Some more tweaks from the final rnaseq template merge

v-clarissa · Mar 17, 2019 · 65f1399 · 65f1399
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diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.gitignore b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.gitignore
@@ -4,3 +4,4 @@ data/
 results/
 .DS_Store
 tests/test_data
+*.pyc
diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/conf/test.config b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/conf/test.config
@@ -8,6 +8,8 @@
  */
 
 params {
+  config_profile_name = 'Test profile'
+  config_profile_description = 'Minimal test dataset to check pipeline function'
   // Limit resources so that this can run on Travis
   max_cpus = 2
   max_memory = 6.GB

diff --git a/...-template/{{cookiecutter.name_noslash}}/docs/configuration/reference_genomes.md b/...-template/{{cookiecutter.name_noslash}}/docs/configuration/reference_genomes.md
@@ -39,7 +39,8 @@ Multiple reference index types are held together with consistent structure for m
 We have put a copy of iGenomes up onto AWS S3 hosting and this pipeline is configured to use this by default.
 The hosting fees for AWS iGenomes are currently kindly funded by a grant from Amazon.
 The pipeline will automatically download the required reference files when you run the pipeline.
-For more information about the AWS iGenomes, see https://ewels.github.io/AWS-iGenomes/
+
+For more information about AWS iGenomes, see [https://ewels.github.io/AWS-iGenomes/](https://ewels.github.io/AWS-iGenomes/).
 
 Downloading the files takes time and bandwidth, so we recommend making a local copy of the iGenomes resource.
 Once downloaded, you can customise the variable `params.igenomes_base` in your custom configuration file to point to the reference location.

diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/installation.md b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/installation.md
@@ -78,7 +78,9 @@ Be warned of two important points about this default configuration:
 ### Docker
 First, install docker on your system: [Docker Installation Instructions](https://docs.docker.com/engine/installation/)
 
-Then, running the pipeline with the option `-profile docker` tells Nextflow to enable Docker for this run. An image containing all of the software requirements will be automatically fetched and used from dockerhub (https://hub.docker.com/r/{{ cookiecutter.name_docker }}).
+Then, running the pipeline with the option `-profile docker` tells Nextflow to enable Docker for this run.
+An image containing all of the software requirements will be automatically fetched and used from dockerhub
+([https://hub.docker.com/r/{{ cookiecutter.name_docker }}](https://hub.docker.com/r/{{ cookiecutter.name_docker }})).
 
 ### Singularity
 If you're not able to use Docker then [Singularity](http://singularity.lbl.gov/) is a great alternative.

diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/output.md b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/output.md
@@ -38,4 +38,4 @@ The pipeline has special steps which allow the software versions used to be repo
 * `Project_multiqc_data/`
   * Directory containing parsed statistics from the different tools used in the pipeline
 
-For more information about how to use MultiQC reports, see http://multiqc.info
+For more information about how to use MultiQC reports, see [http://multiqc.info](http://multiqc.info)
diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/main.nf b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/main.nf
@@ -124,6 +124,7 @@ if(params.readPaths){
 // Header log info
 log.info nfcoreHeader()
 def summary = [:]
+if(workflow.revision) summary['Pipeline Release'] = workflow.revision
 summary['Run Name']         = custom_runName ?: workflow.runName
 // TODO nf-core: Report custom parameters here
 summary['Reads']            = params.reads
@@ -358,7 +359,7 @@ workflow.onComplete {
     c_green = params.monochrome_logs ? '' : "\033[0;32m";
     c_red = params.monochrome_logs ? '' : "\033[0;31m";
     if(workflow.success){
-        log.info "${c_purple}[{{ cookiecutter.name }}]${c_green} Pipeline complete${c_reset}"
+        log.info "${c_purple}[{{ cookiecutter.name }}]${c_green} Pipeline completed successfully${c_reset}"
     } else {
         checkHostname()
         log.info "${c_purple}[{{ cookiecutter.name }}]${c_red} Pipeline completed with errors${c_reset}"

diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
@@ -24,7 +24,6 @@ params {
   help = false
   igenomes_base = "./iGenomes"
   tracedir = "${params.outdir}/pipeline_info"
-  clusterOptions = false
   awsqueue = false
   awsregion = 'eu-west-1'
   igenomesIgnore = false