Applied changes from @apeltzer in nf-core/cookiecutter#57 (#109)

nf_core/pipeline-template/{{cookiecutter.pipeline_slug}}/main.nf

@@ -37,6 +37,10 @@ def helpMessage() {
       --outdir                      The output directory where the results will be saved
       --email                       Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits
       -name                         Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic.
+
+    AWSBatch options:
+      --awsqueue                    The AWSBatch JobQueue that needs to be set when running on AWSBatch
+      --awsregion                   The AWS Region for your AWS Batch job to run on
     """.stripIndent()
 }
 
@@ -65,6 +69,11 @@ if ( params.fasta ){
     fasta = file(params.fasta)
     if( !fasta.exists() ) exit 1, "Fasta file not found: ${params.fasta}"
 }
+// AWSBatch sanity checking
+if(workflow.profile == 'awsbatch'){
+    if (!params.awsqueue || !params.awsregion) exit 1, "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
+    if (!workflow.workDir.startsWith('s3') || !params.outdir.startsWith('s3')) exit 1, "Specify S3 URLs for workDir and outdir parameters on AWSBatch!"
+}
 //
 // NOTE - THIS IS NOT USED IN THIS PIPELINE, EXAMPLE ONLY
 // If you want to use the above in a process, define the following: