
WORKING_DIR: "/project/"
FASTQ_DIR: "/project/test_data/"
LOG_DIR: "/project/logs/"
OUT_DIR: "/project/output/"

##--------------------------------------##
## Packages and script directoty
##--------------------------------------##
DROPSEQ_ROOT: "/path_to_bin/Drop-seq_tools-2.0.0"
PICARD_TOOL_DIR: "/path_to_bin/Drop-seq_tools-2.0.0/3rdParty/picard/picard.jar"
STAR_DIR: "/path_to_bin/STAR-2.6.0a/STAR"
Rscript_DIR: "/usr/bin/Rscript"
SAMTOOLS_DIR: "/path_to_bin/samtools"
SCRIPT_DIR: "/project/script"

##-------------------------------------------------------------##
## Variables declaration: genome, gtf, index and other information
##-------------------------------------------------------------##
FASTA: "/project/genome/hg38.fasta"
INDEX: "/project/annotation/index/"
REFFLAT: "/project/annotation/gencode.v29.refFlat"
EXON_BED: "/project/annotation/exon.unambiguous.bed.gz"
INTRON_BED: "/project/annotation/intron.unambiguous.bed.gz"
AMBIGUOUS_BED: "/project/annotation/ambiguous.bed.gz"
GENES_INFO: "/project/annotation/genes_info"

##-------------------------------##
## parameters
##-------------------------------##
MAPPING_CORES: 32
MERGING_CORES: 16

##-----------------------------------------------##
## samples list
##-----------------------------------------------##
# path to sample sheet (TSV format, columns: sample, condition, ...)
SAMPLES: samples.tsv

#SAMPLES: ['sample1', 'sample2', 'sample3']