From e736dd4678062acb80e4dce77eb665daf846112c Mon Sep 17 00:00:00 2001 From: jasmezz Date: Fri, 11 Aug 2023 14:38:51 +0200 Subject: [PATCH 01/33] Post-release version bump --- 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 25990a0d..c2357764 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/funcscan + This report has been generated by the nf-core/funcscan analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-funcscan-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index 95ffa0c1..887e4a09 100644 --- a/nextflow.config +++ b/nextflow.config @@ -391,7 +391,7 @@ manifest { description = """Pipeline for screening for functional components of assembled contigs""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.1.3' + version = '1.1.4dev' doi = '10.5281/zenodo.7643099' } From caaa6829e105b02f0aceefe1d41a5538d6c761d9 Mon Sep 17 00:00:00 2001 From: jasmezz Date: Fri, 11 Aug 2023 14:40:42 +0200 Subject: [PATCH 02/33] Update changelog --- CHANGELOG.md | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7fa76fc2..e0674f20 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,16 @@ 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). +## v1.1.4dev - [unreleased] + +### `Added` + +### `Fixed` + +### `Dependencies` + +### `Deprecated` + ## v1.1.3 - [2023-08-11] ### `Added` From 83ec5c7e61661f604e0b9b95d43f616c10a10464 Mon Sep 17 00:00:00 2001 From: darcy220606 Date: Tue, 22 Aug 2023 11:28:16 +0200 Subject: [PATCH 03/33] stop prokka from renaming contigs by default --- CHANGELOG.md | 11 +++++++++++ conf/modules.config | 3 +-- nextflow.config | 3 +-- nextflow_schema.json | 18 +++++------------- 4 files changed, 18 insertions(+), 17 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7fa76fc2..b4214bd2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,17 @@ 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). +## v1.1.4dev - [unreleased] + +### `Added` + +### `Fixed` +- [###]() Added new parameter `annotation_prokka_renamecontigs` to allow prokka to retain the original contig headers/locus tag by default (fix by @darcy220606) + +### `Dependencies` + +### `Deprecated` + ## v1.1.3 - [2023-08-11] ### `Added` diff --git a/conf/modules.config b/conf/modules.config index f5472ced..0a2fdbd5 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -65,8 +65,7 @@ process { "--mincontiglen ${params.annotation_prokka_mincontiglen}", "--evalue ${params.annotation_prokka_evalue}", "--coverage ${params.annotation_prokka_coverage}", - "--centre ${params.annotation_prokka_centre}", - "--locustag ${params.annotation_prokka_locustag}", + params.annotation_prokka_renamecontigs ? "--locustag PROKKA --centre CENTER" : "--force" , params.annotation_prokka_singlemode ? '' : '--metagenome' , params.annotation_prokka_cdsrnaolap ? '--cdsrnaolap' : '', params.annotation_prokka_rawproduct ? '--rawproduct' : '', diff --git a/nextflow.config b/nextflow.config index 95ffa0c1..a094f9ec 100644 --- a/nextflow.config +++ b/nextflow.config @@ -62,10 +62,9 @@ params { annotation_prokka_mincontiglen = 1 annotation_prokka_evalue = 1E-06 annotation_prokka_coverage = 80 - annotation_prokka_centre = null annotation_prokka_compliant = false - annotation_prokka_locustag = 'PROKKA' annotation_prokka_addgenes = false + annotation_prokka_renamecontigs = false // Database downloading options save_databases = false diff --git a/nextflow_schema.json b/nextflow_schema.json index 93979e7d..c7f5d1d6 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -297,30 +297,22 @@ "help_text": "Activates [RNAmmer](https://services.healthtech.dtu.dk/service.php?RNAmmer-1.2) instead of the Prokka default [Barrnap](https://github.com/tseemann/barrnap) for rRNA prediction during the annotation process. RNAmmer classifies ribosomal RNA genes in genome sequences by using two levels of Hidden Markov Models. Barrnap uses the nhmmer tool that includes HMMER 3.1 for HMM searching in RNA:DNA style.\n\nFor more information please check Prokka [documentation](https://github.com/tseemann/prokka).\n\n> Modifies tool parameter(s):\n> - Prokka: `--rnammer`", "fa_icon": "fas fa-adjust" }, - "annotation_prokka_centre": { - "type": "string", - "description": "Sequencing centre ID.", - "fa_icon": "fas fa-map-marker-alt", - "help_text": "Add the sequencing center ID used in generating the raw sequences. This flag is typically requested in combination with the `--compliant` flag when contigs need to be renamed due to non-conforming contig headers. For more information please check Prokka [documentation](https://github.com/tseemann/prokka). \n\n> Modifies tool parameter(s):\n> - Prokka: `--centre`" - }, "annotation_prokka_compliant": { "type": "boolean", "fa_icon": "far fa-check-circle", "description": "Force contig name to Genbank/ENA/DDJB naming rules.", "help_text": "Force the contig headers to conform to the Genbank/ENA/DDJB contig header standards. This is activated in combination with `--centre [X]` when contig headers supplied by the user are non-conforming and therefore need to be renamed before Prokka can start annotation. This flag activates `--genes --mincontiglen 200`. For more information please check Prokka [documentation](https://github.com/tseemann/prokka). \n\n> Modifies tool parameter(s):\n> - Prokka: `--compliant`" }, - "annotation_prokka_locustag": { - "type": "string", - "default": "Prokka", - "fa_icon": "fas fa-tags", - "description": "Assign the locus tag for the contig header.", - "help_text": "Assign a special name to the contig. This is used when a specific group of samples are run in a batch. For more information please check Prokka [documentation](https://github.com/tseemann/prokka). \n\n> Modifies tool parameter(s):\n> - Prokka: `--locustag`" - }, "annotation_prokka_addgenes": { "type": "boolean", "fa_icon": "fas fa-dna", "description": "Add the gene features for each CDS hit.", "help_text": "For every CDS annotated, this flag adds the gene that encodes for that CDS region. For more information please check Prokka [documentation](https://github.com/tseemann/prokka). \n\n> Modifies tool parameter(s):\n> - Prokka: `--addgenes`" + }, + "annotation_prokka_renamecontigs": { + "type": "boolean", + "help_text": "This parameter retains the original contig names by activating `PROKKA`'s `--force` flag. If this parameter is set to `true` it activates `PROKKA`'s flags `--locus-tag PROKKA --centre CENTER` so the locus tags (contig names) will be PROKKA_# and the center tag will be CENTER. \n\n> Modifies tool parameter(s):\n> - Prokka: `--locus-tag PROKKA --centre CENTER`\n> - Prokka: `--force`", + "description": "Renames contig names." } }, "fa_icon": "fas fa-tools", From eaf43875557467cf5f3e34a448301cf8ad16e54f Mon Sep 17 00:00:00 2001 From: darcy220606 Date: Tue, 22 Aug 2023 12:02:03 +0200 Subject: [PATCH 04/33] CHANGELOG prettier --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index b4214bd2..a75dbb51 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` ### `Fixed` + - [###]() Added new parameter `annotation_prokka_renamecontigs` to allow prokka to retain the original contig headers/locus tag by default (fix by @darcy220606) ### `Dependencies` From 628111b426ab3340d37e95505997d6b2b0409205 Mon Sep 17 00:00:00 2001 From: darcy220606 Date: Wed, 23 Aug 2023 10:23:21 +0200 Subject: [PATCH 05/33] Fix new parameter --- CHANGELOG.md | 2 +- conf/modules.config | 2 +- nextflow.config | 4 ++-- nextflow_schema.json | 6 +++--- 4 files changed, 7 insertions(+), 7 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a75dbb51..f366a0ee 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` -- [###]() Added new parameter `annotation_prokka_renamecontigs` to allow prokka to retain the original contig headers/locus tag by default (fix by @darcy220606) +- [###]() Added new parameter `annotation_prokka_retaincontigheaders` to allow prokka to retain the original contig headers/locus tag. (by @darcy220606) ### `Dependencies` diff --git a/conf/modules.config b/conf/modules.config index 0a2fdbd5..c94e5324 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -65,7 +65,7 @@ process { "--mincontiglen ${params.annotation_prokka_mincontiglen}", "--evalue ${params.annotation_prokka_evalue}", "--coverage ${params.annotation_prokka_coverage}", - params.annotation_prokka_renamecontigs ? "--locustag PROKKA --centre CENTER" : "--force" , + params.annotation_prokka_retaincontigheaders ? "--force" : "--locustag PROKKA --centre CENTER" , params.annotation_prokka_singlemode ? '' : '--metagenome' , params.annotation_prokka_cdsrnaolap ? '--cdsrnaolap' : '', params.annotation_prokka_rawproduct ? '--rawproduct' : '', diff --git a/nextflow.config b/nextflow.config index a094f9ec..599de35c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -62,9 +62,9 @@ params { annotation_prokka_mincontiglen = 1 annotation_prokka_evalue = 1E-06 annotation_prokka_coverage = 80 - annotation_prokka_compliant = false + annotation_prokka_compliant = true annotation_prokka_addgenes = false - annotation_prokka_renamecontigs = false + annotation_prokka_retaincontigheaders = false // Database downloading options save_databases = false diff --git a/nextflow_schema.json b/nextflow_schema.json index c7f5d1d6..56bef890 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -309,10 +309,10 @@ "description": "Add the gene features for each CDS hit.", "help_text": "For every CDS annotated, this flag adds the gene that encodes for that CDS region. For more information please check Prokka [documentation](https://github.com/tseemann/prokka). \n\n> Modifies tool parameter(s):\n> - Prokka: `--addgenes`" }, - "annotation_prokka_renamecontigs": { + "annotation_prokka_retaincontigheaders": { "type": "boolean", - "help_text": "This parameter retains the original contig names by activating `PROKKA`'s `--force` flag. If this parameter is set to `true` it activates `PROKKA`'s flags `--locus-tag PROKKA --centre CENTER` so the locus tags (contig names) will be PROKKA_# and the center tag will be CENTER. \n\n> Modifies tool parameter(s):\n> - Prokka: `--locus-tag PROKKA --centre CENTER`\n> - Prokka: `--force`", - "description": "Renames contig names." + "help_text": "This parameter allows prokka to retain the original contig names by activating `PROKKA`'s `--force` flag. If this parameter is set to `false` it activates `PROKKA`'s flags `--locus-tag PROKKA --centre CENTER` so the locus tags (contig names) will be PROKKA_# and the center tag will be CENTER. By default `PROKKA` changes contig headers to avoid errors that might rise due to long contig headers, so this must be turned on if the user has short contig names that should be retained by `PROKKA`. \n\n> Modifies tool parameter(s):\n> - Prokka: `--locus-tag PROKKA --centre CENTER`\n> - Prokka: `--force`", + "description": "Retains contig names." } }, "fa_icon": "fas fa-tools", From bb8334c02158a55bd53689bdac91f06869949412 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Fri, 25 Aug 2023 08:55:57 +0200 Subject: [PATCH 06/33] Fix deepARG test profile and use more stable deepARG db URL --- .github/workflows/ci.yml | 52 +++++++++++++++++++++------------------- conf/test_deeparg.config | 5 ++-- 2 files changed, 30 insertions(+), 27 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f45e42aa..ee88aaf1 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -72,31 +72,33 @@ jobs: run: | nextflow run ${GITHUB_WORKSPACE} -profile test_bgc,docker --outdir ./results ${{ matrix.parameters }} - # test_deeparg: #Tests switched off as long as DeepARG servers are unavaiable for database download. - # name: Run pipeline with test data (DeepARG only workflow) - # # Only run on push if this is the nf-core dev branch (merged PRs) - # if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/funcscan') }}" - # runs-on: ubuntu-latest - # strategy: - # matrix: - # NXF_VER: - # - "23.04.0" - # - "latest-everything" - # parameters: - # - "--annotation_tool bakta --annotation_bakta_db_downloadtype light" - # - "--annotation_tool prodigal" - # - "--annotation_tool prokka" - # - "--annotation_tool pyrodigal" + test_deeparg: + name: Run pipeline with test data (DeepARG only workflow) + # Only run on push if this is the nf-core dev branch (merged PRs) + if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/funcscan') }}" + runs-on: ubuntu-latest + strategy: + matrix: + NXF_VER: + - "23.04.0" + - "latest-everything" + parameters: + - "--annotation_tool bakta --annotation_bakta_db_downloadtype light" + - "--annotation_tool prodigal" + - "--annotation_tool prokka" + - "--annotation_tool pyrodigal" - # steps: - # - name: Check out pipeline code - # uses: actions/checkout@v2 + steps: + - name: Check out pipeline code + uses: actions/checkout@v2 - # - name: Install Nextflow - # uses: nf-core/setup-nextflow@v1 - # with: - # version: "${{ matrix.NXF_VER }}" + - name: Install Nextflow + uses: nf-core/setup-nextflow@v1 + with: + version: "${{ matrix.NXF_VER }}" - # - name: Run pipeline with test data (DeepARG workflow) - # run: | - # nextflow run ${GITHUB_WORKSPACE} -profile test_deeparg,docker --outdir ./results ${{ matrix.parameters }} + - name: Run pipeline with test data (DeepARG workflow) + run: | + wget https://zenodo.org/record/8280582/files/deeparg.zip ## download from zenodo due to instability of deepARG server + unzip deeparg.zip + nextflow run ${GITHUB_WORKSPACE} -profile test_deeparg,docker --outdir ./results ${{ matrix.parameters }} --arg_deeparg_data 'deeparg/deeparg/'' diff --git a/conf/test_deeparg.config b/conf/test_deeparg.config index 625d8eb4..ff229340 100644 --- a/conf/test_deeparg.config +++ b/conf/test_deeparg.config @@ -30,8 +30,9 @@ params { arg_skip_fargene = true arg_skip_rgi = true arg_skip_amrfinderplus = true + arg_skip_abricate = true arg_skip_deeparg = false - run_amp_screening = false - run_bgc_screening = false + run_amp_screening = false + run_bgc_screening = false } From f651f88b372c95214add9c094fe0d26b5809fba1 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Fri, 25 Aug 2023 08:57:00 +0200 Subject: [PATCH 07/33] Reduce deepARG test annotaion tool to prevent zenodo DL throttling --- .github/workflows/ci.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ee88aaf1..2d0c597b 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -84,8 +84,6 @@ jobs: - "latest-everything" parameters: - "--annotation_tool bakta --annotation_bakta_db_downloadtype light" - - "--annotation_tool prodigal" - - "--annotation_tool prokka" - "--annotation_tool pyrodigal" steps: From edb6c978a6e35f85bb5c80adde7e2a378ca914f2 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Fri, 25 Aug 2023 09:02:45 +0200 Subject: [PATCH 08/33] Update CHANBGELOG --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e0674f20..e65ca457 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [#307](https://github.com/nf-core/funcscan/pull/307) Fixed stability of deepARG tests by using Zenodo copy of database (❤️ to Gustavo Arango and Liqing Zhang for uploading, fix by @jfy133) + ### `Dependencies` ### `Deprecated` From 079ef0f5e9e00b1b90f71c71f9125e654a9e33e5 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 25 Aug 2023 09:16:58 +0200 Subject: [PATCH 09/33] Apply suggestions from code review --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2d0c597b..cae33590 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -99,4 +99,4 @@ jobs: run: | wget https://zenodo.org/record/8280582/files/deeparg.zip ## download from zenodo due to instability of deepARG server unzip deeparg.zip - nextflow run ${GITHUB_WORKSPACE} -profile test_deeparg,docker --outdir ./results ${{ matrix.parameters }} --arg_deeparg_data 'deeparg/deeparg/'' + nextflow run ${GITHUB_WORKSPACE} -profile test_deeparg,docker --outdir ./results ${{ matrix.parameters }} --arg_deeparg_data 'deeparg/deeparg/' From c749b5eb66be56418fdc90e18d45d74b7fda0a99 Mon Sep 17 00:00:00 2001 From: darcy220606 Date: Fri, 25 Aug 2023 09:38:14 +0200 Subject: [PATCH 10/33] Add review requests --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f366a0ee..231d9274 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` -- [###]() Added new parameter `annotation_prokka_retaincontigheaders` to allow prokka to retain the original contig headers/locus tag. (by @darcy220606) +- [#306](https://github.com/nf-core/funcscan/pull/306) Added new parameter `annotation_prokka_retaincontigheaders` to allow prokka to retain the original contig headers/locus tag. (by @darcy220606) ### `Dependencies` From b7c5237d60095c089c44e76ff6d68aad0de82161 Mon Sep 17 00:00:00 2001 From: jasmezz Date: Fri, 25 Aug 2023 09:39:07 +0200 Subject: [PATCH 11/33] Add DeepARG Zenodo link to usage docs --- docs/usage.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index cf9ba24f..2582618c 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -185,9 +185,10 @@ You can either: 1. Install DeepARG from [bioconda](https://bioconda.github.io/recipes/deeparg/README.html?highlight=deeparg) 2. Run `deeparg download_data -o ////` -Or +Or download the files directly from -1. Download the files directly from the [DeepARG FTP site](https://bench.cs.vt.edu/ftp/data/gustavo1/deeparg/database/) +1. the [DeepARG FTP site](https://bench.cs.vt.edu/ftp/data/gustavo1/deeparg/database/) +2. the [DeepARG database Zenodo archive](https://zenodo.org/record/8280582) Note that more recent database versions maybe available from the [ARGMiner service](https://bench.cs.vt.edu/argminer/#/home). From bc4db0dee77878a0b181a62f6d3fd458fa7192c8 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 25 Aug 2023 11:13:20 +0200 Subject: [PATCH 12/33] Update .github/workflows/ci.yml --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index cae33590..c34546ec 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -99,4 +99,4 @@ jobs: run: | wget https://zenodo.org/record/8280582/files/deeparg.zip ## download from zenodo due to instability of deepARG server unzip deeparg.zip - nextflow run ${GITHUB_WORKSPACE} -profile test_deeparg,docker --outdir ./results ${{ matrix.parameters }} --arg_deeparg_data 'deeparg/deeparg/' + nextflow run ${GITHUB_WORKSPACE} -profile test_deeparg,docker --outdir ./results ${{ matrix.parameters }} --arg_deeparg_data 'deeparg/' From 2d1a2ec5ad7205aa235df50aee57f92970464796 Mon Sep 17 00:00:00 2001 From: jasmezz Date: Wed, 30 Aug 2023 16:58:34 +0200 Subject: [PATCH 13/33] Update amrfinderplus, bakta, and multiqc --- modules.json | 12 ++++++------ modules/nf-core/amrfinderplus/run/main.nf | 19 ++++++++++++------- modules/nf-core/amrfinderplus/update/main.nf | 9 ++++----- modules/nf-core/bakta/bakta/main.nf | 6 +++--- modules/nf-core/bakta/baktadbdownload/main.nf | 6 +++--- .../custom/dumpsoftwareversions/main.nf | 6 +++--- modules/nf-core/multiqc/main.nf | 6 +++--- 7 files changed, 34 insertions(+), 30 deletions(-) diff --git a/modules.json b/modules.json index 2d47f5a7..aa7a4193 100644 --- a/modules.json +++ b/modules.json @@ -27,12 +27,12 @@ }, "amrfinderplus/run": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "868d4c3dc7a3db39d36184173e4fe3484499396e", "installed_by": ["modules"] }, "amrfinderplus/update": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "868d4c3dc7a3db39d36184173e4fe3484499396e", "installed_by": ["modules"] }, "antismash/antismashlite": { @@ -47,12 +47,12 @@ }, "bakta/bakta": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "f05fa7c6753f92be861d606378860dcd5c828880", "installed_by": ["modules"] }, "bakta/baktadbdownload": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "f05fa7c6753f92be861d606378860dcd5c828880", "installed_by": ["modules"] }, "bioawk": { @@ -63,7 +63,7 @@ }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4", "installed_by": ["modules"] }, "deeparg/downloaddata": { @@ -148,7 +148,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80", "installed_by": ["modules"] }, "prodigal": { diff --git a/modules/nf-core/amrfinderplus/run/main.nf b/modules/nf-core/amrfinderplus/run/main.nf index 8077bb48..40df8086 100644 --- a/modules/nf-core/amrfinderplus/run/main.nf +++ b/modules/nf-core/amrfinderplus/run/main.nf @@ -2,10 +2,10 @@ process AMRFINDERPLUS_RUN { tag "$meta.id" label 'process_medium' - conda "bioconda::ncbi-amrfinderplus=3.10.42" + conda "bioconda::ncbi-amrfinderplus=3.11.18" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.42--h6e70893_0': - 'biocontainers/ncbi-amrfinderplus:3.10.42--h6e70893_0' }" + 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.11.18--h283d18e_0': + 'biocontainers/ncbi-amrfinderplus:3.11.18--h283d18e_0' }" input: tuple val(meta), path(fasta) @@ -23,7 +23,8 @@ process AMRFINDERPLUS_RUN { script: def args = task.ext.args ?: '' - def is_compressed = fasta.getName().endsWith(".gz") ? true : false + def is_compressed_fasta = fasta.getName().endsWith(".gz") ? true : false + def is_compressed_db = fasta.getName().endsWith(".gz") ? true : false prefix = task.ext.prefix ?: "${meta.id}" organism_param = meta.containsKey("organism") ? "--organism ${meta.organism} --mutation_all ${prefix}-mutations.tsv" : "" fasta_name = fasta.getName().replace(".gz", "") @@ -34,12 +35,16 @@ process AMRFINDERPLUS_RUN { } } """ - if [ "$is_compressed" == "true" ]; then + if [ "$is_compressed_fasta" == "true" ]; then gzip -c -d $fasta > $fasta_name fi - mkdir amrfinderdb - tar xzvf $db -C amrfinderdb + if [ "$is_compressed_db" == "true" ]; then + mkdir amrfinderdb + tar xzvf $db -C amrfinderdb + else + mv $db amrfinderdb + fi amrfinder \\ $fasta_param $fasta_name \\ diff --git a/modules/nf-core/amrfinderplus/update/main.nf b/modules/nf-core/amrfinderplus/update/main.nf index a043a06a..bf3c5ef6 100644 --- a/modules/nf-core/amrfinderplus/update/main.nf +++ b/modules/nf-core/amrfinderplus/update/main.nf @@ -2,10 +2,10 @@ process AMRFINDERPLUS_UPDATE { tag "update" label 'process_single' - conda "bioconda::ncbi-amrfinderplus=3.10.42" + conda "bioconda::ncbi-amrfinderplus=3.11.18" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.42--h6e70893_0': - 'biocontainers/ncbi-amrfinderplus:3.10.42--h6e70893_0' }" + 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.11.18--h283d18e_0': + 'biocontainers/ncbi-amrfinderplus:3.11.18--h283d18e_0' }" output: path "amrfinderdb.tar.gz", emit: db @@ -17,9 +17,8 @@ process AMRFINDERPLUS_UPDATE { script: def args = task.ext.args ?: '' """ - mkdir amrfinderdb amrfinder_update -d amrfinderdb - tar czvf amrfinderdb.tar.gz -C \$(readlink amrfinderdb/latest) ./ + tar czvf amrfinderdb.tar.gz -C amrfinderdb/\$(readlink amrfinderdb/latest) ./ cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bakta/bakta/main.nf b/modules/nf-core/bakta/bakta/main.nf index 6399f5d0..fd0b76f2 100644 --- a/modules/nf-core/bakta/bakta/main.nf +++ b/modules/nf-core/bakta/bakta/main.nf @@ -2,10 +2,10 @@ process BAKTA_BAKTA { tag "$meta.id" label 'process_medium' - conda "bioconda::bakta=1.7.0" + conda "bioconda::bakta=1.8.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bakta:1.7.0--pyhdfd78af_1' : - 'biocontainers/bakta:1.7.0--pyhdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/bakta:1.8.2--pyhdfd78af_0' : + 'biocontainers/bakta:1.8.2--pyhdfd78af_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/bakta/baktadbdownload/main.nf b/modules/nf-core/bakta/baktadbdownload/main.nf index e62a2bed..de7e2199 100644 --- a/modules/nf-core/bakta/baktadbdownload/main.nf +++ b/modules/nf-core/bakta/baktadbdownload/main.nf @@ -1,10 +1,10 @@ process BAKTA_BAKTADBDOWNLOAD { label 'process_single' - conda "bioconda::bakta=1.7.0" + conda "bioconda::bakta=1.8.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bakta:1.7.0--pyhdfd78af_1' : - 'biocontainers/bakta:1.7.0--pyhdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/bakta:1.8.2--pyhdfd78af_0' : + 'biocontainers/bakta:1.8.2--pyhdfd78af_0' }" output: path "db*" , emit: db 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : + 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 1fc387be..65d7dd0d 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,10 +1,10 @@ process MULTIQC { label 'process_single' - conda "bioconda::multiqc=1.14" + conda "bioconda::multiqc=1.15" container "${ 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 multiqc_files, stageAs: "?/*" From 837442a12c3cb0d35bbda2608960cabb964dfbd9 Mon Sep 17 00:00:00 2001 From: jasmezz Date: Wed, 30 Aug 2023 17:09:31 +0200 Subject: [PATCH 14/33] Update changelog --- CHANGELOG.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e65ca457..f3491edf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Dependencies` +| Tool | Previous version | New version | +| ------------- | ---------------- | ----------- | +| AMRFinderPlus | 3.10.42 | 3.11.18 | +| Bakta | 1.7.0 | 1.8.2 | +| MultiQC | 1.1.4 | 1.1.5 | + ### `Deprecated` ## v1.1.3 - [2023-08-11] From c56197fa67c0df6e1b248892fcf8ba3753c991ca Mon Sep 17 00:00:00 2001 From: jasmezz Date: Wed, 30 Aug 2023 17:13:14 +0200 Subject: [PATCH 15/33] Revert "Update changelog" This reverts commit 837442a12c3cb0d35bbda2608960cabb964dfbd9. --- CHANGELOG.md | 6 ------ 1 file changed, 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f3491edf..e65ca457 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,12 +13,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Dependencies` -| Tool | Previous version | New version | -| ------------- | ---------------- | ----------- | -| AMRFinderPlus | 3.10.42 | 3.11.18 | -| Bakta | 1.7.0 | 1.8.2 | -| MultiQC | 1.1.4 | 1.1.5 | - ### `Deprecated` ## v1.1.3 - [2023-08-11] From d2307668eeb5edc9239e9548a6e9c178aa44e937 Mon Sep 17 00:00:00 2001 From: jasmezz Date: Wed, 30 Aug 2023 17:16:29 +0200 Subject: [PATCH 16/33] Update changelog --- CHANGELOG.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e65ca457..f3491edf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Dependencies` +| Tool | Previous version | New version | +| ------------- | ---------------- | ----------- | +| AMRFinderPlus | 3.10.42 | 3.11.18 | +| Bakta | 1.7.0 | 1.8.2 | +| MultiQC | 1.1.4 | 1.1.5 | + ### `Deprecated` ## v1.1.3 - [2023-08-11] From adaefa507e1049d319359ecd5b70217ffe454804 Mon Sep 17 00:00:00 2001 From: Hugo Tavares Date: Mon, 18 Sep 2023 10:07:19 +0100 Subject: [PATCH 17/33] fix input schema to accept uncompressed fasta; fix #309 --- assets/schema_input.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/assets/schema_input.json b/assets/schema_input.json index 4c70c654..757969c2 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -18,8 +18,8 @@ "type": "string", "format": "file-path", "exists": true, - "pattern": "^\\S+\\.f(ast|n)?a\\.gz$", - "errorMessage": "Fasta file for reads must be provided, cannot contain spaces and must have extension '.fa.gz', '.fna.gz' or '.fasta.gz'", + "pattern": "^\\S+\\.(fasta|fas|fa|fna)(\\.gz)?$", + "errorMessage": "Fasta file for reads must be provided, cannot contain spaces and must have extension '.fasta', '.fas', '.fa' or '.fna' (any of these can be optionally compressed as '.gz')", "unique": true } }, From b2ad76fab1f4c2121b1f76df79ab4d8e65814523 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 25 Sep 2023 15:16:32 +0000 Subject: [PATCH 18/33] 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 | 4 +- conf/modules.config | 9 ++ docs/output.md | 5 +- docs/usage.md | 16 ++- lib/NfcoreTemplate.groovy | 16 +++ lib/WorkflowFuncscan.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/funcscan.nf | 1 + 22 files changed, 253 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 1fcaa542..a5d66311 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/funcscan then the best place to ask is on the nf-core Slack [#funcscan](https://nfcore.slack.com/channels/funcscan) channel ([join our Slack here](https://nf-co.re/join/slack)). +:::info +If you need help using or modifying nf-core/funcscan then the best place to ask is on the nf-core Slack [#funcscan](https://nfcore.slack.com/channels/funcscan) 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 2b8a7c99..446dcd5e 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). -## v1.1.2 - [date] +## v1.1.4dev - [date] Initial release of nf-core/funcscan, created with the [nf-core](https://nf-co.re/) template. diff --git a/CITATIONS.md b/CITATIONS.md index 881ae370..bd67a904 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 38e3a12e..40f60023 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,7 @@ # ![nf-core/funcscan](docs/images/nf-core-funcscan_logo_light.png#gh-light-mode-only) ![nf-core/funcscan](docs/images/nf-core-funcscan_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/funcscan/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/funcscan/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/funcscan/actions?query=workflow%3A%22nf-core+CI%22) +[![GitHub Actions Linting Status](https://github.com/nf-core/funcscan/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/funcscan/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/funcscan/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. +:::