Changeset 9


Ignore:
Timestamp:
Oct 7, 2011, 1:49:24 PM (5 years ago)
Author:
r.w.w.brouwer@…
Message:

Added narwhal.sh controle script

Location:
trunk/narwhal/bin
Files:
1 added
1 edited

Legend:

Unmodified
Added
Removed
  • trunk/narwhal/bin/run_tools.sh

    r8 r9  
    1414    echo $1
    1515    echo "
    16 Usage: workflow.sh -j [maxjobs] -p [profile] RUNFOLDER
     16Usage: run_tools.sh -j [maxjobs] RUNFOLDER
     17
    1718
    1819
     
    3132MAXJOBS=8                                       # run at most 8 parallel processes
    3233RUNFOLDER=""                                    # the run folder to write the results in
     34mismatches=0
    3335
    3436echo "`date` Started"
     
    3739# PARSE THE OPTIONS
    3840#
    39 while getopts 'j:' opt; do
     41while getopts 'j:m:' opt; do
    4042    case $opt in
    4143        'j')
    4244            MAXJOBS=$OPTARG
    4345            ;;
    44         'p')
    45             profile=$OPTARG
     46        'm')
     47            mismatches=$OPTARG
    4648            ;;
    4749    esac
     
    100102if [[ -f $optfile ]] && [[ $(wc -l $optfile) > 0 ]] ; then
    101103        echo "`date` Indexing multiplexed FastQ files from ${optfile}"
    102         parallel -a $optfile --colsep ';' -j $MAXJOBS demultiplex index -f {1}  -i {2} -b {3} -s {4} -c {5}
     104        parallel -a $optfile --colsep ';' -j $MAXJOBS demultiplex index -f {1}  -i {2} -b {3} -s {4} -c {5} -m $mismatches
    103105fi
    104106
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