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config.yaml
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config.yaml
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# Snakemake configuration file
#
# The variables in this file control the behavior of the Snakefile at the root
# of the project. It starts with raw sequencing reads in FASTQ files and
# converts them to gene counts.
# Paths ------------------------------------------------------------------------
# The following paths must be updated to run the scripts on your machine.
# Paths must end with forward slash
# Enter the path (absolute or relative to the Snakefile) to the local directory
# to store the final data files.
dir_data: data/
# Enter the path (absolute or relative to the Snakefile) to the local directory
# to store intermediate output data files.
dir_output: output/
# Enter the absolute path to an external directory to store intermediate files.
# It should also contain a subdirectory fastq/ which contains the raw gzipped
# FASTQ files.
dir_external: /project2/gilad/fucci-seq/
# Enter the path (absolute or relative to the Snakefile) for writing log
# files. Make sure to also update this path for log files in cluster.json
dir_log: log/
# Samples ---------------------------------------------------------------------
# Select which samples to run. You should select a subset when first configuring
# and testing the pipeline.
# C1 chips
chips: ["20170905", "20170906", "20170907", "20170908",
"20170910", "20170912", "20170913", "20170914",
"20170915", "20170916", "20170917", "20170919",
"20170920", "20170921", "20170922", "20170924"]
# rows of chips
rows: ["A", "B", "C", "D", "E", "F", "G", "H"]
# columns of chips
cols: ["01", "02", "03", "04", "05", "06", "07", "08", "09", "10", "11", "12"]
# Annotation -------------------------------------------------------------------
# The following variables control which genome release is used for annotation
# and which chromosomes are considered.
# Specify Ensembl release for genome sequence and annotation
# http://feb2014.archive.ensembl.org/index.html
ensembl_archive: feb2014.archive.ensembl.org
ensembl_rel: 75
ensembl_genome_hs: GRCh37.75
chr_hs: ["1", "2", "3", "4", "5", "6", "7", "8", "9",
"10", "11", "12", "13", "14", "15", "16",
"17", "18", "19", "20", "21", "22",
"X", "Y", "MT"]