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Updated pipeline executable
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souryacs committed Nov 15, 2019
1 parent 59de6c7 commit b43310a
Showing 1 changed file with 3 additions and 3 deletions.
6 changes: 3 additions & 3 deletions pipeline_exec.sh
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ inpfile2=$dirdata'fastafiles/001_R2.fastq.gz'
outdir=$dirdata'Sample_TEST_ATAC'
prefix='001'

`pwd`/bin/pipeline.sh -f $inpfile1 -r $inpfile2 -C `pwd`'/configfile' -n $prefix -g $genome -d $outdir -t 8 -m "16G" -q 20 -D 1 -O 0
`pwd`/bin/pipeline.sh -f $inpfile1 -r $inpfile2 -C `pwd`'/configfile_hg19' -n $prefix -g $genome -d $outdir -t 8 -m "16G" -q 20 -D 1 -O 0

#=================
# script 2 - when fastq files of single end end read are provided as the input
Expand All @@ -31,7 +31,7 @@ inpfile=$dirdata'merged_inp.fastq.gz'
outdir=$dirdata'Sample_TEST_ATAC'
prefix='002'

`pwd`/bin/pipeline.sh -f $inpfile -C `pwd`'/configfile' -n $prefix -g $genome -d $outdir -t 8 -m "16G" -q 20 -D 0 -O 0
`pwd`/bin/pipeline.sh -f $inpfile -C `pwd`'/configfile_hg19' -n $prefix -g $genome -d $outdir -t 8 -m "16G" -q 20 -D 0 -O 0

#=================
# script 3 - when a BAM file is provided as the input
Expand All @@ -45,6 +45,6 @@ inpfile=$dirdata'inp.bam'
outdir=$dirdata'Sample_TEST_ATAC'
prefix='003'

`pwd`/bin/pipeline.sh -f $inpfile -C `pwd`'/configfile' -n $prefix -d $outdir -t 8 -m "16G" -q 20 -D 1 -O 0 -w "hg19"
`pwd`/bin/pipeline.sh -f $inpfile -C `pwd`'/configfile_hg19' -n $prefix -d $outdir -t 8 -m "16G" -q 20 -D 1 -O 0 -w "hg19"


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