{"id":38776,"name":"bulk-rnaseq-nextflow","description":"Bulk RNASeq Workflow","url":"https://github.com/veupathdb/bulk-rnaseq-nextflow","last_synced_at":"2025-09-05T07:52:57.408Z","repository":{"id":248173034,"uuid":"827970122","full_name":"VEuPathDB/bulk-rnaseq-nextflow","owner":"VEuPathDB","description":"Bulk RNASeq Workflow","archived":false,"fork":false,"pushed_at":"2025-07-18T16:18:41.000Z","size":313,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"TEMPLATE","last_synced_at":"2025-08-06T01:31:35.628Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Nextflow","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/VEuPathDB.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATIONS.md","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2024-07-12T19:25:46.000Z","updated_at":"2024-10-11T14:54:26.000Z","dependencies_parsed_at":"2025-02-06T20:30:43.335Z","dependency_job_id":"c30dc159-9d27-4345-963d-bc5e3b5e8916","html_url":"https://github.com/VEuPathDB/bulk-rnaseq-nextflow","commit_stats":null,"previous_names":["jbrestel/bulkrnaseq","veupathdb/bulk-rnaseq-nextflow"],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/VEuPathDB/bulk-rnaseq-nextflow","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VEuPathDB%2Fbulk-rnaseq-nextflow","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VEuPathDB%2Fbulk-rnaseq-nextflow/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VEuPathDB%2Fbulk-rnaseq-nextflow/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VEuPathDB%2Fbulk-rnaseq-nextflow/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/VEuPathDB","download_url":"https://codeload.github.com/VEuPathDB/bulk-rnaseq-nextflow/tar.gz/refs/heads/TEMPLATE","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VEuPathDB%2Fbulk-rnaseq-nextflow/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273728151,"owners_count":25157136,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-09-05T02:00:09.113Z","response_time":402,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"owner":{"login":"VEuPathDB","name":"VEuPathDB Bioinformatics Resource Center","uuid":"903733","kind":"organization","description":"","email":null,"website":"http://veupathdb.org","location":null,"twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/903733?v=4","repositories_count":196,"last_synced_at":"2023-03-24T08:02:13.462Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/VEuPathDB","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-03T20:58:48.270Z","updated_at":"2023-03-24T08:02:14.439Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/VEuPathDB","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/VEuPathDB/repositories"},"packages":[],"commits":{"id":10711132,"full_name":"veupathdb/bulk-rnaseq-nextflow","default_branch":"TEMPLATE","committers":[{"name":"John Brestelli","email":"jbrestell@gmail.com","login":"jbrestel","count":1}],"total_commits":1,"total_committers":1,"total_bot_commits":0,"total_bot_committers":0,"mean_commits":1.0,"dds":0.0,"past_year_committers":[],"past_year_total_commits":0,"past_year_total_committers":0,"past_year_total_bot_commits":0,"past_year_total_bot_committers":0,"past_year_mean_commits":0.0,"past_year_dds":0.0,"last_synced_at":"2025-08-06T01:21:26.276Z","last_synced_commit":"15210a577d87e27b9ecd1e502873cd99f9812578","created_at":"2025-08-06T01:20:14.406Z","updated_at":"2025-08-06T01:21:26.276Z","commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/veupathdb%2Fbulk-rnaseq-nextflow/commits","host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-05T00:00:10.343Z","repositories_count":5480019,"commits_count":853389012,"contributors_count":31098138,"owners_count":906558,"icon_url":"https://github.com/github.png","host_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories"}},"issues_stats":{"full_name":"veupathdb/bulk-rnaseq-nextflow","html_url":"https://github.com/veupathdb/bulk-rnaseq-nextflow","last_synced_at":"2025-08-06T09:39:36.393Z","status":"error","issues_count":null,"pull_requests_count":null,"avg_time_to_close_issue":null,"avg_time_to_close_pull_request":null,"issues_closed_count":null,"pull_requests_closed_count":null,"pull_request_authors_count":null,"issue_authors_count":null,"avg_comments_per_issue":null,"avg_comments_per_pull_request":null,"merged_pull_requests_count":null,"bot_issues_count":null,"bot_pull_requests_count":null,"past_year_issues_count":null,"past_year_pull_requests_count":null,"past_year_avg_time_to_close_issue":null,"past_year_avg_time_to_close_pull_request":null,"past_year_issues_closed_count":null,"past_year_pull_requests_closed_count":null,"past_year_pull_request_authors_count":null,"past_year_issue_authors_count":null,"past_year_avg_comments_per_issue":null,"past_year_avg_comments_per_pull_request":null,"past_year_bot_issues_count":null,"past_year_bot_pull_requests_count":null,"past_year_merged_pull_requests_count":null,"created_at":"2025-08-06T01:20:14.613Z","updated_at":"2025-09-02T17:13:13.644Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/veupathdb%2Fbulk-rnaseq-nextflow","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/veupathdb%2Fbulk-rnaseq-nextflow/issues","issue_labels_count":{"enhancement":1,"bug":1},"pull_request_labels_count":{},"issue_author_associations_count":{"MEMBER":2},"pull_request_author_associations_count":{"MEMBER":1},"issue_authors":{"jbrestel":2},"pull_request_authors":{"sybah2":1},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-05T00:00:10.444Z","repositories_count":10094553,"issues_count":31373669,"pull_requests_count":97058592,"authors_count":10699554,"icon_url":"https://github.com/github.png","host_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories","owners_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/owners","authors_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors"},"past_year_issue_labels_count":{"enhancement":1,"bug":1},"past_year_pull_request_labels_count":{},"past_year_issue_author_associations_count":{"MEMBER":2},"past_year_pull_request_author_associations_count":{},"past_year_issue_authors":{"jbrestel":2},"past_year_pull_request_authors":{},"maintainers":[{"login":"jbrestel","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/jbrestel"},{"login":"sybah2","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/sybah2"}],"active_maintainers":[{"login":"jbrestel","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/jbrestel"}]},"events":{"total":{"IssuesEvent":4,"DeleteEvent":7,"PushEvent":34,"PullRequestEvent":3,"CreateEvent":8},"last_year":{"IssuesEvent":4,"DeleteEvent":7,"PushEvent":34,"PullRequestEvent":3,"CreateEvent":8}},"keywords":[],"dependencies":[{"ecosystem":"actions","filepath":".github/workflows/branch.yml","sha":null,"kind":"manifest","created_at":"2024-07-12T21:59:28.872Z","updated_at":"2024-07-12T21:59:28.872Z","repository_link":"https://github.com/VEuPathDB/bulk-rnaseq-nextflow/blob/TEMPLATE/.github/workflows/branch.yml","dependencies":[{"id":19072905686,"package_name":"mshick/add-pr-comment","ecosystem":"actions","requirements":"b8f338c590a895d50bcbfa6c5859251edc8952fc","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/ci.yml","sha":null,"kind":"manifest","created_at":"2024-07-12T21:59:29.037Z","updated_at":"2024-07-12T21:59:29.037Z","repository_link":"https://github.com/VEuPathDB/bulk-rnaseq-nextflow/blob/TEMPLATE/.github/workflows/ci.yml","dependencies":[{"id":19072905688,"package_name":"actions/checkout","ecosystem":"actions","requirements":"0ad4b8fadaa221de15dcec353f45205ec38ea70b","direct":true,"kind":"composite","optional":false},{"id":19072905689,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":19072905690,"package_name":"jlumbroso/free-disk-space","ecosystem":"actions","requirements":"54081f138730dfa15788a46383842cd2f914a1be","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/clean-up.yml","sha":null,"kind":"manifest","created_at":"2024-07-12T21:59:29.237Z","updated_at":"2024-07-12T21:59:29.237Z","repository_link":"https://github.com/VEuPathDB/bulk-rnaseq-nextflow/blob/TEMPLATE/.github/workflows/clean-up.yml","dependencies":[{"id":19072905696,"package_name":"actions/stale","ecosystem":"actions","requirements":"28ca1036281a5e5922ead5184a1bbf96e5fc984e","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/download_pipeline.yml","sha":null,"kind":"manifest","created_at":"2024-07-12T21:59:29.480Z","updated_at":"2024-07-12T21:59:29.480Z","repository_link":"https://github.com/VEuPathDB/bulk-rnaseq-nextflow/blob/TEMPLATE/.github/workflows/download_pipeline.yml","dependencies":[{"id":19072905697,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":19072905698,"package_name":"jlumbroso/free-disk-space","ecosystem":"actions","requirements":"54081f138730dfa15788a46383842cd2f914a1be","direct":true,"kind":"composite","optional":false},{"id":19072905699,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"82c7e631bb3cdc910f68e0081d67478d79c6982d","direct":true,"kind":"composite","optional":false},{"id":19072905700,"package_name":"eWaterCycle/setup-singularity","ecosystem":"actions","requirements":"931d4e31109e875b13309ae1d07c70ca8fbc8537","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/fix-linting.yml","sha":null,"kind":"manifest","created_at":"2024-07-12T21:59:29.656Z","updated_at":"2024-07-12T21:59:29.656Z","repository_link":"https://github.com/VEuPathDB/bulk-rnaseq-nextflow/blob/TEMPLATE/.github/workflows/fix-linting.yml","dependencies":[{"id":19072905701,"package_name":"actions/checkout","ecosystem":"actions","requirements":"0ad4b8fadaa221de15dcec353f45205ec38ea70b","direct":true,"kind":"composite","optional":false},{"id":19072905702,"package_name":"peter-evans/create-or-update-comment","ecosystem":"actions","requirements":"71345be0265236311c031f5c7866368bd1eff043","direct":true,"kind":"composite","optional":false},{"id":19072905703,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"82c7e631bb3cdc910f68e0081d67478d79c6982d","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/linting.yml","sha":null,"kind":"manifest","created_at":"2024-07-12T21:59:29.830Z","updated_at":"2024-07-12T21:59:29.830Z","repository_link":"https://github.com/VEuPathDB/bulk-rnaseq-nextflow/blob/TEMPLATE/.github/workflows/linting.yml","dependencies":[{"id":19072905704,"package_name":"actions/checkout","ecosystem":"actions","requirements":"0ad4b8fadaa221de15dcec353f45205ec38ea70b","direct":true,"kind":"composite","optional":false},{"id":19072905705,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"82c7e631bb3cdc910f68e0081d67478d79c6982d","direct":true,"kind":"composite","optional":false},{"id":19072905706,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":19072905707,"package_name":"actions/upload-artifact","ecosystem":"actions","requirements":"65462800fd760344b1a7b4382951275a0abb4808","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/linting_comment.yml","sha":null,"kind":"manifest","created_at":"2024-07-12T21:59:30.120Z","updated_at":"2024-07-12T21:59:30.120Z","repository_link":"https://github.com/VEuPathDB/bulk-rnaseq-nextflow/blob/TEMPLATE/.github/workflows/linting_comment.yml","dependencies":[{"id":19072905708,"package_name":"dawidd6/action-download-artifact","ecosystem":"actions","requirements":"09f2f74827fd3a8607589e5ad7f9398816f540fe","direct":true,"kind":"composite","optional":false},{"id":19072905709,"package_name":"marocchino/sticky-pull-request-comment","ecosystem":"actions","requirements":"331f8f5b4215f0445d3c07b4967662a32a2d3e31","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/release-announcements.yml","sha":null,"kind":"manifest","created_at":"2024-07-12T21:59:30.281Z","updated_at":"2024-07-12T21:59:30.281Z","repository_link":"https://github.com/VEuPathDB/bulk-rnaseq-nextflow/blob/TEMPLATE/.github/workflows/release-announcements.yml","dependencies":[{"id":19072905710,"package_name":"rzr/fediverse-action","ecosystem":"actions","requirements":"master","direct":true,"kind":"composite","optional":false},{"id":19072905711,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"82c7e631bb3cdc910f68e0081d67478d79c6982d","direct":true,"kind":"composite","optional":false},{"id":19072905712,"package_name":"zentered/bluesky-post-action","ecosystem":"actions","requirements":"80dbe0a7697de18c15ad22f4619919ceb5ccf597","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"cpan","filepath":"modules/nf-core/fastqc/meta.yml","sha":null,"kind":"manifest","created_at":"2024-07-12T21:59:30.841Z","updated_at":"2024-07-12T21:59:30.841Z","repository_link":"https://github.com/VEuPathDB/bulk-rnaseq-nextflow/blob/TEMPLATE/modules/nf-core/fastqc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/multiqc/meta.yml","sha":null,"kind":"manifest","created_at":"2024-07-12T21:59:30.979Z","updated_at":"2024-07-12T21:59:30.979Z","repository_link":"https://github.com/VEuPathDB/bulk-rnaseq-nextflow/blob/TEMPLATE/modules/nf-core/multiqc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/utils_nextflow_pipeline/meta.yml","sha":null,"kind":"manifest","created_at":"2024-07-12T21:59:31.433Z","updated_at":"2024-07-12T21:59:31.433Z","repository_link":"https://github.com/VEuPathDB/bulk-rnaseq-nextflow/blob/TEMPLATE/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/utils_nfcore_pipeline/meta.yml","sha":null,"kind":"manifest","created_at":"2024-07-12T21:59:31.772Z","updated_at":"2024-07-12T21:59:31.772Z","repository_link":"https://github.com/VEuPathDB/bulk-rnaseq-nextflow/blob/TEMPLATE/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml","sha":null,"kind":"manifest","created_at":"2024-07-12T21:59:31.899Z","updated_at":"2024-07-12T21:59:31.899Z","repository_link":"https://github.com/VEuPathDB/bulk-rnaseq-nextflow/blob/TEMPLATE/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/fastqc/environment.yml","sha":null,"kind":"manifest","created_at":"2025-02-06T20:30:40.132Z","updated_at":"2025-02-06T20:30:40.132Z","repository_link":"https://github.com/VEuPathDB/bulk-rnaseq-nextflow/blob/TEMPLATE/modules/nf-core/fastqc/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/multiqc/environment.yml","sha":null,"kind":"manifest","created_at":"2025-02-06T20:30:40.397Z","updated_at":"2025-02-06T20:30:40.397Z","repository_link":"https://github.com/VEuPathDB/bulk-rnaseq-nextflow/blob/TEMPLATE/modules/nf-core/multiqc/environment.yml","dependencies":[]}],"score":null,"created_at":"2025-09-04T15:51:12.833Z","updated_at":"2025-10-07T08:15:53.858Z","avatar_url":"https://github.com/VEuPathDB.png","language":"Nextflow","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":["https://doi.org/10.5281/zenodo.XXXXXXX","https://doi.org/10.5281/zenodo.XXXXXX","https://dx.doi.org/10.1038/s41587-020-0439-x"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://science.ecosyste.ms/api/v1/projects/38776","html_url":"https://science.ecosyste.ms/projects/38776","bibtex_url":"https://science.ecosyste.ms/projects/38776/export.bibtex","apalike_url":"https://science.ecosyste.ms/projects/38776/export.apalike"}