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## ------------------ fastq to bam config --------------------------- ##
## the file by default, sits in the R pacakge
## You may copy this to ~/flowr/pipelines;
## --------------------------------------------------------------------- ##
## -------------------- file format ------------------------------------ ##
## Following lines, as a tab delimited table, with two columns
#NAME VALUE
## Always use load_opts(); after editing this file !
## Details on this format: https://github.com/sahilseth/params
## ONE can specify as many parameters as you want.
## All of them should get loaded into the R environment
## --------------------------------------------------------------------- ##
## --------------------- A note regarding tools and paths -------------- ##
## You may use module show <name of tool>
## to get full path etc...
## For most tools you may either use FULL PATH
## OR module load <tool>;tool
## for tools which support piping (samtools), you need to supply full path
## Example: (both of them are fine)
## bwa_exe 'module load bwa;bwa'
## bwa_exe
## --------------------------------------------------------------------- ##
## for more details one verbosity levels:
## http://sahilseth.github.io/flowr/rd.html#verbose
verbose 1 #0, 1, 2, 3
## --- paths to tools
bwa_exe 'module load bwa;bwa'
## specify FULL path (samtools is used in pipes)
samtools_exe '/risapps/rhel6/samtools/1.2/bin/samtools'
## minumum version 1.138
picard_jar '/risapps/noarch/picard/1.138/picard.jar'
## --- java paramters
java_exe 'module load jdk/1.7.0_79;java'
java_mem -Xmx16g
java_tmp /tmp
## --- genome reference
ref_dir '/rsrch2/iacs/iacs_dep/sseth/flowr/genomes/Homo_sapiens/NCBI/build37.1'
## path to reference fasta
ref_fasta {{{ref_dir}}}/Sequence/WholeGenomeFasta/genome.fa
## path to bwa index
ref_bwa {{{ref_dir}}}/Sequence/BWAIndex/genome.fa
## --- BWA paramters
bwa_aln_opts -l 40 -k 2 -n 3
bwa_samse_opts -o 1000
bwa_sampe_opts -o 1000
## parameters for read groups
## more details here: https://www.biostars.org/p/43897/
rg_center the_institute
rg_platform Illumina_HiSeq2000
rg_lane 1
## -- CPUs used
## values like <%CPU%> are filled up using the flow definition
cpu_bwa_aln <%CPU%>