{"id":43564,"name":"fastqrepair","description":"A pipeline that can be used to recover corrupted FASTQ.gz files, drop or fix uncompliant reads, remove unpaired reads, and settles reads that became disordered","url":"https://github.com/nf-core/fastqrepair","last_synced_at":"2025-09-05T09:53:00.424Z","repository":{"id":258783356,"uuid":"853439467","full_name":"nf-core/fastqrepair","owner":"nf-core","description":"A pipeline that can be used to recover corrupted FASTQ.gz files, drop or fix uncompliant reads, remove unpaired reads, and settles reads that became disordered","archived":false,"fork":false,"pushed_at":"2025-08-19T09:50:54.000Z","size":3157,"stargazers_count":5,"open_issues_count":3,"forks_count":5,"subscribers_count":189,"default_branch":"master","last_synced_at":"2025-08-19T10:43:40.933Z","etag":null,"topics":["corruption","data-cleaning","data-recovery","fastq","fastq-corrupted","fastq-format","nextflow","nf-core","pipeline","reads-interleaving","recovery-tool","unpaired-reads","well-formed","workflow"],"latest_commit_sha":null,"homepage":"https://nf-co.re/fastqrepair","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/nf-core.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,"zenodo":null}},"created_at":"2024-09-06T16:54:32.000Z","updated_at":"2025-07-14T19:19:21.000Z","dependencies_parsed_at":"2024-12-10T23:24:23.494Z","dependency_job_id":"de5c60d0-420b-4f82-9417-1c4709c95ae7","html_url":"https://github.com/nf-core/fastqrepair","commit_stats":null,"previous_names":["mazzalab/fastqrepair"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/nf-core/fastqrepair","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Ffastqrepair","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Ffastqrepair/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Ffastqrepair/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Ffastqrepair/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nf-core","download_url":"https://codeload.github.com/nf-core/fastqrepair/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Ffastqrepair/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273740853,"owners_count":25159434,"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":"nf-core","name":"nf-core","uuid":"35520196","kind":"organization","description":"A community effort to collect a curated set of analysis pipelines built using Nextflow.","email":"core@nf-co.re","website":"http://nf-co.re","location":null,"twitter":"nf_core","company":null,"icon_url":"https://avatars.githubusercontent.com/u/35520196?v=4","repositories_count":84,"last_synced_at":"2023-03-01T20:50:19.252Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/nf-core","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-12T16:29:01.932Z","updated_at":"2023-03-01T20:50:19.281Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nf-core","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nf-core/repositories"},"packages":[],"commits":{"message":"Repository syncing started."},"issues_stats":{"full_name":"nf-core/fastqrepair","html_url":"https://github.com/nf-core/fastqrepair","last_synced_at":"2025-08-31T12:31:35.900Z","status":null,"issues_count":6,"pull_requests_count":8,"avg_time_to_close_issue":7547544.0,"avg_time_to_close_pull_request":1427557.6666666667,"issues_closed_count":6,"pull_requests_closed_count":6,"pull_request_authors_count":4,"issue_authors_count":3,"avg_comments_per_issue":0.0,"avg_comments_per_pull_request":1.875,"merged_pull_requests_count":5,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":6,"past_year_pull_requests_count":8,"past_year_avg_time_to_close_issue":7547544.0,"past_year_avg_time_to_close_pull_request":1427557.6666666667,"past_year_issues_closed_count":6,"past_year_pull_requests_closed_count":6,"past_year_pull_request_authors_count":4,"past_year_issue_authors_count":3,"past_year_avg_comments_per_issue":0.0,"past_year_avg_comments_per_pull_request":1.875,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":5,"created_at":"2025-08-29T14:20:44.216Z","updated_at":"2025-09-03T05:16:04.187Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Ffastqrepair","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Ffastqrepair/issues","issue_labels_count":{"enhancement":5,"bug":2,"documentation":1},"pull_request_labels_count":{},"issue_author_associations_count":{"COLLABORATOR":6,"NONE":2},"pull_request_author_associations_count":{"MEMBER":6,"COLLABORATOR":5,"NONE":2},"issue_authors":{"mazzalab":6,"jen-reeve":1,"irongraft":1},"pull_request_authors":{"mazzalab":5,"nf-core-bot":4,"mirpedrol":2,"ShimiraOleg":1,"lvclark":1},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-05T00:00:10.444Z","repositories_count":10097364,"issues_count":31428117,"pull_requests_count":97242359,"authors_count":10701128,"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":5,"bug":2,"documentation":1},"past_year_pull_request_labels_count":{},"past_year_issue_author_associations_count":{"COLLABORATOR":6,"NONE":2},"past_year_pull_request_author_associations_count":{"MEMBER":6,"COLLABORATOR":5,"NONE":2},"past_year_issue_authors":{"mazzalab":6,"irongraft":1,"jen-reeve":1},"past_year_pull_request_authors":{"mazzalab":5,"nf-core-bot":4,"mirpedrol":2,"lvclark":1,"ShimiraOleg":1},"maintainers":[{"login":"mazzalab","count":11,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/mazzalab"},{"login":"nf-core-bot","count":4,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/nf-core-bot"},{"login":"mirpedrol","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/mirpedrol"}],"active_maintainers":[{"login":"mazzalab","count":11,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/mazzalab"},{"login":"nf-core-bot","count":4,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/nf-core-bot"},{"login":"mirpedrol","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/mirpedrol"}]},"events":{"total":{"CreateEvent":10,"ReleaseEvent":1,"IssuesEvent":15,"WatchEvent":4,"DeleteEvent":6,"MemberEvent":1,"IssueCommentEvent":22,"PushEvent":78,"PullRequestReviewCommentEvent":155,"PullRequestReviewEvent":99,"PullRequestEvent":22,"ForkEvent":3},"last_year":{"CreateEvent":10,"ReleaseEvent":1,"IssuesEvent":15,"WatchEvent":4,"DeleteEvent":6,"MemberEvent":1,"IssueCommentEvent":22,"PushEvent":78,"PullRequestReviewCommentEvent":155,"PullRequestReviewEvent":99,"PullRequestEvent":22,"ForkEvent":3}},"keywords":["corruption","data-cleaning","data-recovery","fastq","fastq-corrupted","fastq-format","nextflow","nf-core","pipeline","reads-interleaving","recovery-tool","unpaired-reads","well-formed","workflow"],"dependencies":[{"ecosystem":"actions","filepath":".github/workflows/awsfulltest.yml","sha":null,"kind":"manifest","created_at":"2024-10-20T19:26:59.110Z","updated_at":"2024-10-20T19:26:59.110Z","repository_link":"https://github.com/nf-core/fastqrepair/blob/master/.github/workflows/awsfulltest.yml","dependencies":[{"id":20306447851,"package_name":"seqeralabs/action-tower-launch","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":20306447852,"package_name":"actions/upload-artifact","ecosystem":"actions","requirements":"v4","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/awstest.yml","sha":null,"kind":"manifest","created_at":"2024-10-20T19:26:59.474Z","updated_at":"2024-10-20T19:26:59.474Z","repository_link":"https://github.com/nf-core/fastqrepair/blob/master/.github/workflows/awstest.yml","dependencies":[{"id":20306447853,"package_name":"seqeralabs/action-tower-launch","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":20306447854,"package_name":"actions/upload-artifact","ecosystem":"actions","requirements":"v4","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/branch.yml","sha":null,"kind":"manifest","created_at":"2024-10-20T19:26:59.902Z","updated_at":"2024-10-20T19:26:59.902Z","repository_link":"https://github.com/nf-core/fastqrepair/blob/master/.github/workflows/branch.yml","dependencies":[{"id":20306447872,"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":"2024-10-20T19:27:00.458Z","updated_at":"2024-10-20T19:27:00.458Z","repository_link":"https://github.com/nf-core/fastqrepair/blob/master/.github/workflows/ci.yml","dependencies":[{"id":20306447925,"package_name":"actions/checkout","ecosystem":"actions","requirements":"0ad4b8fadaa221de15dcec353f45205ec38ea70b","direct":true,"kind":"composite","optional":false},{"id":20306447926,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":20306447927,"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":"2024-10-20T19:27:02.049Z","updated_at":"2024-10-20T19:27:02.049Z","repository_link":"https://github.com/nf-core/fastqrepair/blob/master/.github/workflows/clean-up.yml","dependencies":[{"id":20306448025,"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":"2024-10-20T19:27:02.533Z","updated_at":"2024-10-20T19:27:02.533Z","repository_link":"https://github.com/nf-core/fastqrepair/blob/master/.github/workflows/download_pipeline.yml","dependencies":[{"id":20306450144,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":20306450145,"package_name":"jlumbroso/free-disk-space","ecosystem":"actions","requirements":"54081f138730dfa15788a46383842cd2f914a1be","direct":true,"kind":"composite","optional":false},{"id":20306450146,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"82c7e631bb3cdc910f68e0081d67478d79c6982d","direct":true,"kind":"composite","optional":false},{"id":20306450147,"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":"2024-10-20T19:27:03.218Z","updated_at":"2024-10-20T19:27:03.218Z","repository_link":"https://github.com/nf-core/fastqrepair/blob/master/.github/workflows/fix-linting.yml","dependencies":[{"id":20306450302,"package_name":"actions/checkout","ecosystem":"actions","requirements":"0ad4b8fadaa221de15dcec353f45205ec38ea70b","direct":true,"kind":"composite","optional":false},{"id":20306450303,"package_name":"peter-evans/create-or-update-comment","ecosystem":"actions","requirements":"71345be0265236311c031f5c7866368bd1eff043","direct":true,"kind":"composite","optional":false},{"id":20306450304,"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":"2024-10-20T19:27:03.529Z","updated_at":"2024-10-20T19:27:03.529Z","repository_link":"https://github.com/nf-core/fastqrepair/blob/master/.github/workflows/linting.yml","dependencies":[{"id":20306450392,"package_name":"actions/checkout","ecosystem":"actions","requirements":"0ad4b8fadaa221de15dcec353f45205ec38ea70b","direct":true,"kind":"composite","optional":false},{"id":20306450393,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"82c7e631bb3cdc910f68e0081d67478d79c6982d","direct":true,"kind":"composite","optional":false},{"id":20306450394,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":20306450395,"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":"2024-10-20T19:27:03.875Z","updated_at":"2024-10-20T19:27:03.875Z","repository_link":"https://github.com/nf-core/fastqrepair/blob/master/.github/workflows/linting_comment.yml","dependencies":[{"id":20306450518,"package_name":"dawidd6/action-download-artifact","ecosystem":"actions","requirements":"09f2f74827fd3a8607589e5ad7f9398816f540fe","direct":true,"kind":"composite","optional":false},{"id":20306450519,"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":"2024-10-20T19:27:04.480Z","updated_at":"2024-10-20T19:27:04.480Z","repository_link":"https://github.com/nf-core/fastqrepair/blob/master/.github/workflows/release-announcements.yml","dependencies":[{"id":20306453082,"package_name":"rzr/fediverse-action","ecosystem":"actions","requirements":"master","direct":true,"kind":"composite","optional":false},{"id":20306453087,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"82c7e631bb3cdc910f68e0081d67478d79c6982d","direct":true,"kind":"composite","optional":false},{"id":20306453088,"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":"2024-10-20T19:27:06.384Z","updated_at":"2024-10-20T19:27:06.384Z","repository_link":"https://github.com/nf-core/fastqrepair/blob/master/modules/nf-core/fastqc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/utils_nextflow_pipeline/meta.yml","sha":null,"kind":"manifest","created_at":"2024-10-20T19:27:06.835Z","updated_at":"2024-10-20T19:27:06.835Z","repository_link":"https://github.com/nf-core/fastqrepair/blob/master/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":"2024-10-20T19:27:07.150Z","updated_at":"2024-10-20T19:27:07.150Z","repository_link":"https://github.com/nf-core/fastqrepair/blob/master/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml","dependencies":[]},{"ecosystem":"actions","filepath":".github/workflows/template_version_comment.yml","sha":null,"kind":"manifest","created_at":"2024-12-10T23:24:12.546Z","updated_at":"2024-12-10T23:24:12.546Z","repository_link":"https://github.com/nf-core/fastqrepair/blob/master/.github/workflows/template_version_comment.yml","dependencies":[{"id":21116220546,"package_name":"actions/checkout","ecosystem":"actions","requirements":"0ad4b8fadaa221de15dcec353f45205ec38ea70b","direct":true,"kind":"composite","optional":false},{"id":21116220547,"package_name":"nichmor/minimal-read-yaml","ecosystem":"actions","requirements":"v0.0.2","direct":true,"kind":"composite","optional":false},{"id":21116220549,"package_name":"mshick/add-pr-comment","ecosystem":"actions","requirements":"b8f338c590a895d50bcbfa6c5859251edc8952fc","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"cpan","filepath":"modules/nf-core/gzrt/meta.yml","sha":null,"kind":"manifest","created_at":"2024-12-10T23:24:18.304Z","updated_at":"2024-12-10T23:24:18.304Z","repository_link":"https://github.com/nf-core/fastqrepair/blob/master/modules/nf-core/gzrt/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/trimmomatic/meta.yml","sha":null,"kind":"manifest","created_at":"2024-12-10T23:24:18.596Z","updated_at":"2024-12-10T23:24:18.596Z","repository_link":"https://github.com/nf-core/fastqrepair/blob/master/modules/nf-core/trimmomatic/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/utils_nfschema_plugin/meta.yml","sha":null,"kind":"manifest","created_at":"2024-12-10T23:24:18.888Z","updated_at":"2024-12-10T23:24:18.888Z","repository_link":"https://github.com/nf-core/fastqrepair/blob/master/subworkflows/nf-core/utils_nfschema_plugin/meta.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/local/wipertools/environment.yml","sha":null,"kind":"manifest","created_at":"2024-12-10T23:24:18.958Z","updated_at":"2024-12-10T23:24:18.958Z","repository_link":"https://github.com/nf-core/fastqrepair/blob/master/modules/local/wipertools/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/fastqc/environment.yml","sha":null,"kind":"manifest","created_at":"2024-12-10T23:24:19.025Z","updated_at":"2024-12-10T23:24:19.025Z","repository_link":"https://github.com/nf-core/fastqrepair/blob/master/modules/nf-core/fastqc/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/gzrt/environment.yml","sha":null,"kind":"manifest","created_at":"2024-12-10T23:24:19.117Z","updated_at":"2024-12-10T23:24:19.117Z","repository_link":"https://github.com/nf-core/fastqrepair/blob/master/modules/nf-core/gzrt/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/trimmomatic/environment.yml","sha":null,"kind":"manifest","created_at":"2024-12-10T23:24:19.196Z","updated_at":"2024-12-10T23:24:19.196Z","repository_link":"https://github.com/nf-core/fastqrepair/blob/master/modules/nf-core/trimmomatic/environment.yml","dependencies":[]}],"score":null,"created_at":"2025-09-04T15:51:18.675Z","updated_at":"2025-10-07T08:17:38.505Z","avatar_url":"https://github.com/nf-core.png","language":"Nextflow","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":["https://doi.org/10.5281/zenodo.14796348","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/43564","html_url":"https://science.ecosyste.ms/projects/43564","bibtex_url":"https://science.ecosyste.ms/projects/43564/export.bibtex","apalike_url":"https://science.ecosyste.ms/projects/43564/export.apalike"}