improve nextflow entrypoint script

* describe arguments
* change variable NEXFLOW_SCRIPT to NEXTFLOW_PROJECT
* add check for AWS_BATCH_* variabes for GUID
* allow github project specifications
* exclude "runs/" from s3

Author: wleepang

src/containers/nextflow/nextflow.aws.sh

@@ -1,12 +1,14 @@
 #!/bin/bash
-echo $@
-NEXTFLOW_SCRIPT=$1
+# $1    S3 URI to Nextflow project files.  If not using S3 set to "".
+# $2..  Additional parameters passed on to the nextflow cli
+
+echo "$@"
+NEXTFLOW_PROJECT=$1
 shift
-NEXTFLOW_PARAMS=$@
+NEXTFLOW_PARAMS="$@"
 
 # Create the default config using environment variables
 # passed into the container
-mkdir -p /opt/config
 NF_CONFIG=~/.nextflow/config
 
 cat << EOF > $NF_CONFIG
@@ -21,13 +23,19 @@ EOF
 # to create a unique path
 GUID="$AWS_BATCH_JOB_ID/$AWS_BATCH_JOB_ATTEMPT"
 
+if [ "$GUID" = "/" ]; then
+    GUID=`date | md5sum | cut -d " " -f 1`
+fi
+
 mkdir -p /opt/work/$GUID
 cd /opt/work/$GUID
 
 # stage workflow definition
-aws s3 sync --only-show-errors --exclude '.*' $NEXTFLOW_SCRIPT .
-
-NF_FILE=$(find . -name "*.nf" -maxdepth 1)
+$NF_FILE=""
+if [ ! -z "$NEXTFLOW_PROJECT" ]; then
+    aws s3 sync --only-show-errors --exclude 'runs/*' --exclude '.*' $NEXTFLOW_PROJECT .
+    NF_FILE=$(find . -maxdepth 1 -name "*.nf")
+fi
 
 echo "== Running Workflow =="
 echo "nextflow run $NF_FILE $NEXTFLOW_PARAMS"