Update wrapper.sh

added script to avoid archiving condor hidden files, archiving twice err and out and added a check to ensure label are provided when their inputs are

wrapper/wrapper.sh

@@ -1,9 +1,22 @@
-ARGS="${refgen} ${indpre} ${refann} ${input1} ${input2} ${input3} ${input3} ${input4} ${input5} ${input6} ${input7} ${input8} ${maskfile_links} ${maskfile_diff} ${insertsize} ${stdev} ${discalign} ${mixalign} ${libtype} ${sensitivity} ${fastqscale} ${minanchor} ${minintron_tophat} ${maxintron_tophat} ${maxalign} ${minreadlength} ${usegtf} ${userescue} ${lab1} ${lab2} ${lab3} ${lab4} ${maxit} ${idpre} ${isofrac} ${intraintrtresh} ${maxintron_cufflinks} ${minintron_cufflinks} ${junctionalpha} ${anchfrac} ${mintransfrag} ${termexonmax} ${trimcovavg} ${trimfrac} ${transfraggap} ${transfraggap_diff} ${userescuecd} ${testalign} ${testfdr} ${normalhits} -proc 12"
+#!/bin/bash
+
+if [ -n "${input5}" ] && [ -z "${lab3}" ]
+  then
+    echo condition 3 label is required
+    exit 1
+fi
+if [ -n "${input7}" ] && [ -z "${lab4}" ]
+  then
+    echo condition 4 label is required
+    exit 1
+fi
+
+ARGS="${refgen} ${indpre} ${refann} ${input1} ${input2} ${input3} ${input3} ${input4} ${input5} ${input6} ${input7} ${input8} ${maskfile_links} ${maskfile_diff} ${insertsize} ${stdev} ${discalign} ${mixalign} ${libtype} ${sensitivity} ${fastqscale} ${minanchor} ${minintron_tophat} ${maxintron_tophat} ${maxalign} ${minreadlength} ${usegtf} ${userescue} ${lab1} ${lab2} ${lab3} ${lab4} ${maxit} ${idpre} ${isofrac} ${intraintrtresh} ${maxintron_cufflinks} ${minintron_cufflinks} ${junctionalpha} ${anchfrac} ${mintransfrag} ${termexonmax} ${trimcovavg} ${trimfrac} ${transfraggap} ${transfraggap} ${userescuecd} ${testalign} ${testfdr} ${normalhits} -proc 12"
 
 function in_for {
-	res=(${1})
-	res=${res[@]:1}
-	res=`for el in ${res}; do echo $el", ";done`
+        res=(${1})
+        res=${res[@]:1}
+        res=`for el in ${res}; do echo $el", ";done`
 }
 
 elenco=("${refgen}" "${refann}" "${input1}" "${input2}" "${input3}" "${input4}" "${input5}" "${input6}" "${input7}" "${input8}" "${maskfile_links}" "${maskfile_diff}")
@@ -17,9 +30,10 @@ INPUTS=${total}
 
 echo  universe                = docker >> lib/condorSubmitEdit.htc
 echo docker_image            =  cyverseuk/tuxedo:v2.1.0 >> lib/condorSubmitEdit.htc ######
-echo arguments				= ${ARGS} >> lib/condorSubmitEdit.htc
+echo arguments                          = ${ARGS} >> lib/condorSubmitEdit.htc
 echo transfer_input_files = ${INPUTS} >> lib/condorSubmitEdit.htc
-cat lib/condorSubmit.htc >> lib/condorSubmitEdit.htc
+echo transfer_output_files = . >> lib/condorSubmitEdit.htc
+cat /mnt/data/rosysnake/lib/condorSubmit.htc >> lib/condorSubmitEdit.htc
 
 less lib/condorSubmitEdit.htc
 
@@ -32,4 +46,12 @@ jobid=`echo $jobid | sed -e 's/\.//'`
 #echo going to monitor job $jobid
 condor_tail -f $jobid
 
+######deleting hidden files
+FILELIST=`ls -d [\_]* .??*`
+for el in "${FILELIST}"
+  do
+    #echo "${el}"
+    echo "${el}" >> .agave.archive
+  done
+
 exit 0