Update file atacseq_runner.sh

atacseq_runner.sh

@@ -333,10 +333,10 @@ for key in "${!OPTS[@]}"; do
 done
 
 
-NFCORE_WF="ATACseq"
-NFCORE_WF_VERSION="2.0"
-NFCORE_WF_COMMIT="971984a48ad4dc5b39fc20b56c5729f4ca20379a"  # the commit for tags/2.0
-CUTANDRUN_DIR="$SCRIPTPATH/$NFCORE_WF"
+NFCORE_WF="nfcore_atacseq"
+NFCORE_WF_VERSION="2.1.2"
+NFCORE_WF_COMMIT="1a1dbe52ffbd82256c941a032b0e22abbd925b8a"  # the commit for tags/2.0 #What is this???
+ATACseq_DIR="$SCRIPTPATH/$NFCORE_WF"
 
 # set max total resources
 max_time="480.h"
@@ -350,20 +350,20 @@ ${max_time}, ${max_cpus} CPUs, ${max_memory} Memory on $(hostname -s).
 
 ## Fix the configs
 # Comment out email notification part from the configure file
-config_cutandrun="${CUTANDRUN_DIR}/workflows/cutandrun.nf"
-if [[ -f $config_cutandrun ]]; then
-  if ! grep "// NfcoreTemplate.email" $config_cutandrun > /dev/null; then
+config_atacseq="${ATACseq_DIR}/workflows/atacseq.nf" ##Check this??
+if [[ -f $config_atacseq ]]; then
+  if ! grep "// NfcoreTemplate.email" $config_atacseq > /dev/null; then
     sed -i "s/NfcoreTemplate.email/\/\/ NfcoreTemplate.email/g" $config_cutandrun
   fi
   if ! grep "// NfcoreTemplate.summary" $config_cutandrun > /dev/null; then
     sed -i "s/NfcoreTemplate.summary/\/\/ NfcoreTemplate.summary/g" $config_cutandrun
   fi
 else
-  echo "Could not find $config_cutandrun!"
+  echo "Could not find $config_atacseq!"
   exit 1
 fi
 
-base_config="${CUTANDRUN_DIR}/conf/base.config"
+base_config="${ATACseq_DIR}/conf/base.config"
 sed -i "s/maxRetries    = 1/maxRetries    = 3/g" $base_config
 
 sed -i "s/ check_max( 4.h  / check_max( 40.h  /g" $base_config
@@ -381,7 +381,7 @@ sed -i "s/ 12.GB / $max_memory /g" $base_config
 sed -i "s/ 36.GB / $max_memory /g" $base_config
 sed -i "s/ 72.GB / $max_memory /g" $base_config
 
-resources_config="${CUTANDRUN_DIR}/conf/resources.config"
+resources_config="${ATACseq_DIR}/conf/resources.config"
 sed -i "s/ check_max( 1.h  / check_max( 10.h  /g" $resources_config
 sed -i "s/ check_max( 4.h  / check_max( 40.h  /g" $resources_config
 
@@ -395,7 +395,7 @@ sed -i "s/ 8.GB / $max_memory /g"  $resources_config
 sed -i "s/ 32.GB / $max_memory /g" $resources_config
 sed -i "s/ 64.GB / $max_memory /g" $resources_config
 
-nextflow_config="${CUTANDRUN_DIR}/nextflow.config"
+nextflow_config="${ATACseq_DIR}/nextflow.config"
 sed -i "s/max_cpus                   = 16/max_cpus                   = $max_cpus/g" $nextflow_config
 sed -i "s/128.GB/$max_memory/g"                                                     $nextflow_config
 sed -i "s/240.h/$max_time/g"                                                        $nextflow_config
@@ -474,17 +474,17 @@ export NXF_SINGULARITY_CACHEDIR="${workdir}/images/singularity"
 
 # run the pipeline
 echo ""
-echo "The working folder is: ${Pwd}"                                     | tee cutandrun_runner.debug.log
-echo "The running command is:"                                           | tee -a cutandrun_runner.debug.log
-echo nextflow run -w ${workdir}/work ${CUTANDRUN_DIR} $RUN_OPTIONS       | tee -a cutandrun_runner.debug.log
-echo ""                                                                  | tee -a cutandrun_runner.debug.log
+echo "The working folder is: ${Pwd}"                                     | tee nfcore_atacseq_runner.debug.log
+echo "The running command is:"                                           | tee -a nfcore_atacseq_runner.debug.log
+echo nextflow run -w ${workdir}/work ${ATACseq_DIR} $RUN_OPTIONS       | tee -a nfcore_atacseq_runner.debug.log
+echo ""                                                                  | tee -a nfcore_atacseq_runner.debug.log
 
 cd ${Pwd}
 # output for debugging
-nextflow config -profile ${OPTS["profile"]} -flat -sort ${CUTANDRUN_DIR} &>> cutandrun_runner.debug.log
+nextflow config -profile ${OPTS["profile"]} -flat -sort ${ATACseq_DIR} &>> nfcore_atacseq_runner.debug.log
 
 # run
-nextflow run  -w ${workdir}/work ${CUTANDRUN_DIR} $RUN_OPTIONS | tee  .nextflow.cutandrun.log &
+nextflow run  -w ${workdir}/work ${ATACseq_DIR} $RUN_OPTIONS | tee  .nextflow.atac.log &
 nextflowPID=$!
 
 update_trace() {
@@ -496,10 +496,10 @@ update_trace() {
 
   if [[ -f $from_trace ]] && [[ -f $to_trace ]]; then
     # from to_trace
-    grep -v "CUTANDRUN:" $to_trace > ./.trace.tmp
+    grep -v "ATACseq:" $to_trace > ./.trace.tmp #check
     echo -e "\n\n" >> ./.trace.tmp
     # from from_trace
-    grep "CUTANDRUN:" $from_trace | awk -F"\t" 'BEGIN {OFS="\t"}; {if ($19) print $1,$2,$3,$4,$5,$6,$7,$10,$11,$15,$16,$17,$18,$19}' | sort -un | sed s"/NFCORE_CUTANDRUN://g" >> ./.trace.tmp
+    grep "ATACseq:" $from_trace | awk -F"\t" 'BEGIN {OFS="\t"}; {if ($19) print $1,$2,$3,$4,$5,$6,$7,$10,$11,$15,$16,$17,$18,$19}' | sort -un | sed s"/NFCORE_ATACseq://g" >> ./.trace.tmp #Check
     # update to_trace
     cat ./.trace.tmp > $to_trace
     # rm tmp file
@@ -518,7 +518,7 @@ while sleep 2; do
   update_trace $from_trace $to_trace
 
   # workflow finished
-  if grep "Completed at:" .nextflow.cutandrun.log &> /dev/null; then
+  if grep "Completed at:" .nextflow.atac.log &> /dev/null; then
     kill -9 $nextflowPID &> /dev/null
     sleep 5
     # update the trace file before leaving