Updated with recent cookiecutter updates

nf_core/pipeline-template/{{cookiecutter.pipeline_slug}}/.travis.yml

@@ -28,8 +28,8 @@ install:
   - cd ${TRAVIS_BUILD_DIR}/tests
 
 env:
-  - NXF_VER=0.30.0
-  - NXF_VER=''
+  - NXF_VER=0.30.0 # Specify a minimum NF version that should be tested and work
+  - NXF_VER='' # Plus: get the latest NF version and check, that it works
 
 script:
   # Lint the pipeline code

nf_core/pipeline-template/{{cookiecutter.pipeline_slug}}/conf/awsbatch.config

@@ -0,0 +1,13 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for AWS Batch
+ * -------------------------------------------------
+ * Imported under the 'awsbatch' Nextflow profile in nextflow.config
+ * Uses docker for software depedencies automagically, so not specified here.
+ */
+
+aws.region = params.awsregion
+process.executor = 'awsbatch'
+process.queue = params.awsqueue
+executor.awscli = '/home/ec2-user/miniconda/bin/aws'
+params.tracedir = './'

nf_core/pipeline-template/{{cookiecutter.pipeline_slug}}/conf/base.config

@@ -26,7 +26,6 @@ process {
     errorStrategy = { task.exitStatus in [143,137] ? 'retry' : 'ignore' }
   }
   $multiqc {
-    executor = 'local'
     errorStrategy = { task.exitStatus in [143,137] ? 'retry' : 'ignore' }
   }
 }

nf_core/pipeline-template/{{cookiecutter.pipeline_slug}}/docs/installation.md

@@ -41,3 +41,9 @@ unzip master.zip -d /my-pipelines/
 cd /my_data/
 nextflow run /my-pipelines/{{ cookiecutter.pipeline_slug }}-master
 ```
+
+To stop nextflow from looking for updates online, you can tell it to run in offline mode by specifying the following environment variable in your ~/.bashrc file:
+
+```bash
+export NXF_OFFLINE='TRUE'
+```

nf_core/pipeline-template/{{cookiecutter.pipeline_slug}}/docs/usage.md

@@ -49,9 +49,8 @@ Use this parameter to choose a configuration profile. Each profile is designed f
 * `docker`
     * A generic configuration profile to be used with [Docker](http://docker.com/)
     * Runs using the `local` executor and pulls software from dockerhub: [`{{ cookiecutter.pipeline_slug }}`](http://hub.docker.com/r/{{ cookiecutter.pipeline_slug }}/)
-* `aws`
-    * A starter configuration for running the pipeline on Amazon Web Services. Uses docker and Spark.
-    * See [`docs/configuration/aws.md`](configuration/aws.md)
+* `awsbatch`
+    * A generic configuration profile to be used with AWS Batch.
 * `standard`
     * The default profile, used if `-profile` is not specified at all. Runs locally and expects all software to be installed and available on the `PATH`.
     * This profile is mainly designed to be used as a starting point for other configurations and is inherited by most of the other profiles.
@@ -132,6 +131,15 @@ Each step in the pipeline has a default set of requirements for number of CPUs,
 ### Custom resource requests
 Wherever process-specific requirements are set in the pipeline, the default value can be changed by creating a custom config file. See the files in [`conf`](../conf) for examples.
 
+## AWS Batch specific parameters
+Running the pipeline on AWS Batch requires a couple of specific parameters to be set according to your AWS Batch configuration. Please use the `-awsbatch` profile and then specify all of the following parameters.
+### `--awsqueue`
+The JobQueue that you intend to use on AWS Batch.
+### `--awsregion`
+The AWS region to run your job in. Default is set to `eu-west-1` but can be adjusted to your needs.
+
+Please make sure to also set the `-w/--work-dir` and `--outdir` parameters to a S3 storage bucket of your choice - you'll get an error message notifying you if you didn't.
+
 ## Other command line parameters
 ### `--outdir`
 The output directory where the results will be saved.

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

@@ -24,7 +24,8 @@ def helpMessage() {
     Mandatory arguments:
       --reads                       Path to input data (must be surrounded with quotes)
       --genome                      Name of iGenomes reference
-      -profile                      Hardware config to use. docker / aws
+      -profile                      Configuration profile to use. Can use multiple (comma separated)
+                                    Available: standard, conda, docker, singularity, awsbatch, test
 
     Options:
       --singleEnd                   Specifies that the input is single end reads
@@ -79,6 +80,12 @@ if( !(workflow.runName ==~ /[a-z]+_[a-z]+/) ){
   custom_runName = workflow.runName
 }
 
+// Check workDir/outdir paths to be S3 buckets if running on AWSBatch
+// related: https://github.com/nextflow-io/nextflow/issues/813
+if( workflow.profile == 'awsbatch') {
+    if(!workflow.workDir.startsWith('s3:') || !params.outdir.startsWith('s3:')) exit 1, "Workdir or Outdir not on S3 - specify S3 Buckets for each to run on AWSBatch!"
+}
+
 /*
  * Create a channel for input read files
  */
@@ -135,6 +142,10 @@ summary['Working dir']    = workflow.workDir
 summary['Output dir']     = params.outdir
 summary['Script dir']     = workflow.projectDir
 summary['Config Profile'] = workflow.profile
+if(workflow.profile == 'awsbatch'){
+   summary['AWS Region'] = params.awsregion
+   summary['AWS Queue'] = params.awsqueue
+}
 if(params.email) summary['E-mail Address'] = params.email
 log.info summary.collect { k,v -> "${k.padRight(15)}: $v" }.join("\n")
 log.info "========================================="

nf_core/pipeline-template/{{cookiecutter.pipeline_slug}}/nextflow.config

@@ -20,7 +20,10 @@ params {
   singleEnd = false
   outdir = './results'
   igenomes_base = "./iGenomes"
+  tracedir = "${params.outdir}/pipeline_info"
   clusterOptions = false
+  awsqueue = false
+  awsregion = 'eu-west-1'
 }
 
 profiles {
@@ -29,11 +32,17 @@ profiles {
     includeConfig 'conf/base.config'
   }
   conda { process.conda = "$baseDir/environment.yml" }
-  docker { docker.enabled = true }
-  singularity { singularity.enabled = true }
-  aws {
+  docker {
+    docker.enabled = true
+    process.container = 'nfcore/{{ cookiecutter.pipeline_slug }}:{{ cookiecutter.version }}'
+  }
+  singularity {
+    enabled = true
+    process.container = 'shub://nf-core/{{ cookiecutter.pipeline_slug }}:{{ cookiecutter.version }}'
+  }
+  awsbatch {
     includeConfig 'conf/base.config'
-    includeConfig 'conf/aws.config'
+    includeConfig 'conf/awsbatch.config'
     includeConfig 'conf/igenomes.config'
   }
   test {
@@ -51,19 +60,19 @@ process.shell = ['/bin/bash', '-euo', 'pipefail']
 
 timeline {
   enabled = true
-  file = "${params.outdir}/pipeline_info/{{ cookiecutter.pipeline_name.replace(' ', '-') }}_timeline.html"
+  file = "${params.tracedir}/pipeline_info/{{ cookiecutter.pipeline_name.replace(' ', '-') }}_timeline.html"
 }
 report {
   enabled = true
-  file = "${params.outdir}/pipeline_info/{{ cookiecutter.pipeline_name.replace(' ', '-') }}_report.html"
+  file = "${params.tracedir}/pipeline_info/{{ cookiecutter.pipeline_name.replace(' ', '-') }}_report.html"
 }
 trace {
   enabled = true
-  file = "${params.outdir}/pipeline_info/{{ cookiecutter.pipeline_name.replace(' ', '-') }}_trace.txt"
+  file = "${params.tracedir}/pipeline_info/{{ cookiecutter.pipeline_name.replace(' ', '-') }}_trace.txt"
 }
 dag {
   enabled = true
-  file = "${params.outdir}/pipeline_info/{{ cookiecutter.pipeline_name.replace(' ', '-') }}_dag.svg"
+  file = "${params.tracedir}/pipeline_info/{{ cookiecutter.pipeline_name.replace(' ', '-') }}_dag.svg"
 }
 
 manifest {