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ewels merged 2 commits into from
Apr 8, 2019
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Removed Gitter everywhere, updated docs and multiqc updates #300

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0b20556
Bugfixes and multiqc updates
drpatelh Apr 8, 2019
796adc2
Update CHANGELOG
drpatelh Apr 8, 2019
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6 changes: 3 additions & 3 deletions .github/CONTRIBUTING.md
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Expand Up @@ -6,7 +6,7 @@ We try to manage the required tasks for nf-core/tools using GitHub issues, you p

However, don't be put off by this template - other more general issues and suggestions are welcome! Contributions to the code are even more welcome ;)

> If you need help using or developing nf-core/tools then the best place to go is the Gitter chatroom where you can ask us questions directly: https://gitter.im/nf-core/Lobby
> If you need help using or developing nf-core/tools then the best place to ask is the nf-core `tools` channel on [Slack](https://nf-core-invite.herokuapp.com/).

## Contribution workflow
If you'd like to write some code for nf-core/tools, the standard workflow
Expand All @@ -24,7 +24,7 @@ If you're not used to this workflow with git, you can start with some [basic doc

## Style guide
Google provides an excellent [style guide](https://github.com/google/styleguide/blob/gh-pages/pyguide.md), which
is an best practise extension of [PEP](https://www.python.org/dev/peps/), the Python Enhancement Proposals. Have a look at the
is an best practise extension of [PEP](https://www.python.org/dev/peps/), the Python Enhancement Proposals. Have a look at the
[docstring](https://github.com/google/styleguide/blob/gh-pages/pyguide.md#38-comments-and-docstrings) section, which is in particular
important, as nf-core tool's code documentation is generated out of these automatically.

Expand Down Expand Up @@ -68,4 +68,4 @@ nf-core lint nf-core-testpipeline
```

## Getting help
For further information/help, please consult the [nf-core/tools documentation](https://github.com/nf-core/tools#documentation) and don't hesitate to get in touch on [Gitter](https://gitter.im/nf-core/Lobby)
For further information/help, please consult the [nf-core/tools documentation](https://github.com/nf-core/tools#documentation) and don't hesitate to get in touch on the nf-core `tools` channel on [Slack](https://nf-core-invite.herokuapp.com/).
4 changes: 3 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -7,7 +7,9 @@
* Fixed markdown linting
* Tools CI testing now runs markdown lint on compiled template pipeline
* Migrated large portions of documentation to the [nf-core website](https://github.com/nf-core/nf-co.re/pull/93)

* Removed Gitter references in `.github/` directories for `tools/` and pipeline template.
* Changed `scrape_software_versions.py` to output `.csv` file
* Added `export_plots` parameter to multiqc config

#### Tools helper code
* Drop [nf-core/rnaseq](https://github.com/nf-core/rnaseq]) from `blacklist.json` to make template sync available
Expand Down
6 changes: 4 additions & 2 deletions nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/CONTRIBUTING.md
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Expand Up @@ -6,7 +6,9 @@ We try to manage the required tasks for {{ cookiecutter.name }} using GitHub iss

However, don't be put off by this template - other more general issues and suggestions are welcome! Contributions to the code are even more welcome ;)

> If you need help using or modifying {{ cookiecutter.name }} then the best place to go is the Gitter chatroom where you can ask us questions directly: https://gitter.im/nf-core/Lobby
> If you need help using or modifying {{ cookiecutter.name }} then the best place to ask is on the pipeline channel on [Slack](https://nf-core-invite.herokuapp.com/).



## Contribution workflow
If you'd like to write some code for {{ cookiecutter.name }}, the standard workflow
Expand Down Expand Up @@ -42,4 +44,4 @@ If there are any failures then the automated tests fail.
These tests are run both with the latest available version of Nextflow and also the minimum required version that is stated in the pipeline code.

## Getting help
For further information/help, please consult the [{{ cookiecutter.name }} documentation](https://github.com/{{ cookiecutter.name }}#documentation) and don't hesitate to get in touch on [Gitter](https://gitter.im/nf-core/Lobby)
For further information/help, please consult the [{{ cookiecutter.name }} documentation](https://github.com/{{ cookiecutter.name }}#documentation) and don't hesitate to get in touch on the pipeline channel on [Slack](https://nf-core-invite.herokuapp.com/).
2 changes: 1 addition & 1 deletion nf_core/pipeline-template/{{cookiecutter.name_noslash}}/CODE_OF_CONDUCT.md
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Expand Up @@ -34,7 +34,7 @@ This Code of Conduct applies both within project spaces and in public spaces whe

## Enforcement

Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team on the [Gitter channel](https://gitter.im/nf-core/Lobby). The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team on [Slack](https://nf-core-invite.herokuapp.com/). The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.

Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.

Expand Down
12 changes: 6 additions & 6 deletions nf_core/pipeline-template/{{cookiecutter.name_noslash}}/README.md
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Expand Up @@ -9,20 +9,20 @@
[![Docker](https://img.shields.io/docker/automated/{{ cookiecutter.name_docker }}.svg)](https://hub.docker.com/r/{{ cookiecutter.name_docker }})

## Introduction
The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.
The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.


## Documentation
The {{ cookiecutter.name }} pipeline comes with documentation about the pipeline, found in the `docs/` directory:

1. [Installation](docs/installation.md)
1. [Installation](https://nf-co.re/usage/installation)
2. Pipeline configuration
* [Local installation](docs/configuration/local.md)
* [Adding your own system](docs/configuration/adding_your_own.md)
* [Reference genomes](docs/configuration/reference_genomes.md)
* [Local installation](https://nf-co.re/usage/local_installation)
* [Adding your own system config](https://nf-co.re/usage/adding_own_config)
* [Reference genomes](https://nf-co.re/usage/reference_genomes)
3. [Running the pipeline](docs/usage.md)
4. [Output and how to interpret the results](docs/output.md)
5. [Troubleshooting](docs/troubleshooting.md)
5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)

<!-- TODO nf-core: Add a brief overview of what the pipeline does and how it works -->

Expand Down
17 changes: 0 additions & 17 deletions nf_core/pipeline-template/{{cookiecutter.name_noslash}}/assets/email_template.txt
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Expand Up @@ -17,23 +17,6 @@ ${errorReport}
} %>


<% if (!success){
out << """####################################################
## {{ cookiecutter.name }} execution completed unsuccessfully! ##
####################################################
The exit status of the task that caused the workflow execution to fail was: $exitStatus.
The full error message was:

${errorReport}
"""
} else {
out << "## {{ cookiecutter.name }} execution completed successfully! ##"
}
%>




The workflow was completed at $dateComplete (duration: $duration)

The command used to launch the workflow was as follows:
Expand Down
2 changes: 2 additions & 0 deletions nf_core/pipeline-template/{{cookiecutter.name_noslash}}/assets/multiqc_config.yaml
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Expand Up @@ -5,3 +5,5 @@ report_comment: >
report_section_order:
{{ cookiecutter.name.lower().replace(' ', '-') }}-software-versions:
order: -1000

export_plots: true
14 changes: 12 additions & 2 deletions nf_core/pipeline-template/{{cookiecutter.name_noslash}}/bin/scrape_software_versions.py
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Expand Up @@ -24,9 +24,14 @@
if match:
results[k] = "v{}".format(match.group(1))

# Remove software set to false in results
for k in results:
if not results[k]:
del(results[k])

# Dump to YAML
print ('''
id: '{{ cookiecutter.name.lower().replace(' ', '-') }}-software-versions'
id: 'software_versions'
section_name: '{{ cookiecutter.name }} Software Versions'
section_href: 'https://github.com/{{ cookiecutter.name }}'
plot_type: 'html'
Expand All @@ -35,5 +40,10 @@
<dl class="dl-horizontal">
''')
for k,v in results.items():
print(" <dt>{}</dt><dd>{}</dd>".format(k,v))
print(" <dt>{}</dt><dd><samp>{}</samp></dd>".format(k,v))
print (" </dl>")

# Write out regexes as csv file:
with open('software_versions.csv', 'w') as f:
for k,v in results.items():
f.write("{}\t{}\n".format(k,v))
2 changes: 1 addition & 1 deletion nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/README.md
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Expand Up @@ -6,7 +6,7 @@ The {{ cookiecutter.name }} documentation is split into the following files:
2. Pipeline configuration
* [Local installation](https://nf-co.re/usage/local_installation)
* [Adding your own system config](https://nf-co.re/usage/adding_own_config)
* [Reference genomes](https://nf-co.re/usage/reference_genomeslocal_)
* [Reference genomes](https://nf-co.re/usage/reference_genomes)
3. [Running the pipeline](usage.md)
4. [Output and how to interpret the results](output.md)
5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)
4 changes: 2 additions & 2 deletions nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/usage.md
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Expand Up @@ -101,7 +101,7 @@ If `-profile` is not specified at all the pipeline will be run locally and expec
* Pulls software from dockerhub: [`{{ cookiecutter.name_docker }}`](http://hub.docker.com/r/{{ cookiecutter.name_docker }}/)
* `singularity`
* A generic configuration profile to be used with [Singularity](http://singularity.lbl.gov/)
* Pulls software from DockerHub
* Pulls software from DockerHub: [`{{ cookiecutter.name_docker }}`](http://hub.docker.com/r/{{ cookiecutter.name_docker }}/)
* `test`
* A profile with a complete configuration for automated testing
* Includes links to test data so needs no other parameters
Expand Down Expand Up @@ -190,7 +190,7 @@ Wherever process-specific requirements are set in the pipeline, the default valu

If you are likely to be running `nf-core` pipelines regularly it may be a good idea to request that your custom config file is uploaded to the `nf-core/configs` git repository. Before you do this please can you test that the config file works with your pipeline of choice using the `-c` parameter (see definition below). You can then create a pull request to the `nf-core/configs` repository with the addition of your config file, associated documentation file (see examples in [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs)), and amending [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) to include your custom profile.

If you have any questions or issues please send us a message on [`Slack`](https://nf-core-invite.herokuapp.com/).
If you have any questions or issues please send us a message on [Slack](https://nf-core-invite.herokuapp.com/).

## 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.
Expand Down
11 changes: 9 additions & 2 deletions nf_core/pipeline-template/{{cookiecutter.name_noslash}}/main.nf
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Expand Up @@ -178,9 +178,15 @@ ${summary.collect { k,v -> " <dt>$k</dt><dd><samp>${v ?: '<span style
* Parse software version numbers
*/
process get_software_versions {
publishDir "${params.outdir}/pipeline_info", mode: 'copy',
saveAs: {filename ->
if (filename.indexOf(".csv") > 0) filename
else null
}

output:
file 'software_versions_mqc.yaml' into software_versions_yaml
file "software_versions.csv"

script:
// TODO nf-core: Get all tools to print their version number here
Expand All @@ -189,7 +195,7 @@ process get_software_versions {
echo $workflow.nextflow.version > v_nextflow.txt
fastqc --version > v_fastqc.txt
multiqc --version > v_multiqc.txt
scrape_software_versions.py > software_versions_mqc.yaml
scrape_software_versions.py &> software_versions_mqc.yaml
"""
}

Expand Down Expand Up @@ -227,12 +233,13 @@ process multiqc {
file multiqc_config from ch_multiqc_config
// TODO nf-core: Add in log files from your new processes for MultiQC to find!
file ('fastqc/*') from fastqc_results.collect().ifEmpty([])
file ('software_versions/*') from software_versions_yaml
file ('software_versions/*') from software_versions_yaml.collect()
file workflow_summary from create_workflow_summary(summary)

output:
file "*multiqc_report.html" into multiqc_report
file "*_data"
file "multiqc_plots"

script:
rtitle = custom_runName ? "--title \"$custom_runName\"" : ''
Expand Down