Create og2.sh

Author: DailyDreaming

og2.sh

@@ -0,0 +1,61 @@
+#!/bin/bash
+
+cd /cromwell_root
+tmpDir=`mkdir -p "/cromwell_root/tmp.43725cb9" && echo "/cromwell_root/tmp.43725cb9"`
+chmod 777 "$tmpDir"
+export _JAVA_OPTIONS=-Djava.io.tmpdir="$tmpDir"
+export TMPDIR="$tmpDir"
+export HOME="$HOME"
+(
+cd /cromwell_root
+
+)
+(
+cd /cromwell_root
+
+
+# Set the exit code of a pipeline to that of the rightmost command
+# to exit with a non-zero status, or zero if all commands of the pipeline exit 
+set -o pipefail
+# cause a bash script to exit immediately when a command fails
+set -e
+# cause the bash shell to treat unset variables as an error and exit immediately
+set -u
+# echo each line of the script to stdout so we can see what is happening
+set -o xtrace
+#to turn off echo do 'set +o xtrace'
+
+echo "Running pre-alignment"
+
+samtools view -T /cromwell_root/topmed_workflow_testing/topmed_variant_caller/reference_files/hg38/hs38DH.fa -uh -F 0x900 /cromwell_root/topmed_workflow_testing/topmed_aligner/input_files/NWD176325.0005.recab.cram \
+  | bam-ext-mem-sort-manager squeeze --in -.ubam --keepDups --rmTags AS:i,BD:Z,BI:Z,XS:i,MC:Z,MD:Z,NM:i,MQ:i --out -.ubam \
+  | samtools sort -l 1 -@ 1 -n -T pre_output_base.samtools_sort_tmp - \
+  | samtools fixmate - - \
+  | bam-ext-mem-sort-manager bam2fastq --in -.bam --outBase pre_output_base --maxRecordLimitPerFq 20000000 --sortByReadNameOnTheFly --readname --gzip
+)  > '/cromwell_root/stdout' 2> '/cromwell_root/stderr'
+echo $? > /cromwell_root/rc.tmp
+(
+# add a .file in every empty directory to facilitate directory delocalization on the cloud
+cd /cromwell_root
+find . -type d -empty -print | xargs -I % touch %/.file
+)
+(
+cd /cromwell_root
+sync
+# make the directory which will keep the matching files
+mkdir /cromwell_root/glob-7cc51463fe16c850aa9228b0db87877e
+
+# create the glob control file that will allow for the globbing to succeed even if there is 0 match
+echo "This file is used by Cromwell to allow for globs that would not match any file.
+By its presence it works around the limitation of some backends that do not allow empty globs.
+Regardless of the outcome of the glob, this file will not be part of the final list of globbed files." > /cromwell_root/glob-7cc51463fe16c850aa9228b0db87877e/cromwell_glob_control_file
+
+# symlink all the files into the glob directory
+( ln -L pre_output_base.* /cromwell_root/glob-7cc51463fe16c850aa9228b0db87877e 2> /dev/null ) || ( ln pre_output_base.* /cromwell_root/glob-7cc51463fe16c850aa9228b0db87877e )
+
+# list all the files (except the control file) that match the glob into a file called glob-[md5 of glob].list
+ls -1 /cromwell_root/glob-7cc51463fe16c850aa9228b0db87877e | grep -v cromwell_glob_control_file > /cromwell_root/glob-7cc51463fe16c850aa9228b0db87877e.list
+
+
+)
+mv /cromwell_root/rc.tmp /cromwell_root/rc