From f667e02b4ff362fc9f09be905fa4e6f0b79be174 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 1 Jul 2026 12:25:57 +0200 Subject: [PATCH 1/2] add check for param blocks to pipeline health --- bin/pipelines.json.js | 6 +- public/pipelines.json | 386 +++++++++++++++--- .../pipelines/src/pages/pipeline_health.astro | 27 +- 3 files changed, 369 insertions(+), 50 deletions(-) diff --git a/bin/pipelines.json.js b/bin/pipelines.json.js index 5a041630c8..d539c1fcab 100644 --- a/bin/pipelines.json.js +++ b/bin/pipelines.json.js @@ -334,7 +334,7 @@ export const writePipelinesJson = async () => { // remove empty values from releases (usually from draft releases) releases = releases.filter((release) => release.tag_name !== "" && release.draft === false); - + console.log(`Releases for ${name}:`, releases.map((release) => release.tag_name)); // remove releases that are already in the pipelines.json file const pipelineIndex = pipelines.remote_workflows.findIndex((workflow) => workflow.name === name); let new_releases = releases; @@ -469,6 +469,10 @@ export const writePipelinesJson = async () => { data[`${branch}_nextflow_config_plugins`] = nextflowConfig.plugins; data[`${branch}_nextflow_config_manifest`] = nextflowConfig.manifest; + + // Check if the root main.nf file declares a `params {` block + const mainNf = await getGitHubFile(name, "main.nf", branch); + data[`${branch}_uses_params_block`] = mainNf ? /params\s*\{/.test(mainNf) : false; } new_releases = await Promise.all( diff --git a/public/pipelines.json b/public/pipelines.json index 3c90a1ab0a..31bd98c052 100644 --- a/public/pipelines.json +++ b/public/pipelines.json @@ -131,12 +131,14 @@ "nf-schema@2.1.1" ], "main_nextflow_config_manifest": {}, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -381,12 +383,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": true, "dev_nextflow_config_plugins": [ "nf-schema@2.7.2" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": true, "releases": [ { "tag_name": "5.1.0", @@ -997,10 +1001,12 @@ "nf-validation@1.1.3" ], "main_nextflow_config_manifest": {}, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-validation@1.1.3" ], "dev_nextflow_config_manifest": {}, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -1398,12 +1404,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.7.2" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "2.18.0", @@ -2573,12 +2581,14 @@ "nf-validation" ], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "2.1.2", @@ -3193,12 +3203,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "main" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "2.6.0", @@ -3825,12 +3837,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -4042,12 +4056,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.0.0", @@ -4332,12 +4348,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.6.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "2.2.1", @@ -4727,12 +4745,14 @@ "has_nf_test_dev": true, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.0.2", @@ -4950,12 +4970,14 @@ "nf-validation@1.1.3" ], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.2.0" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.0.0", @@ -5262,12 +5284,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -5523,12 +5547,14 @@ "nf-validation@1.1.3" ], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "2.1.0", @@ -5909,12 +5935,14 @@ "nf-validation@1.1.3" ], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.1.0", @@ -6413,12 +6441,14 @@ "has_nf_test_dev": true, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -6653,8 +6683,10 @@ "has_nf_test_dev": false, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [], "dev_nextflow_config_manifest": {}, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.0.0", @@ -6859,12 +6891,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "2.0.1", @@ -7181,6 +7215,7 @@ "main_nextflow_config_manifest": { "defaultBranch": "main" }, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-core-utils@0.5.0", "nf-schema@2.7.2" @@ -7188,6 +7223,7 @@ "dev_nextflow_config_manifest": { "defaultBranch": "main" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.0.0", @@ -7315,7 +7351,7 @@ "forks_count": 11, "archived": false, "disabled": false, - "open_issues_count": 8, + "open_issues_count": 9, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -7331,7 +7367,7 @@ ], "visibility": "public", "forks": 11, - "open_issues": 8, + "open_issues": 9, "watchers": 21, "default_branch": "main", "temp_clone_token": "", @@ -7477,12 +7513,14 @@ "main_nextflow_config_manifest": { "defaultBranch": "main" }, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.7.2" ], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "3.0.0", @@ -7889,6 +7927,7 @@ "nf-schema@2.1.1" ], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1", "nf-gpt@0.4.0" @@ -7896,6 +7935,7 @@ "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "2.3.0", @@ -8550,12 +8590,14 @@ "nf-validation@1.1.3" ], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "3.2.2", @@ -9118,12 +9160,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -9310,12 +9354,14 @@ "nf-validation@1.1.3" ], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -9884,12 +9930,14 @@ "main_nextflow_config_manifest": { "defaultBranch": "master" }, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.3.0" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -10059,12 +10107,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -10650,12 +10700,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.7.2" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.2.0", @@ -11107,12 +11159,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.7.0" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.7.1", @@ -12252,12 +12306,14 @@ "main_nextflow_config_manifest": { "defaultBranch": "master" }, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.2.0" ], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.2.1", @@ -12629,12 +12685,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.3.0", @@ -12945,8 +13003,10 @@ "has_nf_test_dev": false, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [], "dev_nextflow_config_manifest": {}, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.2.4", @@ -13291,12 +13351,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "2.0.0", @@ -13737,7 +13799,7 @@ "forks_count": 6, "archived": false, "disabled": false, - "open_issues_count": 48, + "open_issues_count": 47, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -13760,7 +13822,7 @@ ], "visibility": "public", "forks": 6, - "open_issues": 48, + "open_issues": 47, "watchers": 5, "default_branch": "dev", "temp_clone_token": "", @@ -13904,12 +13966,14 @@ "main_nextflow_config_manifest": { "defaultBranch": "main" }, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, + "dev_uses_params_block": true, "releases": [ { "tag_name": "dev", @@ -14103,12 +14167,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.6.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.0.0", @@ -14348,18 +14414,21 @@ "nf-validation" ], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "main_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "main_nextflow_config_manifest": { "defaultBranch": "main" }, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.2.2", @@ -14663,10 +14732,12 @@ "has_nf_test_dev": false, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.3.0" ], "dev_nextflow_config_manifest": {}, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.0.0", @@ -14959,12 +15030,14 @@ "has_nf_test_dev": true, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "2.5.3", @@ -15533,12 +15606,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -15755,6 +15830,7 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1", "nf-co2footprint@1.0.0" @@ -15762,6 +15838,7 @@ "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "3.1.0", @@ -16137,10 +16214,12 @@ "main_nextflow_config_manifest": { "defaultBranch": "master" }, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-validation@1.1.3" ], "dev_nextflow_config_manifest": {}, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -16484,12 +16563,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "main" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.4.2" ], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.0.0", @@ -16713,6 +16794,7 @@ "main_nextflow_config_manifest": { "defaultBranch": "main" }, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1", "nf-fgbio@1.0.0" @@ -16720,6 +16802,7 @@ "dev_nextflow_config_manifest": { "defaultBranch": "main" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "2.0.0", @@ -17134,12 +17217,14 @@ "nf-validation@1.1.3" ], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.12.0", @@ -17576,12 +17661,14 @@ "main_nextflow_config_manifest": { "defaultBranch": "main" }, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -17648,10 +17735,10 @@ "has_wiki": false, "has_pages": false, "has_discussions": false, - "forks_count": 36, + "forks_count": 37, "archived": false, "disabled": false, - "open_issues_count": 20, + "open_issues_count": 22, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -17675,8 +17762,8 @@ "secondary-metabolites" ], "visibility": "public", - "forks": 36, - "open_issues": 20, + "forks": 37, + "open_issues": 22, "watchers": 115, "default_branch": "main", "temp_clone_token": "", @@ -17718,7 +17805,7 @@ "status": "disabled" } }, - "network_count": 36, + "network_count": 37, "subscribers_count": 103, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, @@ -17749,7 +17836,7 @@ "dev_branch_protection_enforce_admins": false, "TEMPLATE_branch_exists": true, "has_required_topics": true, - "open_pr_count": 1, + "open_pr_count": 2, "repository_url": "https://github.com/nf-core/funcscan", "contributors": [ { @@ -17837,12 +17924,14 @@ "main_nextflow_config_manifest": { "defaultBranch": "main" }, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.7.2" ], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "4.0.0", @@ -18773,12 +18862,14 @@ "main_nextflow_config_manifest": { "defaultBranch": "master" }, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -18942,8 +19033,10 @@ "has_nf_test_dev": false, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [], "dev_nextflow_config_manifest": {}, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -19136,12 +19229,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.7.2" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.1.0", @@ -19507,12 +19602,14 @@ "nf-validation@1.1.3" ], "main_nextflow_config_manifest": {}, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -19692,8 +19789,10 @@ "has_nf_test_dev": false, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [], "dev_nextflow_config_manifest": {}, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -19858,12 +19957,14 @@ "main_nextflow_config_manifest": { "defaultBranch": "master" }, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "dev" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -20108,18 +20209,21 @@ "has_nf_test_dev": true, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "main_nextflow_config_plugins": [ "nf-schema@2.2.0" ], "main_nextflow_config_manifest": { "defaultBranch": "main" }, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -20299,12 +20403,14 @@ "main_nextflow_config_manifest": { "defaultBranch": "master" }, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "0.2.0", @@ -20531,12 +20637,14 @@ "has_nf_test_dev": true, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.4.2" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.1.0", @@ -20833,12 +20941,14 @@ "has_nf_test_dev": true, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "2.1.0", @@ -21177,10 +21287,12 @@ "has_nf_test_dev": false, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-validation" ], "dev_nextflow_config_manifest": {}, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.0.0", @@ -21497,12 +21609,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "2.2.0", @@ -21879,8 +21993,10 @@ "has_nf_test_dev": false, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [], "dev_nextflow_config_manifest": {}, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.0.0", @@ -22047,12 +22163,14 @@ "nf-validation@1.1.3" ], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "2.0.0", @@ -22500,12 +22618,14 @@ "has_nf_test_dev": false, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.1.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "0.1.0-alpha", @@ -23279,12 +23399,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.3.0" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -23500,12 +23622,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.0.0", @@ -23813,12 +23937,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.0.2", @@ -24297,12 +24423,14 @@ "main_nextflow_config_manifest": { "defaultBranch": "main" }, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "5.4.2", @@ -26689,12 +26817,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.7.2" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.1.0", @@ -26981,10 +27111,12 @@ "nf-validation" ], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.1.1" ], "dev_nextflow_config_manifest": {}, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.0.3", @@ -27324,12 +27456,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -27505,12 +27639,14 @@ "has_nf_test_dev": true, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-validation@1.1.3" ], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -27697,10 +27833,12 @@ "nf-validation@1.1.3" ], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-validation@1.1.3" ], "dev_nextflow_config_manifest": {}, + "dev_uses_params_block": false, "releases": [ { "tag_name": "2.0.1", @@ -27940,12 +28078,14 @@ "nf-schema@2.1.1" ], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.4.2" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.0.0", @@ -28178,12 +28318,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.7.2" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.4.0", @@ -28688,12 +28830,14 @@ "nf-validation@1.1.3" ], "main_nextflow_config_manifest": {}, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -28881,14 +29025,17 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "main_nextflow_config_plugins": [], "main_nextflow_config_manifest": {}, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.7.0" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "2.0.0", @@ -29336,12 +29483,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "4.2.0", @@ -30353,12 +30502,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "3.2.0", @@ -30970,12 +31121,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.3.0" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -31145,8 +31298,10 @@ "has_nf_test_dev": false, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [], "dev_nextflow_config_manifest": {}, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.0.0", @@ -31329,12 +31484,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.2.0", @@ -31585,12 +31742,14 @@ "main_nextflow_config_manifest": { "defaultBranch": "main" }, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.7.2" ], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -31792,6 +31951,7 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1", "nf-co2footprint@1.0.0", @@ -31800,6 +31960,7 @@ "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.1.1", @@ -32236,12 +32397,14 @@ "has_nf_test_dev": false, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.2.0" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "3.1.0", @@ -32616,12 +32779,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.6.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.3.3", @@ -33014,12 +33179,14 @@ "main_nextflow_config_manifest": { "defaultBranch": "master" }, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.2.0" ], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "2.3.0", @@ -33588,12 +33755,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -33898,10 +34067,12 @@ "has_nf_test_dev": false, "main_nextflow_config_plugins": [], "main_nextflow_config_manifest": {}, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-validation@1.1.3" ], "dev_nextflow_config_manifest": {}, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -34129,12 +34300,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "2.3.0", @@ -34469,12 +34642,14 @@ "main_nextflow_config_manifest": { "defaultBranch": "main" }, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.3.0" ], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -34705,12 +34880,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.1.0", @@ -35066,12 +35243,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.7.2" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "3.0.0", @@ -35665,12 +35844,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.2.0" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.1.3", @@ -36027,12 +36208,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.2.0" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -36254,12 +36437,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "main" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.1.0", @@ -36587,10 +36772,12 @@ "nf-validation" ], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-validation@1.1.3" ], "dev_nextflow_config_manifest": {}, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -36824,6 +37011,7 @@ "main_nextflow_config_manifest": { "defaultBranch": "master" }, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1", "nf-co2footprint@1.0.0-beta", @@ -36832,6 +37020,7 @@ "dev_nextflow_config_manifest": { "defaultBranch": "main" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.1.0", @@ -37180,12 +37369,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.7.2" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "2.0.1", @@ -37517,6 +37708,7 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.7.2", "nf-slack@0.5.1" @@ -37524,6 +37716,7 @@ "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "4.1.2", @@ -38195,12 +38388,14 @@ "main_nextflow_config_manifest": { "defaultBranch": "master" }, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.6.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.1.0", @@ -38497,12 +38692,14 @@ "main_nextflow_config_manifest": { "defaultBranch": "main" }, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.7.2" ], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "2.4.0", @@ -39256,12 +39453,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.7.2" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "2.0.0", @@ -39587,8 +39786,10 @@ "has_nf_test_dev": false, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [], "dev_nextflow_config_manifest": {}, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.0.0", @@ -39818,10 +40019,10 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/provenancereport", "created_at": "2026-06-11T12:54:57Z", - "updated_at": "2026-06-18T13:00:50Z", - "pushed_at": "2026-06-11T13:19:00Z", + "updated_at": "2026-07-01T08:40:30Z", + "pushed_at": "2026-07-01T08:40:24Z", "homepage": null, - "size": 187, + "size": 658, "stargazers_count": 0, "watchers_count": 0, "language": "Nextflow", @@ -39834,7 +40035,7 @@ "forks_count": 1, "archived": false, "disabled": false, - "open_issues_count": 15, + "open_issues_count": 13, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -39843,7 +40044,7 @@ "topics": [], "visibility": "public", "forks": 1, - "open_issues": 15, + "open_issues": 13, "watchers": 0, "default_branch": "dev", "temp_clone_token": "", @@ -39908,41 +40109,50 @@ "workflow", "pipeline" ], - "open_pr_count": 1, + "open_pr_count": 0, "repository_url": "https://github.com/nf-core/provenancereport", "contributors": [ + { + "name": "atrigila", + "count": 10, + "avatar_url": "https://avatars.githubusercontent.com/u/18577080?v=4" + }, { "name": "apeltzer", - "count": 1, + "count": 2, "avatar_url": "https://avatars.githubusercontent.com/u/2359510?v=4" } ], "released_after_tools": false, - "head_sha": "e858f86c3595ba490c60b36b8fe086ef676a8944", + "head_sha": "339adce96b55d735b77fbcb197e1ecdd55673f12", "last_release_is_head": false, "last_release_vs_default_compare_url": "", - "commits_to_dev": 1, - "is_DSL2": false, + "commits_to_dev": 12, + "is_DSL2": true, "has_nf_test": true, "has_nf_test_dev": true, "dev_nextflow_config_plugins": [ - "nf-schema@2.5.1" + "nf-schema@2.5.1", + "nf-prov@1.6.0" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", - "published_at": "2026-06-11T13:18:24Z", - "tag_sha": "e858f86c3595ba490c60b36b8fe086ef676a8944", + "published_at": "2026-07-01T08:40:24Z", + "tag_sha": "339adce96b55d735b77fbcb197e1ecdd55673f12", "has_schema": true, "doc_files": [ "docs/output.md", "docs/usage.md" ], "components": { - "modules": [], + "modules": [ + "quartonotebook" + ], "subworkflows": [ "utils_nextflow_pipeline", "utils_nfcore_pipeline", @@ -40568,8 +40778,10 @@ "has_nf_test_dev": false, "main_nextflow_config_plugins": [], "main_nextflow_config_manifest": {}, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [], "dev_nextflow_config_manifest": {}, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -40773,12 +40985,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.0.0", @@ -40843,9 +41057,9 @@ "url": "https://api.github.com/repos/nf-core/raredisease", "created_at": "2021-06-21T09:40:29Z", "updated_at": "2026-06-25T07:00:32Z", - "pushed_at": "2026-06-30T19:37:43Z", + "pushed_at": "2026-07-01T08:57:15Z", "homepage": "https://nf-co.re/raredisease", - "size": 199806, + "size": 199851, "stargazers_count": 119, "watchers_count": 119, "language": "Nextflow", @@ -40858,7 +41072,7 @@ "forks_count": 69, "archived": false, "disabled": false, - "open_issues_count": 63, + "open_issues_count": 64, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -40876,7 +41090,7 @@ ], "visibility": "public", "forks": 69, - "open_issues": 63, + "open_issues": 64, "watchers": 119, "default_branch": "master", "temp_clone_token": "", @@ -41142,12 +41356,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "3.1.1", @@ -42814,8 +43030,8 @@ }, { "tag_name": "dev", - "published_at": "2026-06-30T19:37:38Z", - "tag_sha": "6fea9aea09786b85d38874766dc7b2243f31ea5c", + "published_at": "2026-07-01T07:45:21Z", + "tag_sha": "f8ea02e68a77d3e781f99e6fbc0e52cdba38fe11", "has_schema": true, "doc_files": [ "docs/output.md", @@ -42873,6 +43089,8 @@ "gatk4_shiftfasta", "gatk4_splitintervals", "gatk4_variantfiltration", + "gatk4_calculatecontamination", + "gatk4_getpileupsummaries", "gawk", "genmod_annotate", "genmod_compound", @@ -43083,12 +43301,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.3.0" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -43256,10 +43476,12 @@ "nf-validation@1.1.3" ], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-validation@1.1.3" ], "dev_nextflow_config_manifest": {}, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.0.1", @@ -43502,10 +43724,12 @@ "nf-validation@1.1.3" ], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "main_nextflow_config_plugins": [ "nf-schema@2.1.1" ], "main_nextflow_config_manifest": {}, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-core-utils@0.4.0", "nf-schema@2.7.2" @@ -43513,6 +43737,7 @@ "dev_nextflow_config_manifest": { "defaultBranch": "main" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "0.1", @@ -43630,7 +43855,7 @@ "forks_count": 6, "archived": false, "disabled": false, - "open_issues_count": 14, + "open_issues_count": 15, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -43641,7 +43866,7 @@ ], "visibility": "public", "forks": 6, - "open_issues": 14, + "open_issues": 15, "watchers": 11, "default_branch": "master", "temp_clone_token": "", @@ -43718,7 +43943,7 @@ "dev_branch_protection_enforce_admins": false, "TEMPLATE_branch_exists": true, "has_required_topics": true, - "open_pr_count": 0, + "open_pr_count": 1, "repository_url": "https://github.com/nf-core/reportho", "contributors": [ { @@ -43756,18 +43981,21 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "main_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "main_nextflow_config_manifest": { "defaultBranch": "master" }, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.1.0", @@ -44016,12 +44244,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.0.0", @@ -44244,12 +44474,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.2.0", @@ -44801,12 +45033,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.0.0", @@ -45283,12 +45517,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.7.2" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": true, "releases": [ { "tag_name": "4.1.3", @@ -46256,9 +46492,9 @@ "url": "https://api.github.com/repos/nf-core/rnaseq", "created_at": "2018-03-29T13:10:58Z", "updated_at": "2026-06-30T08:57:20Z", - "pushed_at": "2026-06-30T13:52:47Z", + "pushed_at": "2026-07-01T07:39:02Z", "homepage": "https://nf-co.re/rnaseq", - "size": 85869, + "size": 85911, "stargazers_count": 1322, "watchers_count": 1322, "language": "Nextflow", @@ -46271,7 +46507,7 @@ "forks_count": 880, "archived": false, "disabled": false, - "open_issues_count": 26, + "open_issues_count": 25, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -46283,7 +46519,7 @@ ], "visibility": "public", "forks": 880, - "open_issues": 26, + "open_issues": 25, "watchers": 1322, "default_branch": "master", "temp_clone_token": "", @@ -46357,7 +46593,7 @@ "dev_branch_protection_enforce_admins": false, "TEMPLATE_branch_exists": true, "has_required_topics": true, - "open_pr_count": 6, + "open_pr_count": 5, "repository_url": "https://github.com/nf-core/rnaseq", "contributors": [ { @@ -46870,12 +47106,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.7.2" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "3.26.0", @@ -49711,8 +49949,8 @@ }, { "tag_name": "dev", - "published_at": "2026-06-18T21:53:08Z", - "tag_sha": "6f6c86071fd3040122063479376e62c30d86a544", + "published_at": "2026-06-30T13:52:46Z", + "tag_sha": "02dfe8bbea3ac9b6c182d174fba815f1be81bf7c", "has_schema": true, "doc_files": [ "docs/output.md", @@ -50002,12 +50240,14 @@ "nf-validation@1.1.3" ], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.7.2" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": true, "releases": [ { "tag_name": "1.0.4", @@ -50493,6 +50733,7 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-core-utils@0.4.0", "nf-schema@2.6.1" @@ -50500,6 +50741,7 @@ "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.3.0", @@ -51283,12 +51525,14 @@ "nf-validation" ], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -51384,7 +51628,7 @@ "has_wiki": false, "has_pages": false, "has_discussions": false, - "forks_count": 537, + "forks_count": 538, "archived": false, "disabled": false, "open_issues_count": 288, @@ -51407,7 +51651,7 @@ "whole-genome-sequencing" ], "visibility": "public", - "forks": 537, + "forks": 538, "open_issues": 288, "watchers": 578, "default_branch": "master", @@ -51452,7 +51696,7 @@ "status": "disabled" } }, - "network_count": 537, + "network_count": 538, "subscribers_count": 133, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, @@ -51876,6 +52120,7 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-core-utils@0.4.0", "nf-fgbio@1.0.0", @@ -51885,6 +52130,7 @@ "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "3.8.1", @@ -55455,6 +55701,7 @@ "nf-validation@1.1.3" ], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1", "nf-anndata@0.3.2" @@ -55462,6 +55709,7 @@ "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -56037,12 +56285,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.3.0", @@ -56751,12 +57001,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "4.1.0", @@ -57359,9 +57611,9 @@ "url": "https://api.github.com/repos/nf-core/seqinspector", "created_at": "2024-03-14T10:40:33Z", "updated_at": "2026-06-25T13:48:12Z", - "pushed_at": "2026-06-30T15:32:06Z", + "pushed_at": "2026-07-01T09:03:04Z", "homepage": "https://nf-co.re/seqinspector", - "size": 7261, + "size": 7718, "stargazers_count": 25, "watchers_count": 25, "language": "Nextflow", @@ -57583,6 +57835,7 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-core-utils@0.4.0", "nf-schema@2.6.1" @@ -57590,6 +57843,7 @@ "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.0.1", @@ -57887,12 +58141,14 @@ "main_nextflow_config_manifest": { "defaultBranch": "main" }, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -58300,8 +58556,10 @@ "has_nf_test_dev": false, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [], "dev_nextflow_config_manifest": {}, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.0.0", @@ -59000,12 +59258,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "2.4.1", @@ -59620,12 +59880,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -59821,12 +60083,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.0.0", @@ -60075,12 +60339,14 @@ "has_nf_test_dev": true, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -60244,10 +60510,12 @@ "has_nf_test_dev": false, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-validation@1.1.3" ], "dev_nextflow_config_manifest": {}, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -60432,9 +60700,9 @@ "url": "https://api.github.com/repos/nf-core/stableexpression", "created_at": "2024-12-20T23:22:55Z", "updated_at": "2026-06-29T10:11:37Z", - "pushed_at": "2026-06-29T14:44:47Z", + "pushed_at": "2026-07-01T10:01:23Z", "homepage": "https://nf-co.re/stableexpression", - "size": 23447, + "size": 23333, "stargazers_count": 9, "watchers_count": 9, "language": "Python", @@ -60564,12 +60832,14 @@ "nf-schema@2.0.0" ], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -60862,12 +61132,14 @@ "main_nextflow_config_manifest": { "defaultBranch": "main" }, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.7.2" ], "dev_nextflow_config_manifest": { "defaultBranch": "main" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "2.0.1", @@ -62532,12 +62804,14 @@ "nf-validation@1.1.3" ], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -62742,12 +63016,14 @@ "nf-validation@1.1.3" ], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -62928,12 +63204,14 @@ "nf-validation@1.1.3" ], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.3.0" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -63142,12 +63420,14 @@ "has_nf_test_dev": true, "main_nextflow_config_plugins": [], "main_nextflow_config_manifest": {}, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -63367,6 +63647,7 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.5.1", "nf-prov@1.2.2" @@ -63374,6 +63655,7 @@ "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.5.0", @@ -63908,8 +64190,10 @@ "has_nf_test_dev": false, "master_nextflow_config_plugins": [], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [], "dev_nextflow_config_manifest": {}, + "dev_uses_params_block": false, "releases": [ { "tag_name": "dev", @@ -64113,12 +64397,14 @@ "main_nextflow_config_manifest": { "defaultBranch": "master" }, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.6.1" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.0.0", @@ -64491,10 +64777,12 @@ "nf-validation" ], "master_nextflow_config_manifest": {}, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-validation@1.1.3" ], "dev_nextflow_config_manifest": {}, + "dev_uses_params_block": false, "releases": [ { "tag_name": "0.1.1", @@ -64741,12 +65029,14 @@ "main_nextflow_config_manifest": { "defaultBranch": "master" }, + "main_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.7.2" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "1.1.2", @@ -65822,12 +66112,14 @@ "master_nextflow_config_manifest": { "defaultBranch": "master" }, + "master_uses_params_block": false, "dev_nextflow_config_plugins": [ "nf-schema@2.7.2" ], "dev_nextflow_config_manifest": { "defaultBranch": "master" }, + "dev_uses_params_block": false, "releases": [ { "tag_name": "3.0.0", diff --git a/sites/pipelines/src/pages/pipeline_health.astro b/sites/pipelines/src/pages/pipeline_health.astro index 0eab097fb4..c74e973c55 100644 --- a/sites/pipelines/src/pages/pipeline_health.astro +++ b/sites/pipelines/src/pages/pipeline_health.astro @@ -168,6 +168,13 @@ const countTrue = (fn) => { ); }) } + Params block @@ -427,6 +434,18 @@ const countTrue = (fn) => { ), ], )} + {/* Params block in main.nf */} + {getCell( + pipeline[`${mainOrMasterBranch}_uses_params_block`], + pipeline.repository_url + `/blob/${mainOrMasterBranch}/main.nf`, + `root main.nf declares a \`params {}\` block in ${mainOrMasterBranch}`, + "border-start", + )} + {getCell( + pipeline["dev_uses_params_block"], + pipeline.repository_url + "/blob/dev/main.nf", + "root main.nf declares a `params {}` block in dev", + )} ); }) @@ -457,8 +476,8 @@ const countTrue = (fn) => { p[(p.main_branch_exists ? "main" : "master") + "_nextflow_config_manifest"] ?.defaultBranch === p.default_branch, ) - } + } + {countTrue((p) => p.has_required_topics)} {countTrue((p) => p.description)} { ], ) } + {countTrue((p) => p[(p.main_branch_exists ? "main" : "master") + "_uses_params_block"])} + {countTrue((p) => p["dev_uses_params_block"])} From c99639f0b7aaae7214d0eb47afe7063f9b179fbb Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 1 Jul 2026 12:29:19 +0200 Subject: [PATCH 2/2] add sarek release --- bin/pipelines.json.js | 1 - public/pipelines.json | 161 +++++++++++++++++++++++++++++++++++++++++- 2 files changed, 158 insertions(+), 4 deletions(-) diff --git a/bin/pipelines.json.js b/bin/pipelines.json.js index d539c1fcab..3910c4710b 100644 --- a/bin/pipelines.json.js +++ b/bin/pipelines.json.js @@ -334,7 +334,6 @@ export const writePipelinesJson = async () => { // remove empty values from releases (usually from draft releases) releases = releases.filter((release) => release.tag_name !== "" && release.draft === false); - console.log(`Releases for ${name}:`, releases.map((release) => release.tag_name)); // remove releases that are already in the pipelines.json file const pipelineIndex = pipelines.remote_workflows.findIndex((workflow) => workflow.name === name); let new_releases = releases; diff --git a/public/pipelines.json b/public/pipelines.json index 31bd98c052..6c0ebe3a2f 100644 --- a/public/pipelines.json +++ b/public/pipelines.json @@ -52103,10 +52103,10 @@ "avatar_url": "https://avatars.githubusercontent.com/u/21218078?v=4" } ], - "released_after_tools": false, + "released_after_tools": true, "head_sha": "b97952e5bac68d5deb93d4a3349a45f146be9830", - "last_release_is_head": false, - "last_release_vs_default_compare_url": "https://github.com/nf-core/sarek/compare/b97952e5bac68d5deb93d4a3349a45f146be9830...4bd2948f98c5bf7b785c91cf6708fffccab25467", + "last_release_is_head": true, + "last_release_vs_default_compare_url": "https://github.com/nf-core/sarek/compare/b97952e5bac68d5deb93d4a3349a45f146be9830...b97952e5bac68d5deb93d4a3349a45f146be9830", "commits_to_dev": 30, "is_DSL2": true, "has_nf_test": true, @@ -52132,6 +52132,161 @@ }, "dev_uses_params_block": false, "releases": [ + { + "tag_name": "3.9.0", + "published_at": "2026-06-30T11:34:06Z", + "tag_sha": "b97952e5bac68d5deb93d4a3349a45f146be9830", + "has_schema": true, + "doc_files": [ + "docs/output.md", + "docs/usage.md", + "docs/usage/variantcalling/interpretation.md", + "docs/usage/variantcalling/introduction.md", + "docs/usage/variantcalling/sarek.md", + "docs/usage/variantcalling/theory.md" + ], + "components": { + "modules": [ + "ascat", + "bbmap_bbsplit", + "bcftools_annotate", + "bcftools_concat", + "bcftools_isec", + "bcftools_merge", + "bcftools_mpileup", + "bcftools_norm", + "bcftools_sort", + "bcftools_stats", + "bcftools_view", + "bwa_index", + "bwa_mem", + "bwamem2_index", + "bwamem2_mem", + "cat_cat", + "cat_fastq", + "cnvkit_antitarget", + "cnvkit_batch", + "cnvkit_call", + "cnvkit_export", + "cnvkit_genemetrics", + "cnvkit_reference", + "controlfreec_assesssignificance", + "controlfreec_freec", + "controlfreec_freec2bed", + "controlfreec_freec2circos", + "controlfreec_makegraph2", + "deepvariant_rundeepvariant", + "dragmap_align", + "dragmap_hashtable", + "ensemblvep_download", + "ensemblvep_vep", + "fastp", + "fastqc", + "fgbio_callmolecularconsensusreads", + "fgbio_copyumifromreadname", + "fgbio_fastqtobam", + "fgbio_groupreadsbyumi", + "freebayes", + "gatk4_applybqsr", + "gatk4_applyvqsr", + "gatk4_baserecalibrator", + "gatk4_calculatecontamination", + "gatk4_cnnscorevariants", + "gatk4_createsequencedictionary", + "gatk4_estimatelibrarycomplexity", + "gatk4_filtermutectcalls", + "gatk4_filtervarianttranches", + "gatk4_gatherbqsrreports", + "gatk4_gatherpileupsummaries", + "gatk4_genomicsdbimport", + "gatk4_genotypegvcfs", + "gatk4_getpileupsummaries", + "gatk4_haplotypecaller", + "gatk4_intervallisttobed", + "gatk4_learnreadorientationmodel", + "gatk4_markduplicates", + "gatk4_mergemutectstats", + "gatk4_mergevcfs", + "gatk4_mutect2", + "gatk4_variantrecalibrator", + "gatk4spark_applybqsr", + "gatk4spark_baserecalibrator", + "gatk4spark_markduplicates", + "gawk", + "goleft_indexcov", + "gunzip", + "lofreq_callparallel", + "manta_germline", + "manta_somatic", + "manta_tumoronly", + "mosdepth", + "msisensor2_msi", + "msisensorpro_msisomatic", + "msisensorpro_scan", + "multiqc", + "muse_call", + "muse_sump", + "ngscheckmate_ncm", + "parabricks_fq2bam", + "rbt_vcfsplit", + "samtools_bam2fq", + "samtools_collatefastq", + "samtools_convert", + "samtools_faidx", + "samtools_index", + "samtools_merge", + "samtools_mpileup", + "samtools_stats", + "samtools_view", + "sentieon_applyvarcal", + "sentieon_bwamem", + "sentieon_dedup", + "sentieon_dnamodelapply", + "sentieon_dnascope", + "sentieon_gvcftyper", + "sentieon_haplotyper", + "sentieon_tnscope", + "sentieon_varcal", + "snpeff_download", + "snpeff_snpeff", + "snpsift_annmem", + "snpsift_annmemcreate", + "spring_decompress", + "strelka_germline", + "strelka_somatic", + "svdb_merge", + "tabix_bgziptabix", + "tabix_tabix", + "tiddit_sv", + "untar", + "unzip", + "varlociraptor_callvariants", + "varlociraptor_estimatealignmentproperties", + "varlociraptor_preprocess", + "vcflib_vcffilter", + "vcftools", + "yte" + ], + "subworkflows": [ + "bam_ngscheckmate", + "cache_download_ensemblvep_snpeff", + "utils_annotation_cache", + "utils_nextflow_pipeline", + "utils_nfcore_pipeline", + "utils_nfschema_plugin", + "vcf_annotate_snpeff" + ] + }, + "nextflow_version": "!>=25.10.2", + "nf_core_version": "3.5.1", + "plugins": [ + "nf-core-utils@0.4.0", + "nf-fgbio@1.0.0", + "nf-prov@1.7.0", + "nf-schema@2.7.2" + ], + "co2footprint_files": null + }, { "tag_name": "3.8.1", "published_at": "2026-02-12T08:50:37Z",