From 65f1399da46fac85bb5462c0d1ed956cefc31d22 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Sun, 17 Mar 2019 18:03:58 +0100 Subject: [PATCH 1/4] Some more tweaks from the final rnaseq template merge --- .../{{cookiecutter.name_noslash}}/.gitignore | 1 + .../{{cookiecutter.name_noslash}}/conf/test.config | 2 ++ .../docs/configuration/reference_genomes.md | 3 ++- .../{{cookiecutter.name_noslash}}/docs/installation.md | 4 +++- .../{{cookiecutter.name_noslash}}/docs/output.md | 2 +- .../pipeline-template/{{cookiecutter.name_noslash}}/main.nf | 3 ++- .../{{cookiecutter.name_noslash}}/nextflow.config | 1 - 7 files changed, 11 insertions(+), 5 deletions(-) diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.gitignore b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.gitignore index 46f69e414b..5b54e3e6c2 100644 --- 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 index 661cb5e72c..3b221bb358 100644 --- 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/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/configuration/reference_genomes.md b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/configuration/reference_genomes.md index 622a2e052d..eade099839 100644 --- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/configuration/reference_genomes.md +++ b/nf_core/pipeline-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 index 5475c064c4..76779af573 100644 --- 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 index 034aa90199..c9b9b9e4e1 100644 --- 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 index 2cad5a6af9..8178ac77ab 100644 --- 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${c_reset}" diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config index 71896df174..956c38a409 100644 --- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config +++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config @@ -24,7 +24,6 @@ params { help = false igenomes_base = "./iGenomes" tracedir = "${params.outdir}/pipeline_info" - clusterOptions = false awsqueue = false awsregion = 'eu-west-1' igenomesIgnore = false From 65a19647a24285fd82036893021eb19fefa15c01 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Sun, 17 Mar 2019 18:06:45 +0100 Subject: [PATCH 2/4] Run markdown lint on the compiled pipeline --- .travis.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 32485e0fce..b3894a6c64 100644 --- 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 From 2a4453a3d60c84aa74ec6eeaf3baad1544b703b5 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Sun, 17 Mar 2019 18:08:19 +0100 Subject: [PATCH 3/4] Changelog --- CHANGELOG.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5b9a343f34..8d4fb34752 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,7 +2,9 @@ ## v1.6dev -_..nothing yet.._ +#### Template pipeline +* Fixed markdown linting +* Tools CI testing now runs markdown lint on compiled template pipeline ## [v1.5](https://github.com/nf-core/tools/releases/tag/1.5) - 2019-03-13 Iron Shark From c8b8b5aa340579d3edc9fcf237284d3d4ae4cb2d Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Sun, 17 Mar 2019 18:10:26 +0100 Subject: [PATCH 4/4] Fixed template multiqc config bug --- .../{{cookiecutter.name_noslash}}/nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config index 956c38a409..6f0d53a0bb 100644 --- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config +++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config @@ -16,7 +16,7 @@ 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