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Unverified Commit 28aeafaa authored by Phil Ewels's avatar Phil Ewels Committed by GitHub
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Merge pull request #79 from ewels/nf-core-template-merge-1.11

nf-core template merge v1.11
parents c7475fc9 3abd228c
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...@@ -59,4 +59,4 @@ For further information/help, please consult the [nf-core/hic documentation](htt ...@@ -59,4 +59,4 @@ For further information/help, please consult the [nf-core/hic documentation](htt
don't hesitate to get in touch on the nf-core Slack [#hic](https://nfcore.slack.com/channels/hic) channel don't hesitate to get in touch on the nf-core Slack [#hic](https://nfcore.slack.com/channels/hic) channel
([join our Slack here](https://nf-co.re/join/slack)). ([join our Slack here](https://nf-co.re/join/slack)).
For further information/help, please consult the [nf-core/hic documentation](https://nf-co.re/hic/docs) and don't hesitate to get in touch on the nf-core Slack [#hic](https://nfcore.slack.com/channels/hic) channel ([join our Slack here](https://nf-co.re/join/slack)). For further information/help, please consult the [nf-core/hic documentation](https://nf-co.re/hic/usage) and don't hesitate to get in touch on the nf-core Slack [#hic](https://nfcore.slack.com/channels/hic) channel ([join our Slack here](https://nf-co.re/join/slack)).
...@@ -35,7 +35,7 @@ Steps to reproduce the behaviour: ...@@ -35,7 +35,7 @@ Steps to reproduce the behaviour:
## Container engine ## Container engine
- Engine: <!-- [e.g. Conda, Docker or Singularity] --> - Engine: <!-- [e.g. Conda, Docker, Singularity or Podman] -->
- version: <!-- [e.g. 1.0.0] --> - version: <!-- [e.g. 1.0.0] -->
- Image tag: <!-- [e.g. nfcore/hic:1.0.0] --> - Image tag: <!-- [e.g. nfcore/hic:1.0.0] -->
......
name: nf-core AWS full size tests name: nf-core AWS full size tests
# This workflow is triggered on push to the master branch. # This workflow is triggered on published releases.
# It can be additionally triggered manually with GitHub actions workflow dispatch.
# It runs the -profile 'test_full' on AWS batch # It runs the -profile 'test_full' on AWS batch
on: on:
release: release:
types: [published] types: [published]
workflow_dispatch:
jobs: jobs:
run-awstest: run-awstest:
......
name: nf-core AWS test name: nf-core AWS test
# This workflow is triggered on push to the master branch. # This workflow is triggered on push to the master branch.
# It runs the -profile 'test' on AWS batch # It can be additionally triggered manually with GitHub actions workflow dispatch.
# It runs the -profile 'test' on AWS batch.
on: on:
push: workflow_dispatch:
branches:
- master
jobs: jobs:
run-awstest: run-awstest:
...@@ -36,4 +35,4 @@ jobs: ...@@ -36,4 +35,4 @@ jobs:
--job-name nf-core-hic \ --job-name nf-core-hic \
--job-queue $AWS_JOB_QUEUE \ --job-queue $AWS_JOB_QUEUE \
--job-definition $AWS_JOB_DEFINITION \ --job-definition $AWS_JOB_DEFINITION \
--container-overrides '{"command": ["nf-core/hic", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/hic/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/hic/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'hic/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}' --container-overrides '{"command": ["nf-core/hic", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/hic/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/hic/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
...@@ -34,13 +34,13 @@ jobs: ...@@ -34,13 +34,13 @@ jobs:
- name: Build new docker image - name: Build new docker image
if: env.GIT_DIFF if: env.GIT_DIFF
run: docker build --no-cache . -t nfcore/hic:1.2.2 run: docker build --no-cache . -t nfcore/hic:dev
- name: Pull docker image - name: Pull docker image
if: ${{ !env.GIT_DIFF }} if: ${{ !env.GIT_DIFF }}
run: | run: |
docker pull nfcore/hic:dev docker pull nfcore/hic:dev
docker tag nfcore/hic:dev nfcore/hic:1.2.2 docker tag nfcore/hic:dev nfcore/hic:dev
- name: Install Nextflow - name: Install Nextflow
run: | run: |
......
...@@ -3,6 +3,11 @@ ...@@ -3,6 +3,11 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
## v1.3.0dev
* Template update for nf-core/tools v1.11
* Minor fix to summary log messages in pipeline header
## v1.2.2 - 2020-09-02 ## v1.2.2 - 2020-09-02
### `Added` ### `Added`
......
FROM nfcore/base:1.10.2 FROM nfcore/base:1.11
LABEL authors="Nicolas Servant" \ LABEL authors="Nicolas Servant" \
description="Docker image containing all software requirements for the nf-core/hic pipeline" description="Docker image containing all software requirements for the nf-core/hic pipeline"
...@@ -10,10 +9,10 @@ COPY environment.yml / ...@@ -10,10 +9,10 @@ COPY environment.yml /
RUN conda env create --quiet -f /environment.yml && conda clean -a RUN conda env create --quiet -f /environment.yml && conda clean -a
# Add conda installation dir to PATH (instead of doing 'conda activate') # Add conda installation dir to PATH (instead of doing 'conda activate')
ENV PATH /opt/conda/envs/nf-core-hic-1.2.2/bin:$PATH ENV PATH /opt/conda/envs/nf-core-hic-1.3.0dev/bin:$PATH
# Dump the details of the installed packages to a file for posterity # Dump the details of the installed packages to a file for posterity
RUN conda env export --name nf-core-hic-1.2.2 > nf-core-hic-1.2.2.yml RUN conda env export --name nf-core-hic-1.3.0dev > nf-core-hic-1.3.0dev.yml
# Instruct R processes to use these empty files instead of clashing with a local version # Instruct R processes to use these empty files instead of clashing with a local version
RUN touch .Rprofile RUN touch .Rprofile
......
...@@ -42,17 +42,14 @@ sites (bowtie2) ...@@ -42,17 +42,14 @@ sites (bowtie2)
## Quick Start ## Quick Start
i. Install [`nextflow`](https://nf-co.re/usage/installation) 1. Install [`nextflow`](https://nf-co.re/usage/installation)
ii. Install either [`Docker`](https://docs.docker.com/engine/installation/) 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) or [`Podman`](https://podman.io/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_
or [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/)
for full pipeline reproducibility (please only use [`Conda`](https://conda.io/miniconda.html)
as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))
iii. Download the pipeline and test it on a minimal dataset with a single command 3. Download the pipeline and test it on a minimal dataset with a single command
```bash ```bash
nextflow run nf-core/hic -profile test,<docker/singularity/conda/institute> nextflow run nf-core/hic -profile test,<docker/singularity/podman/conda/institute>
``` ```
> Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) > Please check [nf-core/configs](https://github.com/nf-core/configs#documentation)
...@@ -61,35 +58,19 @@ If so, you can simply use `-profile <institute>` in your command. ...@@ -61,35 +58,19 @@ If so, you can simply use `-profile <institute>` in your command.
This will enable either `docker` or `singularity` and set the appropriate execution This will enable either `docker` or `singularity` and set the appropriate execution
settings for your local compute environment. settings for your local compute environment.
iv. Start running your own analysis! 4. Start running your own analysis!
```bash ```bash
nextflow run nf-core/hic -profile <docker/singularity/conda/institute> --reads '*_R{1,2}.fastq.gz' --genome GRCh37 nextflow run nf-core/hic -profile <docker/singularity/podman/conda/institute> --input '*_R{1,2}.fastq.gz' --genome GRCh37
``` ```
See [usage docs](https://nf-co.re/hic/usage) for all of the available options when running See [usage docs](https://nf-co.re/hic/usage) for all of the available options when running the pipeline.
the pipeline.
## Documentation ## Documentation
The nf-core/hic pipeline comes with documentation about the pipeline, The nf-core/hic pipeline comes with documentation about the pipeline: [usage](https://nf-co.re/hic/usage) and [output](https://nf-co.re/hic/output).
found in the `docs/` directory:
1. [Installation](https://nf-co.re/usage/installation) For further information or help, don't hesitate to get in touch on [Slack](https://nfcore.slack.com/channels/hic).
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_genomes)
3. [Running the pipeline](docs/usage.md)
4. [Output and how to interpret the results](docs/output.md)
5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)
The nf-core/hic pipeline comes with documentation about the pipeline which
you can read at [https://nf-co.re/hic/usage](https://nf-co.re/hic/usage) or
find in the [`docs/` directory](docs).
For further information or help, don't hesitate to get in touch on
[Slack](https://nfcore.slack.com/channels/hic).
You can join with [this invite](https://nf-co.re/join/slack). You can join with [this invite](https://nf-co.re/join/slack).
## Credits ## Credits
......
# nf-core/hic: Output # nf-core/hic: Output
This document describes the output produced by the pipeline. ## :warning: Please read this documentation on the nf-core website: [https://nf-co.re/hic/output](https://nf-co.re/hic/output)
Most of the plots are taken from the MultiQC report, which
summarises results at the end of the pipeline. > _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._
## Introduction
This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.
The directories listed below will be created in the results directory The directories listed below will be created in the results directory
after the pipeline has finished. All paths are relative to the top-level after the pipeline has finished. All paths are relative to the top-level
...@@ -191,12 +195,16 @@ reported in the MultiQC output for future traceability. ...@@ -191,12 +195,16 @@ reported in the MultiQC output for future traceability.
**Output files:** **Output files:**
* `Project_multiqc_report.html` * `multiqc/`
* MultiQC report - a standalone HTML file that can be viewed in your * `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
web browser * `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
* `Project_multiqc_data/` * `multiqc_plots/`: directory containing static images from the report in various formats.
* Directory containing parsed statistics from the different tools used
in the pipeline ## Pipeline information
[Nextflow](https://www.nextflow.io/docs/latest/tracing.html) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.
**Output files:**
* `pipeline_info/` * `pipeline_info/`
* Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, * Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`,
......
# nf-core/hic: Usage # nf-core/hic: Usage
## :warning: Please read this documentation on the nf-core website: [https://nf-co.re/hic/usage](https://nf-co.re/hic/usage)
> _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._
## Introduction
## Running the pipeline ## Running the pipeline
The typical command for running the pipeline is as follows: The typical command for running the pipeline is as follows:
...@@ -74,9 +80,7 @@ fails after three times then the pipeline is stopped. ...@@ -74,9 +80,7 @@ fails after three times then the pipeline is stopped.
Use this parameter to choose a configuration profile. Profiles can give Use this parameter to choose a configuration profile. Profiles can give
configuration presets for different compute environments. configuration presets for different compute environments.
Several generic profiles are bundled with the pipeline which instruct Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Conda) - see below.
the pipeline to use software packaged using different methods
(Docker, Singularity, Conda) - see below.
> We highly recommend the use of Docker or Singularity containers for full > We highly recommend the use of Docker or Singularity containers for full
pipeline reproducibility, however when this is not possible, Conda is also supported. pipeline reproducibility, however when this is not possible, Conda is also supported.
...@@ -104,9 +108,11 @@ installed and available on the `PATH`. This is _not_ recommended. ...@@ -104,9 +108,11 @@ installed and available on the `PATH`. This is _not_ recommended.
* `singularity` * `singularity`
* A generic configuration profile to be used with [Singularity](https://sylabs.io/docs/) * A generic configuration profile to be used with [Singularity](https://sylabs.io/docs/)
* Pulls software from Docker Hub: [`nfcore/hic`](https://hub.docker.com/r/nfcore/hic/) * Pulls software from Docker Hub: [`nfcore/hic`](https://hub.docker.com/r/nfcore/hic/)
* `podman`
* A generic configuration profile to be used with [Podman](https://podman.io/)
* Pulls software from Docker Hub: [`nfcore/hic`](https://hub.docker.com/r/nfcore/hic/)
* `conda` * `conda`
* Please only use Conda as a last resort i.e. when it's not possible to run the * Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity or Podman.
pipeline with Docker or Singularity.
* A generic configuration profile to be used with [Conda](https://conda.io/docs/) * A generic configuration profile to be used with [Conda](https://conda.io/docs/)
* Pulls most software from [Bioconda](https://bioconda.github.io/) * Pulls most software from [Bioconda](https://bioconda.github.io/)
* `test` * `test`
...@@ -151,15 +157,7 @@ process { ...@@ -151,15 +157,7 @@ process {
See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html)
for more information. for more information.
If you are likely to be running `nf-core` pipelines regularly it may be a 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 above). 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.
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 If you have any questions or issues please send us a message on
[Slack](https://nf-co.re/join/slack) on the [Slack](https://nf-co.re/join/slack) on the
...@@ -215,7 +213,7 @@ A normal glob pattern, enclosed in quotation marks, can then be used for `--inpu ...@@ -215,7 +213,7 @@ A normal glob pattern, enclosed in quotation marks, can then be used for `--inpu
For example: For example:
```bash ```bash
--single_end --reads '*.fastq' --single_end --input '*.fastq'
``` ```
It is not possible to run a mixture of single-end and paired-end files in one run. It is not possible to run a mixture of single-end and paired-end files in one run.
......
# You can use this file to create a conda environment for this pipeline: # You can use this file to create a conda environment for this pipeline:
# conda env create -f environment.yml # conda env create -f environment.yml
name: nf-core-hic-1.2.2 name: nf-core-hic-1.3.0dev
channels: channels:
- conda-forge - conda-forge
- bioconda - bioconda
......
...@@ -255,24 +255,17 @@ summary['Min Insert Size'] = params.min_insert_size ...@@ -255,24 +255,17 @@ summary['Min Insert Size'] = params.min_insert_size
summary['Max Insert Size'] = params.max_insert_size summary['Max Insert Size'] = params.max_insert_size
summary['Min CIS dist'] = params.min_cis_dist summary['Min CIS dist'] = params.min_cis_dist
summary['Maps resolution'] = params.bin_size summary['Maps resolution'] = params.bin_size
summary['Max Memory'] = params.max_memory summary['Max Resources'] = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job"
summary['Max CPUs'] = params.max_cpus if (workflow.containerEngine) summary['Container'] = "$workflow.containerEngine - $workflow.container"
summary['Max Time'] = params.max_time
summary['Output dir'] = params.outdir summary['Output dir'] = params.outdir
summary['Launch dir'] = workflow.launchDir
summary['Working dir'] = workflow.workDir summary['Working dir'] = workflow.workDir
summary['Container Engine'] = workflow.containerEngine
if(workflow.containerEngine)
summary['Container'] = workflow.container
summary['Current home'] = "$HOME"
summary['Current user'] = "$USER"
summary['Current path'] = "$PWD"
summary['Working dir'] = workflow.workDir
summary['Output dir'] = params.outdir
summary['Script dir'] = workflow.projectDir summary['Script dir'] = workflow.projectDir
summary['Config Profile'] = workflow.profile summary['User'] = workflow.userName
if(workflow.profile == 'awsbatch'){ if (workflow.profile.contains('awsbatch')) {
summary['AWS Region'] = params.awsregion summary['AWS Region'] = params.awsregion
summary['AWS Queue'] = params.awsqueue summary['AWS Queue'] = params.awsqueue
summary['AWS CLI'] = params.awscli
} }
summary['Config Profile'] = workflow.profile summary['Config Profile'] = workflow.profile
if (params.config_profile_description) summary['Config Profile Description'] = params.config_profile_description if (params.config_profile_description) summary['Config Profile Description'] = params.config_profile_description
......
...@@ -80,7 +80,7 @@ params { ...@@ -80,7 +80,7 @@ params {
// Container slug. Stable releases should specify release tag! // Container slug. Stable releases should specify release tag!
// Developmental code should specify :dev // Developmental code should specify :dev
process.container = 'nfcore/hic:1.2.2' process.container = 'nfcore/hic:dev'
// Load base.config by default for all pipelines // Load base.config by default for all pipelines
includeConfig 'conf/base.config' includeConfig 'conf/base.config'
...@@ -108,6 +108,9 @@ profiles { ...@@ -108,6 +108,9 @@ profiles {
singularity.enabled = true singularity.enabled = true
singularity.autoMounts = true singularity.autoMounts = true
} }
podman {
podman.enabled = true
}
test { includeConfig 'conf/test.config' } test { includeConfig 'conf/test.config' }
} }
...@@ -150,7 +153,7 @@ manifest { ...@@ -150,7 +153,7 @@ manifest {
description = 'Analysis of Chromosome Conformation Capture data (Hi-C)' description = 'Analysis of Chromosome Conformation Capture data (Hi-C)'
mainScript = 'main.nf' mainScript = 'main.nf'
nextflowVersion = '>=19.10.0' nextflowVersion = '>=19.10.0'
version = '1.2.2' version = '1.3.0dev'
} }
// Function to ensure that resource requirements don't go beyond // Function to ensure that resource requirements don't go beyond
......
{ {
"$schema": "https://json-schema.org/draft-07/schema", "$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/nf-core/hic/master/nextflow_schema.json", "$id": "https://raw.githubusercontent.com/nf-core/hic/master/nextflow_schema.json",
"title": "nf-core/hic pipeline parameters", "title": "nf-core/hic pipeline parameters",
"description": "Analysis of Chromosome Conformation Capture data (Hi-C)", "description": "Analysis of Chromosome Conformation Capture data (Hi-C)",
...@@ -295,7 +295,7 @@ ...@@ -295,7 +295,7 @@
"link", "link",
"copy", "copy",
"copyNoFollow", "copyNoFollow",
"mov" "move"
] ]
}, },
"name": { "name": {
......
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