{"id":55752,"name":"rnaseq","description":"RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.","url":"https://github.com/vrc-cvd/rnaseq","last_synced_at":"2025-09-05T14:01:13.705Z","repository":{"id":285929070,"uuid":"946542175","full_name":"vrc-cvd/rnaseq","owner":"vrc-cvd","description":"RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.","archived":false,"fork":false,"pushed_at":"2025-03-11T10:20:48.000Z","size":6541,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-04-03T12:25:22.757Z","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/vrc-cvd.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","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}},"created_at":"2025-03-11T09:56:45.000Z","updated_at":"2025-03-11T10:20:53.000Z","dependencies_parsed_at":"2025-04-03T12:39:03.091Z","dependency_job_id":null,"html_url":"https://github.com/vrc-cvd/rnaseq","commit_stats":null,"previous_names":["vrc-cvd/rnaseq"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/vrc-cvd/rnaseq","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vrc-cvd%2Frnaseq","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vrc-cvd%2Frnaseq/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vrc-cvd%2Frnaseq/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vrc-cvd%2Frnaseq/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/vrc-cvd","download_url":"https://codeload.github.com/vrc-cvd/rnaseq/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vrc-cvd%2Frnaseq/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273768118,"owners_count":25164464,"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":"vrc-cvd","name":null,"uuid":"202773714","kind":"user","description":null,"email":"","website":null,"location":null,"twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/202773714?v=4","repositories_count":1,"last_synced_at":"2025-04-03T12:22:49.698Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/vrc-cvd","funding_links":[],"total_stars":0,"followers":0,"following":0,"created_at":"2025-04-03T12:22:49.720Z","updated_at":"2025-04-03T12:22:49.720Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/vrc-cvd","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/vrc-cvd/repositories"},"packages":[],"commits":{"message":"Repository syncing started."},"issues_stats":{"full_name":"vrc-cvd/rnaseq","html_url":"https://github.com/vrc-cvd/rnaseq","last_synced_at":null,"status":null,"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":"2025-09-05T14:00:20.651Z","updated_at":"2025-09-05T14:00:20.651Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/vrc-cvd%2Frnaseq","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/vrc-cvd%2Frnaseq/issues","issue_labels_count":{},"pull_request_labels_count":{},"issue_author_associations_count":{},"pull_request_author_associations_count":{},"issue_authors":{},"pull_request_authors":{},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-05T00:00:10.444Z","repositories_count":10100117,"issues_count":31473266,"pull_requests_count":97445500,"authors_count":10702683,"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":{},"past_year_pull_request_labels_count":{},"past_year_issue_author_associations_count":{},"past_year_pull_request_author_associations_count":{},"past_year_issue_authors":{},"past_year_pull_request_authors":{},"maintainers":[],"active_maintainers":[]},"events":{"total":{"MemberEvent":5,"CreateEvent":2},"last_year":{"MemberEvent":5,"CreateEvent":2}},"keywords":[],"dependencies":[{"ecosystem":"actions","filepath":".github/workflows/branch.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:35:32.288Z","updated_at":"2025-04-03T12:35:32.288Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/.github/workflows/branch.yml","dependencies":[{"id":22531900249,"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":"2025-04-03T12:35:32.344Z","updated_at":"2025-04-03T12:35:32.344Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/.github/workflows/ci.yml","dependencies":[{"id":22531900250,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v4","direct":true,"kind":"composite","optional":false},{"id":22531900251,"package_name":"adamrtalbot/detect-nf-test-changes","ecosystem":"actions","requirements":"v0.0.2","direct":true,"kind":"composite","optional":false},{"id":22531900293,"package_name":"actions/checkout","ecosystem":"actions","requirements":"0ad4b8fadaa221de15dcec353f45205ec38ea70b","direct":true,"kind":"composite","optional":false},{"id":22531900294,"package_name":"actions/setup-java","ecosystem":"actions","requirements":"8df1039502a15bceb9433410b1a100fbe190c53b","direct":true,"kind":"composite","optional":false},{"id":22531900295,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":22531900351,"package_name":"eWaterCycle/setup-apptainer","ecosystem":"actions","requirements":"main","direct":true,"kind":"composite","optional":false},{"id":22531900406,"package_name":"nf-core/setup-nf-test","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":22531901241,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v4","direct":true,"kind":"composite","optional":false},{"id":22531901242,"package_name":"jlumbroso/free-disk-space","ecosystem":"actions","requirements":"54081f138730dfa15788a46383842cd2f914a1be","direct":true,"kind":"composite","optional":false},{"id":22531903451,"package_name":"pcolby/tap-summary","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":22531905078,"package_name":"mikepenz/action-junit-report","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/clean-up.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:35:41.018Z","updated_at":"2025-04-03T12:35:41.018Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/.github/workflows/clean-up.yml","dependencies":[{"id":22531905647,"package_name":"actions/stale","ecosystem":"actions","requirements":"28ca1036281a5e5922ead5184a1bbf96e5fc984e","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/cloud_tests_full.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:35:41.073Z","updated_at":"2025-04-03T12:35:41.073Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/.github/workflows/cloud_tests_full.yml","dependencies":[{"id":22531905648,"package_name":"seqeralabs/action-tower-launch","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":22531906965,"package_name":"actions/upload-artifact","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/cloud_tests_small.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:35:42.339Z","updated_at":"2025-04-03T12:35:42.339Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/.github/workflows/cloud_tests_small.yml","dependencies":[{"id":22531907008,"package_name":"seqeralabs/action-tower-launch","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":22531907009,"package_name":"actions/upload-artifact","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/download_pipeline.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:35:42.402Z","updated_at":"2025-04-03T12:35:42.402Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/.github/workflows/download_pipeline.yml","dependencies":[{"id":22531907040,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":22531907041,"package_name":"jlumbroso/free-disk-space","ecosystem":"actions","requirements":"54081f138730dfa15788a46383842cd2f914a1be","direct":true,"kind":"composite","optional":false},{"id":22531907042,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"82c7e631bb3cdc910f68e0081d67478d79c6982d","direct":true,"kind":"composite","optional":false},{"id":22531907043,"package_name":"eWaterCycle/setup-apptainer","ecosystem":"actions","requirements":"4bb22c52d4f63406c49e94c804632975787312b3","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/fix-linting.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:35:42.458Z","updated_at":"2025-04-03T12:35:42.458Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/.github/workflows/fix-linting.yml","dependencies":[{"id":22531907046,"package_name":"actions/checkout","ecosystem":"actions","requirements":"0ad4b8fadaa221de15dcec353f45205ec38ea70b","direct":true,"kind":"composite","optional":false},{"id":22531907047,"package_name":"peter-evans/create-or-update-comment","ecosystem":"actions","requirements":"71345be0265236311c031f5c7866368bd1eff043","direct":true,"kind":"composite","optional":false},{"id":22531908043,"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":"2025-04-03T12:35:44.720Z","updated_at":"2025-04-03T12:35:44.720Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/.github/workflows/linting.yml","dependencies":[{"id":22531908044,"package_name":"actions/checkout","ecosystem":"actions","requirements":"0ad4b8fadaa221de15dcec353f45205ec38ea70b","direct":true,"kind":"composite","optional":false},{"id":22531908045,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"82c7e631bb3cdc910f68e0081d67478d79c6982d","direct":true,"kind":"composite","optional":false},{"id":22531908046,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":22531908047,"package_name":"pietrobolcato/action-read-yaml","ecosystem":"actions","requirements":"1.1.0","direct":true,"kind":"composite","optional":false},{"id":22531908258,"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":"2025-04-03T12:35:45.610Z","updated_at":"2025-04-03T12:35:45.610Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/.github/workflows/linting_comment.yml","dependencies":[{"id":22531908264,"package_name":"dawidd6/action-download-artifact","ecosystem":"actions","requirements":"bf251b5aa9c2f7eeb574a96ee720e24f801b7c11","direct":true,"kind":"composite","optional":false},{"id":22531908416,"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":"2025-04-03T12:35:46.551Z","updated_at":"2025-04-03T12:35:46.551Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/.github/workflows/release-announcements.yml","dependencies":[{"id":22531908417,"package_name":"rzr/fediverse-action","ecosystem":"actions","requirements":"master","direct":true,"kind":"composite","optional":false},{"id":22531910015,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"82c7e631bb3cdc910f68e0081d67478d79c6982d","direct":true,"kind":"composite","optional":false},{"id":22531910016,"package_name":"zentered/bluesky-post-action","ecosystem":"actions","requirements":"80dbe0a7697de18c15ad22f4619919ceb5ccf597","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/template_version_comment.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:35:49.462Z","updated_at":"2025-04-03T12:35:49.462Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/.github/workflows/template_version_comment.yml","dependencies":[{"id":22531910109,"package_name":"actions/checkout","ecosystem":"actions","requirements":"0ad4b8fadaa221de15dcec353f45205ec38ea70b","direct":true,"kind":"composite","optional":false},{"id":22531910110,"package_name":"nichmor/minimal-read-yaml","ecosystem":"actions","requirements":"v0.0.2","direct":true,"kind":"composite","optional":false},{"id":22531910146,"package_name":"mshick/add-pr-comment","ecosystem":"actions","requirements":"b8f338c590a895d50bcbfa6c5859251edc8952fc","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"cpan","filepath":"modules/nf-core/bbmap/bbsplit/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:28.357Z","updated_at":"2025-04-03T12:36:28.357Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/bbmap/bbsplit/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/bedtools/genomecov/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:28.410Z","updated_at":"2025-04-03T12:36:28.410Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/bedtools/genomecov/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/bracken/bracken/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:28.462Z","updated_at":"2025-04-03T12:36:28.462Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/bracken/bracken/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/cat/fastq/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:28.509Z","updated_at":"2025-04-03T12:36:28.509Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/cat/fastq/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/custom/catadditionalfasta/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:28.552Z","updated_at":"2025-04-03T12:36:28.552Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/custom/catadditionalfasta/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/custom/getchromsizes/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:28.595Z","updated_at":"2025-04-03T12:36:28.595Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/custom/getchromsizes/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/custom/tx2gene/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:28.638Z","updated_at":"2025-04-03T12:36:28.638Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/custom/tx2gene/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/dupradar/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:28.693Z","updated_at":"2025-04-03T12:36:28.693Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/dupradar/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/fastp/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:28.736Z","updated_at":"2025-04-03T12:36:28.736Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/fastp/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/fastqc/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:28.778Z","updated_at":"2025-04-03T12:36:28.778Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/fastqc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/fq/lint/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:28.824Z","updated_at":"2025-04-03T12:36:28.824Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/fq/lint/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/fq/subsample/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:28.866Z","updated_at":"2025-04-03T12:36:28.866Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/fq/subsample/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/gffread/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:28.918Z","updated_at":"2025-04-03T12:36:28.918Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/gffread/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/gunzip/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:28.983Z","updated_at":"2025-04-03T12:36:28.983Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/gunzip/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/hisat2/align/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:29.034Z","updated_at":"2025-04-03T12:36:29.034Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/hisat2/align/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/hisat2/build/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:29.075Z","updated_at":"2025-04-03T12:36:29.075Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/hisat2/build/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/hisat2/extractsplicesites/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:29.117Z","updated_at":"2025-04-03T12:36:29.117Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/hisat2/extractsplicesites/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/kallisto/index/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:29.159Z","updated_at":"2025-04-03T12:36:29.159Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/kallisto/index/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/kallisto/quant/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:29.202Z","updated_at":"2025-04-03T12:36:29.202Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/kallisto/quant/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/kraken2/kraken2/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:29.254Z","updated_at":"2025-04-03T12:36:29.254Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/kraken2/kraken2/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/multiqc/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:29.296Z","updated_at":"2025-04-03T12:36:29.296Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/multiqc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/picard/markduplicates/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:29.338Z","updated_at":"2025-04-03T12:36:29.338Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/picard/markduplicates/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/preseq/lcextrap/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:29.381Z","updated_at":"2025-04-03T12:36:29.381Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/preseq/lcextrap/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/qualimap/rnaseq/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:29.423Z","updated_at":"2025-04-03T12:36:29.423Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/qualimap/rnaseq/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/rsem/calculateexpression/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:29.465Z","updated_at":"2025-04-03T12:36:29.465Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/rsem/calculateexpression/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/rsem/preparereference/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:29.509Z","updated_at":"2025-04-03T12:36:29.509Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/rsem/preparereference/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/rseqc/bamstat/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:29.556Z","updated_at":"2025-04-03T12:36:29.556Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/rseqc/bamstat/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/rseqc/inferexperiment/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:29.602Z","updated_at":"2025-04-03T12:36:29.602Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/rseqc/inferexperiment/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/rseqc/innerdistance/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:29.645Z","updated_at":"2025-04-03T12:36:29.645Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/rseqc/innerdistance/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/rseqc/junctionannotation/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:29.692Z","updated_at":"2025-04-03T12:36:29.692Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/rseqc/junctionannotation/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/rseqc/junctionsaturation/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:29.738Z","updated_at":"2025-04-03T12:36:29.738Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/rseqc/junctionsaturation/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/rseqc/readdistribution/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:29.783Z","updated_at":"2025-04-03T12:36:29.783Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/rseqc/readdistribution/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/rseqc/readduplication/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:29.831Z","updated_at":"2025-04-03T12:36:29.831Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/rseqc/readduplication/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/rseqc/tin/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:29.881Z","updated_at":"2025-04-03T12:36:29.881Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/rseqc/tin/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/salmon/index/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:29.928Z","updated_at":"2025-04-03T12:36:29.928Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/salmon/index/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/salmon/quant/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:29.971Z","updated_at":"2025-04-03T12:36:29.971Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/salmon/quant/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/samtools/flagstat/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:30.035Z","updated_at":"2025-04-03T12:36:30.035Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/samtools/flagstat/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/samtools/idxstats/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:30.079Z","updated_at":"2025-04-03T12:36:30.079Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/samtools/idxstats/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/samtools/index/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:30.124Z","updated_at":"2025-04-03T12:36:30.124Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/samtools/index/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/samtools/sort/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:30.170Z","updated_at":"2025-04-03T12:36:30.170Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/samtools/sort/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/samtools/stats/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:30.213Z","updated_at":"2025-04-03T12:36:30.213Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/samtools/stats/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/sortmerna/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:30.256Z","updated_at":"2025-04-03T12:36:30.256Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/sortmerna/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/star/align/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:30.298Z","updated_at":"2025-04-03T12:36:30.298Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/star/align/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/star/genomegenerate/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:30.351Z","updated_at":"2025-04-03T12:36:30.351Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/star/genomegenerate/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/stringtie/stringtie/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:30.408Z","updated_at":"2025-04-03T12:36:30.408Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/stringtie/stringtie/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/subread/featurecounts/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:30.451Z","updated_at":"2025-04-03T12:36:30.451Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/subread/featurecounts/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/summarizedexperiment/summarizedexperiment/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:30.507Z","updated_at":"2025-04-03T12:36:30.507Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/summarizedexperiment/summarizedexperiment/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/trimgalore/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:30.550Z","updated_at":"2025-04-03T12:36:30.550Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/trimgalore/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/tximeta/tximport/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:30.594Z","updated_at":"2025-04-03T12:36:30.594Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/tximeta/tximport/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/ucsc/bedclip/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:30.639Z","updated_at":"2025-04-03T12:36:30.639Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/ucsc/bedclip/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/ucsc/bedgraphtobigwig/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:30.683Z","updated_at":"2025-04-03T12:36:30.683Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/ucsc/bedgraphtobigwig/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/umicollapse/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:30.727Z","updated_at":"2025-04-03T12:36:30.727Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/umicollapse/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/umitools/dedup/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:30.769Z","updated_at":"2025-04-03T12:36:30.769Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/umitools/dedup/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/umitools/extract/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:30.813Z","updated_at":"2025-04-03T12:36:30.813Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/umitools/extract/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/umitools/prepareforrsem/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:30.854Z","updated_at":"2025-04-03T12:36:30.854Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/umitools/prepareforrsem/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/untar/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:30.899Z","updated_at":"2025-04-03T12:36:30.899Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/untar/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:30.943Z","updated_at":"2025-04-03T12:36:30.943Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/bam_dedup_stats_samtools_umitools/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:30.987Z","updated_at":"2025-04-03T12:36:30.987Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/bam_dedup_umi/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:31.032Z","updated_at":"2025-04-03T12:36:31.032Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/subworkflows/nf-core/bam_dedup_umi/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/bam_markduplicates_picard/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:31.073Z","updated_at":"2025-04-03T12:36:31.073Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/subworkflows/nf-core/bam_markduplicates_picard/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/bam_rseqc/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:31.121Z","updated_at":"2025-04-03T12:36:31.121Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/subworkflows/nf-core/bam_rseqc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/bam_sort_stats_samtools/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:31.170Z","updated_at":"2025-04-03T12:36:31.170Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/bam_stats_samtools/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:31.214Z","updated_at":"2025-04-03T12:36:31.214Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/subworkflows/nf-core/bam_stats_samtools/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:31.260Z","updated_at":"2025-04-03T12:36:31.260Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/fastq_align_hisat2/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:31.304Z","updated_at":"2025-04-03T12:36:31.304Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/subworkflows/nf-core/fastq_align_hisat2/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/fastq_fastqc_umitools_fastp/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:31.349Z","updated_at":"2025-04-03T12:36:31.349Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/subworkflows/nf-core/fastq_fastqc_umitools_fastp/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:31.397Z","updated_at":"2025-04-03T12:36:31.397Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:31.460Z","updated_at":"2025-04-03T12:36:31.460Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/fastq_subsample_fq_salmon/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:31.507Z","updated_at":"2025-04-03T12:36:31.507Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/subworkflows/nf-core/fastq_subsample_fq_salmon/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/quantify_pseudo_alignment/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:31.564Z","updated_at":"2025-04-03T12:36:31.564Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/subworkflows/nf-core/quantify_pseudo_alignment/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/utils_nextflow_pipeline/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:31.611Z","updated_at":"2025-04-03T12:36:31.611Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/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":"2025-04-03T12:36:31.658Z","updated_at":"2025-04-03T12:36:31.658Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/utils_nfschema_plugin/meta.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:31.722Z","updated_at":"2025-04-03T12:36:31.722Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/subworkflows/nf-core/utils_nfschema_plugin/meta.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/local/deseq2_qc/environment.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:31.773Z","updated_at":"2025-04-03T12:36:31.773Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/local/deseq2_qc/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/local/gtf2bed/environment.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:31.818Z","updated_at":"2025-04-03T12:36:31.818Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/local/gtf2bed/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/local/gtf_filter/environment.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:31.867Z","updated_at":"2025-04-03T12:36:31.867Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/local/gtf_filter/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/local/multiqc_custom_biotype/environment.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:31.912Z","updated_at":"2025-04-03T12:36:31.912Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/local/multiqc_custom_biotype/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/local/preprocess_transcripts_fasta_gencode/environment.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:31.957Z","updated_at":"2025-04-03T12:36:31.957Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/local/preprocess_transcripts_fasta_gencode/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/local/rsem_merge_counts/environment.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:32.014Z","updated_at":"2025-04-03T12:36:32.014Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/local/rsem_merge_counts/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/local/star_align_igenomes/environment.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:32.065Z","updated_at":"2025-04-03T12:36:32.065Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/local/star_align_igenomes/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/local/star_genomegenerate_igenomes/environment.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:32.112Z","updated_at":"2025-04-03T12:36:32.112Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/local/star_genomegenerate_igenomes/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/bbmap/bbsplit/environment.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:32.164Z","updated_at":"2025-04-03T12:36:32.164Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/bbmap/bbsplit/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/bedtools/genomecov/environment.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:32.204Z","updated_at":"2025-04-03T12:36:32.204Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/bedtools/genomecov/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/bracken/bracken/environment.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:32.254Z","updated_at":"2025-04-03T12:36:32.254Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/bracken/bracken/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/cat/fastq/environment.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:32.305Z","updated_at":"2025-04-03T12:36:32.305Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/cat/fastq/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/custom/catadditionalfasta/environment.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:32.349Z","updated_at":"2025-04-03T12:36:32.349Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/custom/catadditionalfasta/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/custom/getchromsizes/environment.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:32.393Z","updated_at":"2025-04-03T12:36:32.393Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/custom/getchromsizes/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/custom/tx2gene/environment.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:32.435Z","updated_at":"2025-04-03T12:36:32.435Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/custom/tx2gene/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/dupradar/environment.yml","sha":null,"kind":"manifest","created_at":"2025-04-03T12:36:32.478Z","updated_at":"2025-04-03T12:36:32.478Z","repository_link":"https://github.com/vrc-cvd/rnaseq/blob/main/modules/nf-core/dupradar/environment.yml","dependencies":[]}],"score":null,"created_at":"2025-09-04T15:51:31.768Z","updated_at":"2025-10-07T08:22:03.039Z","avatar_url":"https://github.com/vrc-cvd.png","language":"Nextflow","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":["https://doi.org/10.5281/zenodo.1400710","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/55752","html_url":"https://science.ecosyste.ms/projects/55752","bibtex_url":"https://science.ecosyste.ms/projects/55752/export.bibtex","apalike_url":"https://science.ecosyste.ms/projects/55752/export.apalike"}