From e8cb375dd9b69704a5c21b8cc9aff2a6c88db309 Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Thu, 24 Aug 2023 10:11:36 +0200 Subject: [PATCH 01/15] bump version to 2.5.0dev --- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 3b0c72ff..f272acb5 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/scrnaseq + This report has been generated by the nf-core/scrnaseq analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-scrnaseq-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index 39d968b2..c69ed641 100644 --- a/nextflow.config +++ b/nextflow.config @@ -262,7 +262,7 @@ manifest { description = """Pipeline for processing 10x Genomics single cell rnaseq data""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.4.0' + version = '2.5.0dev' doi = '10.5281/zenodo.3568187' } From cf89f52464634de7072e74e5d3b2ae777253baea Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Thu, 24 Aug 2023 14:13:56 +0200 Subject: [PATCH 02/15] Update cellranger module --- CHANGELOG.md | 2 ++ modules.json | 6 +++--- .../cellranger/count/templates/cellranger_count.py | 11 ++++++++++- modules/nf-core/custom/dumpsoftwareversions/main.nf | 6 +++--- modules/nf-core/universc/README.md | 2 +- modules/nf-core/universc/main.nf | 12 ++++++++---- 6 files changed, 27 insertions(+), 12 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f1866715..ca49111e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unpublished Version / DEV] +- Fix false-positive filename check in cellranger module ([#TODO](TODO)) + ## v2.4.0 - 2023-08-16 Lime Platinum Crab - Fix typo causing empty version imformation for mtx_conversion subworkflow ([#254](https://github.com/nf-core/scrnaseq/pull/254)) diff --git a/modules.json b/modules.json index 95175143..823185bc 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "cellranger/count": { "branch": "master", - "git_sha": "716ef3019b66772a817b417078edce2f7b337858", + "git_sha": "1288cb1bff6f478affa34bf866e8ff13110607de", "installed_by": ["modules"] }, "cellranger/mkgtf": { @@ -22,7 +22,7 @@ }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4", "installed_by": ["modules"] }, "fastqc": { @@ -62,7 +62,7 @@ }, "universc": { "branch": "master", - "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b", + "git_sha": "cf67a6d7d043e2bd6a3099be84c72046fc71508f", "installed_by": ["modules"] } } diff --git a/modules/nf-core/cellranger/count/templates/cellranger_count.py b/modules/nf-core/cellranger/count/templates/cellranger_count.py index b121a538..464d2a91 100644 --- a/modules/nf-core/cellranger/count/templates/cellranger_count.py +++ b/modules/nf-core/cellranger/count/templates/cellranger_count.py @@ -3,6 +3,7 @@ from pathlib import Path from textwrap import dedent import shlex +import re def chunk_iter(seq, size): @@ -25,13 +26,21 @@ def chunk_iter(seq, size): fastq_all = Path("./fastq_all") fastq_all.mkdir(exist_ok=True) +# Match R1 in the filename, but only if it is followed by a non-digit or non-character +# match "file_R1.fastq.gz", "file.R1_000.fastq.gz", etc. but +# do not match "SRR12345", "file_INFIXR12", etc +filename_pattern = r'([^a-zA-Z0-9])R1([^a-zA-Z0-9])' for i, (r1, r2) in enumerate(chunk_iter(fastqs, 2)): - if r1.name.replace("R1", "R2") != r2.name: + # double escapes are required because nextflow processes this python 'template' + if re.sub(filename_pattern, r'\\1R2\\2', r1.name) != r2.name: raise AssertionError( dedent( f"""\ We expect R1 and R2 of the same sample to have the same filename except for R1/R2. + This has been checked by replacing "R1" with "R2" in the first filename and comparing it to the second filename. + If you believe this check shouldn't have failed on your filenames, please report an issue on GitHub! + Files involved: - {r1} - {r2} diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index ebc87273..c9d014b1 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.14" + conda "bioconda::multiqc=1.15" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : + 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/universc/README.md b/modules/nf-core/universc/README.md index e5da6f3b..793f4f13 100644 --- a/modules/nf-core/universc/README.md +++ b/modules/nf-core/universc/README.md @@ -48,7 +48,7 @@ process { container = "nf-core/universc:1.2.5.1" } withName: CELLRANGER_MKREF{ - container = "nf-core/universc:1.2.5.1" + container = "nf-core/universc:1.2.5.1" } ... } diff --git a/modules/nf-core/universc/main.nf b/modules/nf-core/universc/main.nf index 6d6cc020..de8394a0 100644 --- a/modules/nf-core/universc/main.nf +++ b/modules/nf-core/universc/main.nf @@ -2,10 +2,6 @@ process UNIVERSC { tag "$meta.id" label 'process_medium' - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "UNIVERSC module does not support Conda. Please use Docker / Singularity / Podman instead." - } container "nf-core/universc:1.2.5.1" if (workflow.containerEngine == 'docker'){ containerOptions = "--privileged" @@ -31,6 +27,10 @@ process UNIVERSC { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "UNIVERSC module does not support Conda. Please use Docker / Singularity / Podman instead." + } def args = task.ext.args ?: '' def sample_arg = meta.samples.unique().join(",") def reference_name = reference.name @@ -63,6 +63,10 @@ process UNIVERSC { stub: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "UNIVERSC module does not support Conda. Please use Docker / Singularity / Podman instead." + } """ mkdir -p "sample-${meta.id}/outs/" touch sample-${meta.id}/outs/fake_file.txt From 0bf2013bc1aea9bd7f2ee35b4d9d93eb3b283d0a Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Thu, 24 Aug 2023 14:16:10 +0200 Subject: [PATCH 03/15] Fix black --- .../nf-core/cellranger/count/templates/cellranger_count.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/cellranger/count/templates/cellranger_count.py b/modules/nf-core/cellranger/count/templates/cellranger_count.py index 464d2a91..2172927b 100644 --- a/modules/nf-core/cellranger/count/templates/cellranger_count.py +++ b/modules/nf-core/cellranger/count/templates/cellranger_count.py @@ -29,11 +29,11 @@ def chunk_iter(seq, size): # Match R1 in the filename, but only if it is followed by a non-digit or non-character # match "file_R1.fastq.gz", "file.R1_000.fastq.gz", etc. but # do not match "SRR12345", "file_INFIXR12", etc -filename_pattern = r'([^a-zA-Z0-9])R1([^a-zA-Z0-9])' +filename_pattern = r"([^a-zA-Z0-9])R1([^a-zA-Z0-9])" for i, (r1, r2) in enumerate(chunk_iter(fastqs, 2)): # double escapes are required because nextflow processes this python 'template' - if re.sub(filename_pattern, r'\\1R2\\2', r1.name) != r2.name: + if re.sub(filename_pattern, r"\\1R2\\2", r1.name) != r2.name: raise AssertionError( dedent( f"""\ From 4d676eb9a5c26b007d041716b54229c15c745b63 Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Thu, 21 Sep 2023 12:58:37 +0200 Subject: [PATCH 04/15] bump version for patch release --- CHANGELOG.md | 4 ++-- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ca49111e..4b4ef989 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,9 +3,9 @@ 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). -## [Unpublished Version / DEV] +## v2.4.1 - 2023-09-21 -- Fix false-positive filename check in cellranger module ([#TODO](TODO)) +- Fix false-positive filename check in cellranger module ([#261](https://github.com/nf-core/scrnaseq/pull/261)) ## v2.4.0 - 2023-08-16 Lime Platinum Crab diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index f272acb5..a1c4a586 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/scrnaseq + This report has been generated by the nf-core/scrnaseq analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-scrnaseq-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index c69ed641..1e1fe757 100644 --- a/nextflow.config +++ b/nextflow.config @@ -262,7 +262,7 @@ manifest { description = """Pipeline for processing 10x Genomics single cell rnaseq data""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.5.0dev' + version = '2.4.1' doi = '10.5281/zenodo.3568187' } From d8444791f3aa1325422eb8405c4b8e46472ffa0a Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Thu, 21 Sep 2023 13:21:46 +0200 Subject: [PATCH 05/15] Fix whitelist logic for dropseq --- modules/local/simpleaf_quant.nf | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/modules/local/simpleaf_quant.nf b/modules/local/simpleaf_quant.nf index eb95979e..0c879ceb 100644 --- a/modules/local/simpleaf_quant.nf +++ b/modules/local/simpleaf_quant.nf @@ -34,12 +34,15 @@ process SIMPLEAF_QUANT { // check if users are using one of the mutually excludable parameters: // e.g -k,--knee | -e,--expect-cells | -f, --forced-cells // - if (args_list.any { it in ['-k', '--knee', '-e', '--expect-cells', '-f', '--forced-cells']} || meta.expected_cells) { - unfiltered_command = "" - save_whitelist = "" - } else { - unfiltered_command = "-u whitelist.uncompressed.txt" - save_whitelist = "mv whitelist.uncompressed.txt ${prefix}_alevin_results/" + unzip_whitelist = "" + unfiltered_command = "" + save_whitelist = "" + if (!(args_list.any { it in ['-k', '--knee', '-e', '--expect-cells', '-f', '--forced-cells']} || meta.expected_cells)) { + if (whitelist) { + unzip_whitelist = "gzip -dcf $whitelist > whitelist.uncompressed.txt" + unfiltered_command = "-u whitelist.uncompressed.txt" + save_whitelist = "mv whitelist.uncompressed.txt ${prefix}_alevin_results/" + } } // expected cells @@ -55,7 +58,7 @@ process SIMPLEAF_QUANT { simpleaf set-paths # run simpleaf quant - gzip -dcf $whitelist > whitelist.uncompressed.txt + $unzip_whitelist simpleaf quant \\ -1 ${forward.join( "," )} \\ -2 ${reverse.join( "," )} \\ From 6224bd9c1827848a29ce7c311fbc64af24df5e7b Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Thu, 21 Sep 2023 13:22:29 +0200 Subject: [PATCH 06/15] Update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ca49111e..00a75677 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unpublished Version / DEV] - Fix false-positive filename check in cellranger module ([#TODO](TODO)) +- Fix whitelist logic for dropseq ([#267](https://github.com/nf-core/scrnaseq/pull/267)) ## v2.4.0 - 2023-08-16 Lime Platinum Crab From 07dd4a73d85650dd40a9bc3c2b3d2dd34f7d6d1a Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 26 Sep 2023 08:09:03 +0000 Subject: [PATCH 07/15] Template update for nf-core/tools version 2.10 --- .devcontainer/devcontainer.json | 1 + .github/CONTRIBUTING.md | 4 +- .github/workflows/linting.yml | 2 +- .github/workflows/release-announcments.yml | 68 +++++++++ CHANGELOG.md | 2 +- CITATIONS.md | 2 +- CODE_OF_CONDUCT.md | 133 ++++++++++++++---- README.md | 21 +-- assets/multiqc_config.yml | 6 +- conf/modules.config | 9 ++ docs/output.md | 5 +- docs/usage.md | 16 ++- lib/NfcoreTemplate.groovy | 16 +++ lib/WorkflowScrnaseq.groovy | 2 +- main.nf | 3 + modules.json | 6 +- .../custom/dumpsoftwareversions/main.nf | 2 +- modules/nf-core/fastqc/main.nf | 8 +- modules/nf-core/multiqc/main.nf | 2 +- nextflow.config | 9 +- nextflow_schema.json | 15 -- workflows/scrnaseq.nf | 1 + 22 files changed, 255 insertions(+), 78 deletions(-) create mode 100644 .github/workflows/release-announcments.yml diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index ea27a584..4ecfbfe3 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -2,6 +2,7 @@ "name": "nfcore", "image": "nfcore/gitpod:latest", "remoteUser": "gitpod", + "runArgs": ["--privileged"], // Configure tool-specific properties. "customizations": { diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index a7783031..a66c8d8b 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -9,7 +9,9 @@ Please use the pre-filled template to save time. 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/scrnaseq then the best place to ask is on the nf-core Slack [#scrnaseq](https://nfcore.slack.com/channels/scrnaseq) channel ([join our Slack here](https://nf-co.re/join/slack)). +:::info +If you need help using or modifying nf-core/scrnaseq then the best place to ask is on the nf-core Slack [#scrnaseq](https://nfcore.slack.com/channels/scrnaseq) channel ([join our Slack here](https://nf-co.re/join/slack)). +::: ## Contribution workflow diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 888cb4bc..b8bdd214 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -78,7 +78,7 @@ jobs: - uses: actions/setup-python@v4 with: - python-version: "3.8" + python-version: "3.11" architecture: "x64" - name: Install dependencies diff --git a/.github/workflows/release-announcments.yml b/.github/workflows/release-announcments.yml new file mode 100644 index 00000000..6ad33927 --- /dev/null +++ b/.github/workflows/release-announcments.yml @@ -0,0 +1,68 @@ +name: release-announcements +# Automatic release toot and tweet anouncements +on: + release: + types: [published] + workflow_dispatch: + +jobs: + toot: + runs-on: ubuntu-latest + steps: + - uses: rzr/fediverse-action@master + with: + access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} + host: "mstdn.science" # custom host if not "mastodon.social" (default) + # GitHub event payload + # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release + message: | + Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! + + Please see the changelog: ${{ github.event.release.html_url }} + + send-tweet: + runs-on: ubuntu-latest + + steps: + - uses: actions/setup-python@v4 + with: + python-version: "3.10" + - name: Install dependencies + run: pip install tweepy==4.14.0 + - name: Send tweet + shell: python + run: | + import os + import tweepy + + client = tweepy.Client( + access_token=os.getenv("TWITTER_ACCESS_TOKEN"), + access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"), + consumer_key=os.getenv("TWITTER_CONSUMER_KEY"), + consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"), + ) + tweet = os.getenv("TWEET") + client.create_tweet(text=tweet) + env: + TWEET: | + Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! + + Please see the changelog: ${{ github.event.release.html_url }} + TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }} + TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }} + TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }} + TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }} + + bsky-post: + runs-on: ubuntu-latest + steps: + - uses: zentered/bluesky-post-action@v0.0.2 + with: + post: | + Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! + + Please see the changelog: ${{ github.event.release.html_url }} + env: + BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }} + BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }} + # diff --git a/CHANGELOG.md b/CHANGELOG.md index 49a9920c..6d0db033 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). -## v2.4.0dev - [date] +## v2.4.1 - [date] Initial release of nf-core/scrnaseq, created with the [nf-core](https://nf-co.re/) template. diff --git a/CITATIONS.md b/CITATIONS.md index 298fec73..bd70fa4e 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,7 +12,7 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) - > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. + > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index f4fd052f..c089ec78 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -1,18 +1,20 @@ -# Code of Conduct at nf-core (v1.0) +# Code of Conduct at nf-core (v1.4) ## Our Pledge -In the interest of fostering an open, collaborative, and welcoming environment, we as contributors and maintainers of nf-core, pledge to making participation in our projects and community a harassment-free experience for everyone, regardless of: +In the interest of fostering an open, collaborative, and welcoming environment, we as contributors and maintainers of nf-core pledge to making participation in our projects and community a harassment-free experience for everyone, regardless of: - Age +- Ability - Body size +- Caste - Familial status - Gender identity and expression - Geographical location - Level of experience - Nationality and national origins - Native language -- Physical and neurological ability +- Neurodiversity - Race or ethnicity - Religion - Sexual identity and orientation @@ -22,80 +24,133 @@ Please note that the list above is alphabetised and is therefore not ranked in a ## Preamble -> Note: This Code of Conduct (CoC) has been drafted by the nf-core Safety Officer and been edited after input from members of the nf-core team and others. "We", in this document, refers to the Safety Officer and members of the nf-core core team, both of whom are deemed to be members of the nf-core community and are therefore required to abide by this Code of Conduct. This document will amended periodically to keep it up-to-date, and in case of any dispute, the most current version will apply. +:::note +This Code of Conduct (CoC) has been drafted by Renuka Kudva, Cris Tuñí, and Michael Heuer, with input from the nf-core Core Team and Susanna Marquez from the nf-core community. "We", in this document, refers to the Safety Officers and members of the nf-core Core Team, both of whom are deemed to be members of the nf-core community and are therefore required to abide by this Code of Conduct. This document will be amended periodically to keep it up-to-date. In case of any dispute, the most current version will apply. +::: -An up-to-date list of members of the nf-core core team can be found [here](https://nf-co.re/about). Our current safety officer is Renuka Kudva. +An up-to-date list of members of the nf-core core team can be found [here](https://nf-co.re/about). + +Our Safety Officers are Saba Nafees, Cris Tuñí, and Michael Heuer. nf-core is a young and growing community that welcomes contributions from anyone with a shared vision for [Open Science Policies](https://www.fosteropenscience.eu/taxonomy/term/8). Open science policies encompass inclusive behaviours and we strive to build and maintain a safe and inclusive environment for all individuals. -We have therefore adopted this code of conduct (CoC), which we require all members of our community and attendees in nf-core events to adhere to in all our workspaces at all times. Workspaces include but are not limited to Slack, meetings on Zoom, Jitsi, YouTube live etc. +We have therefore adopted this CoC, which we require all members of our community and attendees of nf-core events to adhere to in all our workspaces at all times. Workspaces include, but are not limited to, Slack, meetings on Zoom, gather.town, YouTube live etc. -Our CoC will be strictly enforced and the nf-core team reserve the right to exclude participants who do not comply with our guidelines from our workspaces and future nf-core activities. +Our CoC will be strictly enforced and the nf-core team reserves the right to exclude participants who do not comply with our guidelines from our workspaces and future nf-core activities. -We ask all members of our community to help maintain a supportive and productive workspace and to avoid behaviours that can make individuals feel unsafe or unwelcome. Please help us maintain and uphold this CoC. +We ask all members of our community to help maintain supportive and productive workspaces and to avoid behaviours that can make individuals feel unsafe or unwelcome. Please help us maintain and uphold this CoC. -Questions, concerns or ideas on what we can include? Contact safety [at] nf-co [dot] re +Questions, concerns, or ideas on what we can include? Contact members of the Safety Team on Slack or email safety [at] nf-co [dot] re. ## Our Responsibilities -The safety officer is responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behaviour. +Members of the Safety Team (the Safety Officers) are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behaviour. -The safety officer in consultation with the nf-core core team have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. +The Safety Team, in consultation with the nf-core core team, have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this CoC, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. -Members of the core team or the safety officer who violate the CoC will be required to recuse themselves pending investigation. They will not have access to any reports of the violations and be subject to the same actions as others in violation of the CoC. +Members of the core team or the Safety Team who violate the CoC will be required to recuse themselves pending investigation. They will not have access to any reports of the violations and will be subject to the same actions as others in violation of the CoC. -## When are where does this Code of Conduct apply? +## When and where does this Code of Conduct apply? -Participation in the nf-core community is contingent on following these guidelines in all our workspaces and events. This includes but is not limited to the following listed alphabetically and therefore in no order of preference: +Participation in the nf-core community is contingent on following these guidelines in all our workspaces and events, such as hackathons, workshops, bytesize, and collaborative workspaces on gather.town. These guidelines include, but are not limited to, the following (listed alphabetically and therefore in no order of preference): - Communicating with an official project email address. - Communicating with community members within the nf-core Slack channel. - Participating in hackathons organised by nf-core (both online and in-person events). -- Participating in collaborative work on GitHub, Google Suite, community calls, mentorship meetings, email correspondence. -- Participating in workshops, training, and seminar series organised by nf-core (both online and in-person events). This applies to events hosted on web-based platforms such as Zoom, Jitsi, YouTube live etc. +- Participating in collaborative work on GitHub, Google Suite, community calls, mentorship meetings, email correspondence, and on the nf-core gather.town workspace. +- Participating in workshops, training, and seminar series organised by nf-core (both online and in-person events). This applies to events hosted on web-based platforms such as Zoom, gather.town, Jitsi, YouTube live etc. - Representing nf-core on social media. This includes both official and personal accounts. ## nf-core cares 😊 -nf-core's CoC and expectations of respectful behaviours for all participants (including organisers and the nf-core team) include but are not limited to the following (listed in alphabetical order): +nf-core's CoC and expectations of respectful behaviours for all participants (including organisers and the nf-core team) include, but are not limited to, the following (listed in alphabetical order): - Ask for consent before sharing another community member’s personal information (including photographs) on social media. - Be respectful of differing viewpoints and experiences. We are all here to learn from one another and a difference in opinion can present a good learning opportunity. -- Celebrate your accomplishments at events! (Get creative with your use of emojis 🎉 🥳 💯 🙌 !) +- Celebrate your accomplishments! (Get creative with your use of emojis 🎉 🥳 💯 🙌 !) - Demonstrate empathy towards other community members. (We don’t all have the same amount of time to dedicate to nf-core. If tasks are pending, don’t hesitate to gently remind members of your team. If you are leading a task, ask for help if you feel overwhelmed.) - Engage with and enquire after others. (This is especially important given the geographically remote nature of the nf-core community, so let’s do this the best we can) - Focus on what is best for the team and the community. (When in doubt, ask) -- Graciously accept constructive criticism, yet be unafraid to question, deliberate, and learn. +- Accept feedback, yet be unafraid to question, deliberate, and learn. - Introduce yourself to members of the community. (We’ve all been outsiders and we know that talking to strangers can be hard for some, but remember we’re interested in getting to know you and your visions for open science!) -- Show appreciation and **provide clear feedback**. (This is especially important because we don’t see each other in person and it can be harder to interpret subtleties. Also remember that not everyone understands a certain language to the same extent as you do, so **be clear in your communications to be kind.**) +- Show appreciation and **provide clear feedback**. (This is especially important because we don’t see each other in person and it can be harder to interpret subtleties. Also remember that not everyone understands a certain language to the same extent as you do, so **be clear in your communication to be kind.**) - Take breaks when you feel like you need them. -- Using welcoming and inclusive language. (Participants are encouraged to display their chosen pronouns on Zoom or in communication on Slack.) +- Use welcoming and inclusive language. (Participants are encouraged to display their chosen pronouns on Zoom or in communication on Slack) ## nf-core frowns on 😕 -The following behaviours from any participants within the nf-core community (including the organisers) will be considered unacceptable under this code of conduct. Engaging or advocating for any of the following could result in expulsion from nf-core workspaces. +The following behaviours from any participants within the nf-core community (including the organisers) will be considered unacceptable under this CoC. Engaging or advocating for any of the following could result in expulsion from nf-core workspaces: - Deliberate intimidation, stalking or following and sustained disruption of communication among participants of the community. This includes hijacking shared screens through actions such as using the annotate tool in conferencing software such as Zoom. - “Doxing” i.e. posting (or threatening to post) another person’s personal identifying information online. - Spamming or trolling of individuals on social media. -- Use of sexual or discriminatory imagery, comments, or jokes and unwelcome sexual attention. -- Verbal and text comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, ability, physical appearance, body size, race, age, religion or work experience. +- Use of sexual or discriminatory imagery, comments, jokes, or unwelcome sexual attention. +- Verbal and text comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, ability, physical appearance, body size, race, age, religion, or work experience. ### Online Trolling -The majority of nf-core interactions and events are held online. Unfortunately, holding events online comes with the added issue of online trolling. This is unacceptable, reports of such behaviour will be taken very seriously, and perpetrators will be excluded from activities immediately. +The majority of nf-core interactions and events are held online. Unfortunately, holding events online comes with the risk of online trolling. This is unacceptable — reports of such behaviour will be taken very seriously and perpetrators will be excluded from activities immediately. -All community members are required to ask members of the group they are working within for explicit consent prior to taking screenshots of individuals during video calls. +All community members are **required** to ask members of the group they are working with for explicit consent prior to taking screenshots of individuals during video calls. -## Procedures for Reporting CoC violations +## Procedures for reporting CoC violations If someone makes you feel uncomfortable through their behaviours or actions, report it as soon as possible. -You can reach out to members of the [nf-core core team](https://nf-co.re/about) and they will forward your concerns to the safety officer(s). +You can reach out to members of the Safety Team (Saba Nafees, Cris Tuñí, and Michael Heuer) on Slack. Alternatively, contact a member of the nf-core core team [nf-core core team](https://nf-co.re/about), and they will forward your concerns to the Safety Team. + +Issues directly concerning members of the Core Team or the Safety Team will be dealt with by other members of the core team and the safety manager — possible conflicts of interest will be taken into account. nf-core is also in discussions about having an ombudsperson and details will be shared in due course. + +All reports will be handled with the utmost discretion and confidentiality. + +You can also report any CoC violations to safety [at] nf-co [dot] re. In your email report, please do your best to include: + +- Your contact information. +- Identifying information (e.g. names, nicknames, pseudonyms) of the participant who has violated the Code of Conduct. +- The behaviour that was in violation and the circumstances surrounding the incident. +- The approximate time of the behaviour (if different than the time the report was made). +- Other people involved in the incident, if applicable. +- If you believe the incident is ongoing. +- If there is a publicly available record (e.g. mailing list record, a screenshot). +- Any additional information. + +After you file a report, one or more members of our Safety Team will contact you to follow up on your report. + +## Who will read and handle reports + +All reports will be read and handled by the members of the Safety Team at nf-core. + +If members of the Safety Team are deemed to have a conflict of interest with a report, they will be required to recuse themselves as per our Code of Conduct and will not have access to any follow-ups. + +To keep this first report confidential from any of the Safety Team members, please submit your first report by direct messaging on Slack/direct email to any of the nf-core members you are comfortable disclosing the information to, and be explicit about which member(s) you do not consent to sharing the information with. + +## Reviewing reports + +After receiving the report, members of the Safety Team will review the incident report to determine whether immediate action is required, for example, whether there is immediate threat to participants’ safety. + +The Safety Team, in consultation with members of the nf-core core team, will assess the information to determine whether the report constitutes a Code of Conduct violation, for them to decide on a course of action. + +In the case of insufficient information, one or more members of the Safety Team may contact the reporter, the reportee, or any other attendees to obtain more information. -Issues directly concerning members of the core team will be dealt with by other members of the core team and the safety manager, and possible conflicts of interest will be taken into account. nf-core is also in discussions about having an ombudsperson, and details will be shared in due course. +Once additional information is gathered, the Safety Team will collectively review and decide on the best course of action to take, if any. The Safety Team reserves the right to not act on a report. -All reports will be handled with utmost discretion and confidentially. +## Confidentiality + +All reports, and any additional information included, are only shared with the team of safety officers (and possibly members of the core team, in case the safety officer is in violation of the CoC). We will respect confidentiality requests for the purpose of protecting victims of abuse. + +We will not name harassment victims, beyond discussions between the safety officer and members of the nf-core team, without the explicit consent of the individuals involved. + +## Enforcement + +Actions taken by the nf-core’s Safety Team may include, but are not limited to: + +- Asking anyone to stop a behaviour. +- Asking anyone to leave the event and online spaces either temporarily, for the remainder of the event, or permanently. +- Removing access to the gather.town and Slack, either temporarily or permanently. +- Communicating to all participants to reinforce our expectations for conduct and remind what is unacceptable behaviour; this may be public for practical reasons. +- Communicating to all participants that an incident has taken place and how we will act or have acted — this may be for the purpose of letting event participants know we are aware of and dealing with the incident. +- Banning anyone from participating in nf-core-managed spaces, future events, and activities, either temporarily or permanently. +- No action. ## Attribution and Acknowledgements @@ -106,6 +161,22 @@ All reports will be handled with utmost discretion and confidentially. ## Changelog -### v1.0 - March 12th, 2021 +### v1.4 - February 8th, 2022 + +- Included a new member of the Safety Team. Corrected a typographical error in the text. + +### v1.3 - December 10th, 2021 + +- Added a statement that the CoC applies to nf-core gather.town workspaces. Corrected typographical errors in the text. + +### v1.2 - November 12th, 2021 + +- Removed information specific to reporting CoC violations at the Hackathon in October 2021. + +### v1.1 - October 14th, 2021 + +- Updated with names of new Safety Officers and specific information for the hackathon in October 2021. + +### v1.0 - March 15th, 2021 - Complete rewrite from original [Contributor Covenant](http://contributor-covenant.org/) CoC. diff --git a/README.md b/README.md index 5e620efc..3f35dfd8 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,7 @@ # ![nf-core/scrnaseq](docs/images/nf-core-scrnaseq_logo_light.png#gh-light-mode-only) ![nf-core/scrnaseq](docs/images/nf-core-scrnaseq_logo_dark.png#gh-dark-mode-only) -[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/scrnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) +[![GitHub Actions CI Status](https://github.com/nf-core/scrnaseq/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/scrnaseq/actions?query=workflow%3A%22nf-core+CI%22) +[![GitHub Actions Linting Status](https://github.com/nf-core/scrnaseq/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/scrnaseq/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/scrnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) @@ -29,10 +30,11 @@ ## Usage -> **Note** -> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how -> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) -> with `-profile test` before running the workflow on actual data. +:::note +If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how +to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) +with `-profile test` before running the workflow on actual data. +:::