8000 Create TEMPLATE branch for automated syncing by drpatelh · Pull Request #30 · nf-core/atacseq · GitHub
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Apr 11, 2019
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6 changes: 4 additions & 2 deletions .github/CONTRIBUTING.md
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,9 @@ We try to manage the required tasks for nf-core/atacseq using GitHub issues, you

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 nf-core/atacseq then the best place to ask is the nf-core `atacseq` channel on [Slack](https://nf-core-invite.herokuapp.com/).
> If you need help using or modifying nf-core/atacseq 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 nf-core/atacseq, 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 [nf-core/atacseq documentation](https://github.com/nf-core/atacseq#documentation) and don't hesitate to get in touch on the nf-core `atacseq` channel on [Slack](https://nf-core-invite.herokuapp.com/).
For further information/help, please consult the [nf-core/atacseq documentation](https://github.com/nf-core/atacseq#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 .github/ISSUE_TEMPLATE/bug_report.md
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Expand Up @@ -25,7 +25,7 @@ A clear and concise description of what you expected to happen.
#### Container engine:
- Engine: [e.g. Conda, Docker or Singularity]
- version: [e.g. 1.0.0]
- Image tag: [e.g. nfcore/imcyto:1.0.0]
- Image tag: [e.g. nfcore/atacseq:1.0.0]

#### Additional context
Add any other context about the problem here.
2 changes: 1 addition & 1 deletion CHANGELOG.md
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@@ -1,4 +1,4 @@
# nf-core/atacseq: Changelog

## v1.0dev - [date]
## v1.0.0 - [date]
Initial release of nf-core/atacseq, created with the [nf-core](http://nf-co.re/) template.
4 changes: 2 additions & 2 deletions Dockerfile 8000
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@@ -1,6 +1,6 @@
FROM nfcore/base
LABEL authors="harshil.patel@crick.ac.uk" \
description="Docker image containing all requirements for the nfcore/atacseq pipeline"
LABEL authors="Harshil Patel" \
description="Docker image containing all requirements for nf-core/atacseq pipeline"

COPY environment.yml /
RUN conda env create -f /environment.yml && conda clean -a
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9 changes: 9 additions & 0 deletions assets/multiqc_config.yaml
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@@ -0,0 +1,9 @@
report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/atacseq" target="_blank">nf-core/atacseq</a>
analysis pipeline. For information about how to interpret these results, please see the
<a href="https://github.com/nf-core/atacseq" target="_blank">documentation</a>.
report_section_order:
nf-core/atacseq-software-versions:
order: -1000

export_plots: true
2 changes: 1 addition & 1 deletion bin/scrape_software_versions.py
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Expand Up @@ -48,7 +48,7 @@
if match:
results[k] = "v{}".format(match.group(1))

# Strip HOMER
# Remove software set to false in results
for k in results:
if not results[k]:
del(results[k])
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7 changes: 4 additions & 3 deletions docs/usage.md
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Expand Up @@ -192,7 +192,7 @@ The pipeline config files come bundled with paths to the illumina iGenomes refer
### `--genome` (using iGenomes)
There are 31 different species supported in the iGenomes references. To run the pipeline, you must specify which to use with the `--genome` flag.

You can find the keys to specify the genomes in the [`iGenomes config file`](../conf/igenomes.config). Common genomes that are supported are:
You can find the keys to specify the genomes in the [iGenomes config file](../conf/igenomes.config). Common genomes that are supported are:

* Human
* `--genome GRCh37`
Expand Down Expand Up @@ -364,7 +364,8 @@ You can also supply a run name to resume a specific run: `-resume [run-name]`. U
Specify the path to a specific config file (this is a core NextFlow command).

**NB:** Single hyphen (core Nextflow option)
**NB:** You can use this config to override pipeline defaults.

Note - you can use this to override pipeline defaults.

### `--custom_config_version`
Provide git commit id for custom Institutional configs hosted at `nf-core/configs`. This was implemented for reproducibility purposes. Default is set to `master`.
Expand All @@ -388,7 +389,7 @@ unzip master.zip

## Run the pipeline
cd /path/to/my/data
nextflow run /path/to/atacseq_pipeline/ --custom_config_base /path/to/my/configs/configs-master/
nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/
```

> Note that the nf-core/tools helper package has a `download` command to download all required pipeline
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8 changes: 7 additions & 1 deletion main.nf
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Expand Up @@ -1775,7 +1775,6 @@ workflow.onComplete {
if(workflow.commitId) email_fields['summary']['Pipeline repository Git Commit'] = workflow.commitId
if(workflow.revision) email_fields['summary']['Pipeline Git branch/tag'] = workflow.revision
if(workflow.container) email_fields['summary']['Docker image'] = workflow.container
email_fields['skipped_poor_alignment'] = skipped_poor_alignment
email_fields['summary']['Nextflow Version'] = workflow.nextflow.version
email_fields['summary']['Nextflow Build'] = workflow.nextflow.build
email_fields['summary']['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
Expand Down Expand Up @@ -1839,6 +1838,13 @@ workflow.onComplete {
c_purple = params.monochrome_logs ? '' : "\033[0;35m";
c_green = params.monochrome_logs ? '' : "\033[0;32m";
c_red = params.monochrome_logs ? '' : "\033[0;31m";

if (workflow.stats.ignoredCountFmt > 0 && workflow.success) {
log.info "${c_purple}Warning, pipeline completed, but with errored process(es) ${c_reset}"
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Maybe you want to get rid of this line, which is always reporting an error ...

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Yep. Ill do that when I bump-versions in the dev branch.

log.info "${c_red}Number of ignored errored process(es) : ${workflow.stats.ignoredCountFmt} ${c_reset}"
log.info "${c_green}Number of successfully ran process(es) : ${workflow.stats.succeedCountFmt} ${c_reset}"
}

if(workflow.success){
log.info "${c_purple}[nf-core/atacseq]${c_green} Pipeline completed successfully${c_reset}"
} else {
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8 changes: 4 additions & 4 deletions nextflow.config
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Expand Up @@ -105,19 +105,19 @@ process.shell = ['/bin/bash', '-euo', 'pipefail']

timeline {
enabled = true
file = "${params.tracedir}/nf-core/execution_timeline.html"
file = "${params.tracedir}/execution_timeline.html"
}
report {
enabled = true
file = "${params.tracedir}/nf-core/execution_report.html"
file = "${params.tracedir}/execution_report.html"
}
trace {
enabled = true
file = "${params.tracedir}/nf-core/execution_trace.txt"
file = "${params.tracedir}/execution_trace.txt"
}
dag {
enabled = true
file = "${params.tracedir}/nf-core/pipeline_dag.svg"
file = "${params.tracedir}/pipeline_dag.svg"
}

manifest {
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