parameters.csv

########################################################################
## General parameters for SLURM settings and cluster directory paths
#
queue,medium
defaultInterpreter,#!/bin/bash
stage,module load
checkStage,module list
WORKDIR,/groups/
root,${WORKDIR}
group,umcg-wijmenga
tmp,tmp04
resDir,/groups/umcg-wijmenga/tmp04/resources/
toolDir,/apps/software/
projectDir,/groups/umcg-wijmenga/tmp04/umcg-hbrugge/projects/10xpipelineTemplate/
jdkVersion,1.8.0_25
### SplitBam
bamToolsPath,/groups/umcg-wijmenga/tmp04/umcg-hbrugge/apps/bam-per-cell-1.0.jar
bamPath,/groups/umcg-wijmenga/tmp04/umcg-mdam/bamFile6kcells10XGenomics/pbmc6k_possorted_genome_bam.bam
barcodePath,/groups/umcg-wijmenga/tmp04/umcg-mdam/bamFile6kcells10XGenomics/barcodes.tsv
splitBamDir,${projectDir}/splitBam
### DedupBam
umiToolsDir,/groups/umcg-wijmenga/tmp04/umcg-hbrugge/apps/UMI-tools/umi_tools/dedup.py
deduppedBamDir,${projectDir}/deduppedBam
pythonVersion,2.7.11-foss-2015b
cythonVersion,0.22-foss-2015b-Python-2.7.9
futureVersion,0.15.2-foss-2015b-Python-2.7.9
pysamVersion,0.9.0-foss-2015b-Python-2.7.11
pandasVersion,0.18.0-foss-2015b-Python-2.7.11
numpyVersion,1.10.4-foss-2015b-Python-2.7.11
scipyVersion,0.17.0-foss-2015b-Python-2.7.11
matplotlibVersion,1.5.1-foss-2015b-Python-2.7.11
### FeatureCounts
featureCountsPath,/home/umcg-hbrugge/group-home/tools/subread-1.5.1-Linux-x86_64/bin/featureCounts
humanGtf,/apps/data/ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/Homo_sapiens.GRCh37.75.gtf
countsDir,${projectDir}/counts/
### CountsToMatrix
countsToMatrixPath,/groups/umcg-wijmenga/tmp04/umcg-hbrugge/apps/counts-to-matrix-1.0.jar
matrixDir,${projectDir}matrix/