From 1ee1d693d811f0d7c0d951cd2c9144c75cde5216 Mon Sep 17 00:00:00 2001 From: nf-core-bot <core@nf-co.re> Date: Tue, 27 Oct 2020 09:25:20 +0000 Subject: [PATCH] Template update for nf-core/tools version 1.11 --- .github/CONTRIBUTING.md | 2 +- .github/ISSUE_TEMPLATE/bug_report.md | 2 +- .github/workflows/awsfulltest.yml | 4 +++- .github/workflows/awstest.yml | 9 ++++----- CHANGELOG.md | 2 +- Dockerfile | 6 +++--- README.md | 10 +++++----- assets/nf-core-hic_logo.png | Bin 10282 -> 288 bytes docs/README.md | 2 -- docs/images/nf-core-hic_logo.png | Bin 17777 -> 288 bytes docs/output.md | 8 +++++++- docs/usage.md | 13 ++++++++++--- environment.yml | 2 +- nextflow.config | 5 ++++- nextflow_schema.json | 4 ++-- 15 files changed, 42 insertions(+), 27 deletions(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 078248e..53f8478 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -54,4 +54,4 @@ These tests are run both with the latest available version of `Nextflow` and als ## Getting help -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)). diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md index a97d339..14a7e8b 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.md +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -36,7 +36,7 @@ Steps to reproduce the behaviour: ## Container engine -- Engine: <!-- [e.g. Conda, Docker or Singularity] --> +- Engine: <!-- [e.g. Conda, Docker, Singularity or Podman] --> - version: <!-- [e.g. 1.0.0] --> - Image tag: <!-- [e.g. nfcore/hic:1.0.0] --> diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 26d2e7e..76e9d38 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -1,10 +1,12 @@ 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 on: release: types: [published] + workflow_dispatch: jobs: run-awstest: diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 78ee5bc..cd8579f 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -1,11 +1,10 @@ name: nf-core AWS test # 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: - push: - branches: - - master + workflow_dispatch: jobs: run-awstest: @@ -37,4 +36,4 @@ jobs: --job-name nf-core-hic \ --job-queue $AWS_JOB_QUEUE \ --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": "'"$TOWER_ACCESS_TOKEN"'"}]}' diff --git a/CHANGELOG.md b/CHANGELOG.md index 5e1f95f..62f0e5f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v1.2.1 - [date] +## v1.2.2 - [date] Initial release of nf-core/hic, created with the [nf-core](https://nf-co.re/) template. diff --git a/Dockerfile b/Dockerfile index f7e704c..d7a7b24 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM nfcore/base:1.10.2 +FROM nfcore/base:1.11 LABEL authors="Nicolas Servant" \ description="Docker image containing all software requirements for the nf-core/hic pipeline" @@ -7,10 +7,10 @@ COPY environment.yml / RUN conda env create --quiet -f /environment.yml && conda clean -a # Add conda installation dir to PATH (instead of doing 'conda activate') -ENV PATH /opt/conda/envs/nf-core-hic-1.2.1/bin:$PATH +ENV PATH /opt/conda/envs/nf-core-hic-1.2.2/bin:$PATH # Dump the details of the installed packages to a file for posterity -RUN conda env export --name nf-core-hic-1.2.1 > nf-core-hic-1.2.1.yml +RUN conda env export --name nf-core-hic-1.2.2 > nf-core-hic-1.2.2.yml # Instruct R processes to use these empty files instead of clashing with a local version RUN touch .Rprofile diff --git a/README.md b/README.md index 8ef1c64..13e8e7c 100644 --- a/README.md +++ b/README.md @@ -18,12 +18,12 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool 1. Install [`nextflow`](https://nf-co.re/usage/installation) -2. Install either [`Docker`](https://docs.docker.com/engine/installation/) 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))_ +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))_ 3. Download the pipeline and test it on a minimal dataset with a single command: ```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) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment. @@ -33,14 +33,14 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool <!-- TODO nf-core: Update the example "typical command" below used to run the pipeline --> ```bash - nextflow run nf-core/hic -profile <docker/singularity/conda/institute> --input '*_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](docs/usage.md) for all of the available options when running the pipeline. +See [usage docs](https://nf-co.re/hic/usage) for all of the available options when running the pipeline. ## Documentation -The nf-core/hic pipeline comes with documentation about the pipeline which you can read at [https://nf-core/hic/docs](https://nf-core/hic/docs) or find in the [`docs/` directory](docs). +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). <!-- TODO nf-core: Add a brief overview of what the pipeline does and how it works --> diff --git a/assets/nf-core-hic_logo.png b/assets/nf-core-hic_logo.png index 6b364161664e70224fac3a83fb9f02ed0acbd9f8..dee3db82069b61e9a5380d940355f47ff565057c 100644 GIT binary patch literal 288 zcmaKn!EVAZ5Jd0(iYfQTPzk9AD^kHmL`q9kxd)CWS%D=(itV(`-**E&_qa1VJ8y-0 z(7UzWHwIh#TBG?`)zuoaM=2{~H&SY=@6J;(m(sk=N};CBQf<wP=D}9BHYJwxXS`GD zhu9KofA$$wV#T#5>Xf{12_<hSwc6?ZbZAljlVMlb6XBZ<$!CI3$aMbfql-R_7%uJ* z2)Re1_~p5F<aR{54wN!n0yEH0OVm-v@*i86*b31Ea*5M%ggZKaL2#L3!Gt$92A!T1 Ezej^vdH?_b literal 10282 zcmb_?Ra_iT(Cy+L+zApSIKhJxAUFgGZUKTW?k))yoZxQ3g1fuB`!2gcaCcec?*F?F z_vJo*57RRbJ*Q6Bbanlv>ikkumBYcLzytsQI12JI8UO%7Jp8#59Th(2u(M#nZx~MU zdaeM#n}Po>gk-iilmGxNKtblySFfxSu&-a1R`&hHw9xbfLwYe?n7&za%37EP<~wb* zz<sPo>E+Kvts|dxPD$|bxbEj}F3nkvlx9iWA|iDpB~cKFzw3SdUR39$=Z2C`6w(lq 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the different command-line flags. * [Output](output.md) diff --git a/docs/images/nf-core-hic_logo.png b/docs/images/nf-core-hic_logo.png index e5fead372861ff430d7f1428e15dad9b045523e8..dee3db82069b61e9a5380d940355f47ff565057c 100644 GIT binary patch literal 288 zcmaKn!EVAZ5Jd0(iYfQTPzk9AD^kHmL`q9kxd)CWS%D=(itV(`-**E&_qa1VJ8y-0 z(7UzWHwIh#TBG?`)zuoaM=2{~H&SY=@6J;(m(sk=N};CBQf<wP=D}9BHYJwxXS`GD zhu9KofA$$wV#T#5>Xf{12_<hSwc6?ZbZAljlVMlb6XBZ<$!CI3$aMbfql-R_7%uJ* z2)Re1_~p5F<aR{54wN!n0yEH0OVm-v@*i86*b31Ea*5M%ggZKaL2#L3!Gt$92A!T1 Ezej^vdH?_b literal 17777 zcmd43Ra9GD)HaF~D^77O#fn35Z-Ewv;=v_Iad$6JXt5S|iWhg+LJ95=JXj%kf(8h3 z==*)=+?|{M>dzP%JK1B&v^D42YtCnX{iv>h|D5_c3JMColA^p83JMwk1qJmPHs;fv zi$3M?rwfj&qJakr3c;U$U(^&%0vZ&Qmncf|?{s{#kJo~-vvhMF9~Z=itx9J18<X=% zxtfymlRrmC|M~?0SanhS_}udA<;GgINM%I_kJ({D&0+Z=etRGp*_??<WBqE`UVSvz zt5+{yS(X(i8!EFGtC!C1duA$4+}yh*D%pt7vbI&LR$D<d=q=uq4twQrwy`d-L3cgg z%KzW<DF;%Upb`@kE5+}OrZxE8`{(j|lz2f5T!v|b|NO{kRs~%lTqd2?&a8x`w(1Rj 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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 after the pipeline has finished. All paths are relative to the top-level results directory. @@ -40,7 +46,7 @@ For more information about how to use MultiQC reports, see [https://multiqc.info **Output files:** -* `multiqc/` +* `multiqc/` * `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser. * `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline. * `multiqc_plots/`: directory containing static images from the report in various formats. diff --git a/docs/usage.md b/docs/usage.md index 2141915..76803dd 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -1,5 +1,9 @@ # 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 <!-- TODO nf-core: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website. --> @@ -47,7 +51,7 @@ This version number will be logged in reports when you run the pipeline, so that Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments. -Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Conda) - see below. +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. > We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. @@ -64,8 +68,11 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof * `singularity` * 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/) +* `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` - * Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker or Singularity. + * Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity or Podman. * A generic configuration profile to be used with [Conda](https://conda.io/docs/) * Pulls most software from [Bioconda](https://bioconda.github.io/) * `test` @@ -98,7 +105,7 @@ process { See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for more information. -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 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. If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs). diff --git a/environment.yml b/environment.yml index bda1cbf..5762739 100644 --- a/environment.yml +++ b/environment.yml @@ -1,6 +1,6 @@ # You can use this file to create a conda environment for this pipeline: # conda env create -f environment.yml -name: nf-core-hic-1.2.1 +name: nf-core-hic-1.2.2 channels: - conda-forge - bioconda diff --git a/nextflow.config b/nextflow.config index 7c450f1..42d1074 100644 --- a/nextflow.config +++ b/nextflow.config @@ -71,6 +71,9 @@ profiles { singularity.enabled = true singularity.autoMounts = true } + podman { + podman.enabled = true + } test { includeConfig 'conf/test.config' } } @@ -113,7 +116,7 @@ manifest { description = 'Analysis of Chromosome Conformation Capture data (Hi-C)' mainScript = 'main.nf' nextflowVersion = '>=19.10.0' - version = '1.2.1' + version = '1.2.2' } // Function to ensure that resource requirements don't go beyond diff --git a/nextflow_schema.json b/nextflow_schema.json index ccbfe4b..21e29d7 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,5 +1,5 @@ { - "$schema": "https://json-schema.org/draft-07/schema", + "$schema": "http://json-schema.org/draft-07/schema", "$id": "https://raw.githubusercontent.com/nf-core/hic/master/nextflow_schema.json", "title": "nf-core/hic pipeline parameters", "description": "Analysis of Chromosome Conformation Capture data (Hi-C)", @@ -101,7 +101,7 @@ "link", "copy", "copyNoFollow", - "mov" + "move" ] }, "name": { -- GitLab