Add cd'ing to correct directory

The BLAHP submit wrapper creates a temp directory and cd's there
before running the executable. This breaks Pegasus jobs for a
sharedfs site as it expects to be in the shared-scratch dir
via the `remote_iwd` Condor ClassAd.  This dir is available via
the PEGASUS_SCRATCH_DIR env variable in the job, so cd there as a
workaround.

chipathlon/jobs/scripts/download_fastq.py

-#!/usr/bin/python
+#!/bin/env python 
 import chipathlon.utils
 import argparse
 

chipathlon/jobs/scripts/sort_wrapper.sh

 #!/bin/bash
 
+cd $PEGASUS_SCRATCH_DIR
 /bin/sort -k 8gr,8gr "$1" | awk 'BEGIN{OFS="\t"}{$r="PEAK_"NR; print $0;}' > "$2"

chipathlon/jobs/scripts/zcat_wrapper.sh

 #!/bin/bash
 
+cd $PEGASUS_SCRATCH_DIR
 /bin/zcat "$1" | awk 'BEGIN{OFS="\t"}{print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' > "$2"

chipathlon/jobs/wrappers/bedtools_wrapper.sh

 #!/bin/bash
 
+cd $PEGASUS_SCRATCH_DIR
 . /util/opt/lmod/lmod/init/profile
 module load bedtools
 bedtools "$@"

chipathlon/jobs/wrappers/bowtie2_wrapper.sh

 #!/bin/bash
 
+cd $PEGASUS_SCRATCH_DIR
 . /util/opt/lmod/lmod/init/profile
 module load bowtie
 bowtie2 "$@"

chipathlon/jobs/wrappers/bwa_wrapper.sh

 #!/bin/bash
 
+cd $PEGASUS_SCRATCH_DIR
 . /util/opt/lmod/lmod/init/profile
 module load bwa
 bwa "$@"

chipathlon/jobs/wrappers/macs2_wrapper.sh

 #!/bin/bash
 
+cd $PEGASUS_SCRATCH_DIR
 . /util/opt/lmod/lmod/init/profile
 module load python/2.7 macs2
 macs2 "$@"

chipathlon/jobs/wrappers/picard_wrapper.sh

@@ -2,6 +2,7 @@
 set -eu -o pipefail
 set -o pipefail
 
+cd $PEGASUS_SCRATCH_DIR
 . /util/opt/lmod/lmod/init/profile
 module load picard
 

chipathlon/jobs/wrappers/r_spp_nodups_wrapper.sh

 #!/bin/bash
 
+cd $PEGASUS_SCRATCH_DIR
 . /util/opt/lmod/lmod/init/profile
 module load R spp
 Rscript ${SPP_NODUPS} "$@"

chipathlon/jobs/wrappers/samtools_wrapper.sh

 #!/bin/bash
 
+cd $PEGASUS_SCRATCH_DIR
 . /util/opt/lmod/lmod/init/profile
 module load samtools
 samtools "$@"