nf-core · ewels · Mar 19, 2019 · Mar 17, 2019 · Mar 17, 2019 · Mar 17, 2019
diff --git a/.travis.yml b/.travis.yml
@@ -26,10 +26,13 @@ install:
   - sudo apt-get install npm && npm install -g markdownlint-cli # For documentation linting
 
 script:
+  # Test the main code in this repo
   - pytest --cov=nf_core .
+  - markdownlint . -c ${TRAVIS_BUILD_DIR}/.github/markdownlint.yml
+  # Test the pipeline template code
   - nf-core create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"
   - nf-core lint nf-core-testpipeline
-  - markdownlint . -c ${TRAVIS_BUILD_DIR}/.github/markdownlint.yml
+  - markdownlint nf-core-testpipeline -c nf-core-testpipeline/.github/markdownlint.yml
 
 after_success:
   - codecov --rcfile=${TRAVIS_BUILD_DIR}/.github/coveragerc

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,8 +2,11 @@
 
 ## v1.6dev
 
-_..nothing yet.._
-#### Syncing Functionality
+#### Template pipeline
+* Fixed markdown linting
+* Tools CI testing now runs markdown lint on compiled template pipeline
+
+#### Tools helper code
 * Drop [nf-core/rnaseq](https://github.com/nf-core/rnaseq]) from `blacklist.json` to make template sync available
 
 ## [v1.5](https://github.com/nf-core/tools/releases/tag/1.5) - 2019-03-13 Iron Shark

diff --git a/README.md b/README.md
@@ -50,7 +50,7 @@ The command `nf-core list` shows all available nf-core pipelines along with thei
 
 An example of the output from the command is as follows:
 
-```bash
+```txt
 $ nf-core list
 
                                           ,--./,-.
@@ -75,7 +75,7 @@ nf-core/vipr       dev        -            -              No
 
 To narrow down the list, supply one or more additional keywords to filter the pipelines based on matches in titles, descriptions and topics:
 
-```bash
+```txt
 nf-core list rna rna-seq
 
                                           ,--./,-.
@@ -103,7 +103,7 @@ To make this process easier and ensure accurate retrieval of correctly versioned
 
 By default, the pipeline will just download the pipeline code. If you specify the flag `--singularity`, it will also download any singularity image files that are required.
 
-```bash
+```txt
 $ nf-core download methylseq --singularity
 
                                           ,--./,-.
@@ -124,7 +124,7 @@ INFO: Downloading 1 singularity container
 nf-core-methylseq-1.0.simg [762.28MB]  [####################################]  780573/780572
 ```
 
-```bash
+```txt
 $ tree -L 2 nf-core-methylseq-1.0/
 
 nf-core-methylseq-1.0/
@@ -150,7 +150,7 @@ nf-core-methylseq-1.0/
 ## Pipeline software licences
 Sometimes it's useful to see the software licences of the tools used in a pipeline. You can use the `licences` subcommand to fetch and print the software licence from each conda / PyPI package used in an nf-core pipeline.
 
-```bash
+```txt
 $ nf-core licences rnaseq
 
                                           ,--./,-.
@@ -191,7 +191,7 @@ With a given pipeline name, description and author, it makes a starter pipeline
 After creating the files, the command initialises the folder as a git repository and makes an initial commit. This first "vanilla" commit which is identical to the output from the templating tool is important, as it allows us to keep your pipeline in sync with the base template in the future.
 See the [nf-core syncing docs](http://nf-co.re/sync) for more information.
 
-```bash
+```txt
 $ nf-core create
 
                                           ,--./,-.
@@ -217,7 +217,7 @@ INFO: Done. Remember to add a remote and push to GitHub:
 Once you have run the command, create a new empty repository on GitHub under your username (not the `nf-core` organisation, yet).
 On your computer, add this repository as a git remote and push to it:
 
-```bash
+```txt
 git remote add origin https://github.com/ewels/nf-core-nextbigthing.git
 git push --set-upstream origin master
 ```
@@ -235,7 +235,7 @@ This is the same test that is used on the automated continuous integration tests
 
 For example, the current version looks something like this:
 
-```bash
+```txt
 $ cd path/to/my_pipeline
 $ nf-core lint .
 
@@ -268,7 +268,7 @@ The command uses results from the linting process, so will only work with workfl
 
 Usage is `nf-core bump-version <pipeline_dir> <new_version>`, eg:
 
-```bash
+```txt
 $ cd path/to/my_pipeline
 $ nf-core bump-version . 1.0
 

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
@@ -126,6 +126,7 @@ 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
@@ -360,7 +361,7 @@ 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
@@ -16,15 +16,14 @@ params {
 
   // Boilerplate options
   name = false
-  multiqc_config = "$baseDir/conf/multiqc_config.yaml"
+  multiqc_config = "$baseDir/assets/multiqc_config.yaml"
   email = false
   maxMultiqcEmailFileSize = 25.MB
   plaintext_email = false
   monochrome_logs = false
   help = false
   igenomes_base = "./iGenomes"
   tracedir = "${params.outdir}/pipeline_info"
-  clusterOptions = false
   awsqueue = false
   awsregion = 'eu-west-1'
   igenomesIgnore = false