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config_CRISPR.ini
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##############################################################
## Description ##
##############################################################
#
# Edit this file to create custom configurations to use with
# sh_CRISPR.sh. Any change to this file will override default
# script settings.
#
##############################################################
## Configurable variables ##
##############################################################
#
#
## General options
#
# Maximum number of threads (or CPUs) to request and allocate to programs.
# In some case less than this value may automatically be allowed.
threads=$(nproc --all --ignore=1)
#
# Maximum amount of memory (in GB) to request and allocate to programs.
# In some case less than this value may automatically be allowed.
mem="128"
#
# Log folder, will be created in your destination folder.
logs="logs"
#
# Advanced: Path to temporary folder. Useful if your cluster system have a fast local I/O disk.
# Leave empty to use the destination folder. In all cases temporary files will be purged at the end of the script.
tmp="\${L_SCRATCH_JOB}"
#
# Debug mode.
# For troubleshooting only. Will keep all intermediate files,
# sbatch files and logs.
# 0 = No ; 1 = Yes
debug="0"
#
#
## SLURM options
#
# email to use to receive SLURM notifications.
# By default only send FAIL notifications for all jobs and FAIL,END for the last one.
SLURMemail=""
#
# SLURM account, partition and qos settings if required.
SLURMaccount=""
SLURMpartition=""
SLURMqos=""
#
# Custom commands to run before any other program.
# Use it to load modules for example:
# customcmd="module load R"
customcmd=""
#
#
## Screen options
#
# day0-label.
# Specify the label for control sample (usually day 0 or plasmid).
# If using MAGeCK it will also turn on the negative selection QC for every other sample label.
# The negative selection QC will compare each other sample with day0 sample, and thus estimate the degree of negative selections in essential genes.
# If using casTLE, only the first TWO replicates will be used.
# day0="Plasmid,Control_t0_rep1,Control_t0_rep2,Treated_t0_rep1,Treated_t0_rep2"
day0=""
#
# Tests groups.
# Enter your sample names (not including ".fastq" or ".fastq.gz") for comparisons.
# Delimit replicate samples by a COMMA and groups by a SPACE.
# If using casTLE, only the first TWO replicates will be used.
# testgroups="Control_rep1,Control_rep2 Treated_condA_rep1,Treated_condA_rep Treated_condB_rep1,Treated_condB_rep2"
testgroups=""
#
#
## casTLE options
# download the last version from https://bitbucket.org/dmorgens/castle/
#
# Use casTLE.
# 0 = No ; 1 = Yes
usecastle="0"
#
# Python version.
# Are you using python2.7 (original) or python3 (included in this repo) casTLE scripts?
# If you also use MAGeCK python3 is REQUIRED
# use "python" or "python3"
python="python3"
#
# casTLE folder location.
castlepath="/Tools/dmorgens-castle"
#
# Number of permutations to generate p-values.
# For a first pass, use 5x the permutations (so for 20,000 genes that is 100,000 permutations).
# For publication, use 50x (Default, takes time).
permutations="1000000"
#
# Perform permutations on the individual result files.
# Permutations are always calculated for the combo file.
# 0 = No ; 1 = Yes
permres="0"
#
# Output format for graphs.
# If left empty default value is png.
# (png, pdf, eps)
graphformat="pdf"
#
# Screen performed in mouse cells.
# Default is 0, for human cells.
# 0 = No ; 1 = Yes
mouse="0"
#
# Path to bowtie, bowtie-build needs to be in the same folder (probably is already the case).
# bowtie="/usr/local/bin/bowtie"
bowtie="/usr/local/bin/bowtie"
#
# Type of screen. Will be used to create Indices for the guides.
screentype="Cas9-10"
#
# Name of the guides index file. Will be saved in the Indices folder.
# It will overwrite any files with this name prefix.
outputbowtieindex=""
#
# Oligo file location.
# Leave empty if it was previously used and the corresponding Index are already generated for this type of screen.
oligofile=""
#
#
## MAGeCK options.
# download the last version from https://sourceforge.net/projects/mageck/
#
# Use MAGeCK.
# 0 = No ; 1 = Yes
usemageck="1"
#
# MAGeCK list of sgRNA names (see https://sourceforge.net/p/mageck/wiki/input/#sgrna-library-file ) location.
magecksgRNAlibrary=""
#
# Use the reverse complement of the MAGeCK list of sgRNA names.
# 0 = No ; 1 = Yes
mageckrevcomplib="0"
#
# MAGeCK list of control sgRNA names (see https://sourceforge.net/p/mageck/wiki/input/#negative-control-sgrna-list ) location.
mageckcontrolsgrna=""
#
# GMT file for MAGeCK pathway analysis (see https://sourceforge.net/p/mageck/wiki/input/#pathway-file-gmt ) location.
gmtfile=""
#
# Matrix file for mle analysis ( see https://sourceforge.net/p/mageck/wiki/input/#design-matrix-file ) location.
# By default will look for a "matrix.txt" file stored with the FastQ files.
matrixfile=$([ -f "${1}"/matrix.txt ] && echo "${1}/matrix.txt")
#
#
## Notifications options
#
# Event name used in your webhooks or IFTTT recipes.
# The IFTTT maker channel will look for the combination private key + event name to then trigger your recipe.
# You can then create a recipe to send an email, a text message or a push notification.
# In the case of a Slack webhook this will be used in the message title
notifevent="CRISPR"
#
# Trigger a Slack Webhook when script is done.
# You must create an "Incoming WebHooks" associated to your slack workspace on https://slack.com/apps
# Copy your full private webhook URL here. Leave blank to disable this function.
# slackwebhookURL="https://hooks.slack.com/services/T5HF5GTUK85/AHUIK456HJG/GSD27f5gGQ7SD5r2fg" # Not a real webhook URL, you have to use your own private one.
slackwebhookURL=""
#
# Trigger IFTTT when script is done.
# You must register the "Maker channel" on https://ifttt.com/maker and create an event (limit of 3 free event since September 2020...)
# Copy your private key here. Leave blank to disable this function.
# iftttkey="AbCd_15CdhUIvbsFJTHGMcfgjsdHRTgcyjt" # Not a real key, you have to use your own private one.
iftttkey=""
#
#
##############################################################
## Setup done. Go home there is nothing below this point! ##
##############################################################