{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":172603759,"defaultBranch":"master","name":"nf-flu","ownerLogin":"peterk87","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2019-02-25T23:45:39.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/4203424?v=4","public":true,"private":false,"isOrgOwned":false},"refInfo":{"name":"","listCacheKey":"v0:1723226233.0","currentOid":""},"activityList":{"items":[{"before":"ee8844cd7cef13c8d2c503749bcbeaa8301e0b58","after":"0d30dd9b825726aefc9c9028541b4889c9259c1c","ref":"refs/heads/dev","pushedAt":"2024-08-09T17:58:51.000Z","pushType":"push","commitsCount":12,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"},"commit":{"message":"Merge pull request #76 from peterk87/fix/75-cat-illumina-fastq\n\nFix cat_illumina_fastq header match Perl regex","shortMessageHtmlLink":"Merge pull request #76 from peterk87/fix/75-cat-illumina-fastq"}},{"before":"b36b2667c99b0d143fbf34f7b2b6b1c35510271c","after":null,"ref":"refs/heads/fix/75-cat-illumina-fastq","pushedAt":"2024-08-09T17:57:13.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"}},{"before":"968641e84e128796fede67e70ca1c273e2b81bb1","after":"b36b2667c99b0d143fbf34f7b2b6b1c35510271c","ref":"refs/heads/fix/75-cat-illumina-fastq","pushedAt":"2024-08-08T01:37:55.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"},"commit":{"message":"Update VADR from 1.6.3 to 1.6.4 Bioconda version; add model setup step","shortMessageHtmlLink":"Update VADR from 1.6.3 to 1.6.4 Bioconda version; add model setup step"}},{"before":"296f1942885903c8a42f13f3b89214794d2298d9","after":"968641e84e128796fede67e70ca1c273e2b81bb1","ref":"refs/heads/fix/75-cat-illumina-fastq","pushedAt":"2024-08-07T20:54:49.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"},"commit":{"message":"Update CHANGELOG.md and ci.yml","shortMessageHtmlLink":"Update CHANGELOG.md and ci.yml"}},{"before":"4006b1153b7d2e18e7d208a4b4cbeec536a2e25c","after":"296f1942885903c8a42f13f3b89214794d2298d9","ref":"refs/heads/fix/75-cat-illumina-fastq","pushedAt":"2024-08-07T20:10:04.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"},"commit":{"message":"ci: update .github/workflows/ci.yml","shortMessageHtmlLink":"ci: update .github/workflows/ci.yml"}},{"before":"25747b689d43834a005c6f478ea84cb27c7f0055","after":"4006b1153b7d2e18e7d208a4b4cbeec536a2e25c","ref":"refs/heads/fix/75-cat-illumina-fastq","pushedAt":"2024-08-07T20:06:35.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"},"commit":{"message":"ci: update .github/workflows/ci.yml to cache .nextflow/ and test with latest stable version of Nextflow 24.04.4","shortMessageHtmlLink":"ci: update .github/workflows/ci.yml to cache .nextflow/ and test with…"}},{"before":"301e7a3318e1b79ce8ba692a74480760e113a232","after":"25747b689d43834a005c6f478ea84cb27c7f0055","ref":"refs/heads/fix/75-cat-illumina-fastq","pushedAt":"2024-08-07T19:41:08.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"},"commit":{"message":"fix bcftools exclude filter for v1.20","shortMessageHtmlLink":"fix bcftools exclude filter for v1.20"}},{"before":"6a73f9e3f6138a3b9dbddc3f004673dd0ade3f69","after":"301e7a3318e1b79ce8ba692a74480760e113a232","ref":"refs/heads/fix/75-cat-illumina-fastq","pushedAt":"2024-08-07T19:00:48.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"},"commit":{"message":"update process container/conda directives; symlink publishdir mode for test profiles","shortMessageHtmlLink":"update process container/conda directives; symlink publishdir mode fo…"}},{"before":"3f385550b5aa1b19199deb107c2e5f024775244f","after":"6a73f9e3f6138a3b9dbddc3f004673dd0ade3f69","ref":"refs/heads/fix/75-cat-illumina-fastq","pushedAt":"2024-08-07T18:25:06.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"},"commit":{"message":"fix: ignore markdownlint no space in inline code span issue","shortMessageHtmlLink":"fix: ignore markdownlint no space in inline code span issue"}},{"before":"960dba3adf707b7fa7b9244fd4b7ca2dd91398e2","after":"3f385550b5aa1b19199deb107c2e5f024775244f","ref":"refs/heads/fix/75-cat-illumina-fastq","pushedAt":"2024-08-07T18:19:56.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"},"commit":{"message":"forgot to add modules/local/mqc_versions_table.nf","shortMessageHtmlLink":"forgot to add modules/local/mqc_versions_table.nf"}},{"before":"0c681ebb655134f175d3d1e3890a4e5e4131dd43","after":"960dba3adf707b7fa7b9244fd4b7ca2dd91398e2","ref":"refs/heads/fix/75-cat-illumina-fastq","pushedAt":"2024-08-07T18:14:59.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"},"commit":{"message":"Add mqc_versions_table v0.2.0 binary and update CHANGELOG.md","shortMessageHtmlLink":"Add mqc_versions_table v0.2.0 binary and update CHANGELOG.md"}},{"before":null,"after":"0c681ebb655134f175d3d1e3890a4e5e4131dd43","ref":"refs/heads/fix/75-cat-illumina-fastq","pushedAt":"2024-08-01T20:55:34.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"},"commit":{"message":"fix: cat_illumina_fastq header match Perl regex","shortMessageHtmlLink":"fix: cat_illumina_fastq header match Perl regex"}},{"before":"db8f3e7fdbc55dc823b305bd06e57014195ab3d5","after":"ee8844cd7cef13c8d2c503749bcbeaa8301e0b58","ref":"refs/heads/dev","pushedAt":"2024-07-29T16:26:23.000Z","pushType":"push","commitsCount":21,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"},"commit":{"message":"Merge pull request #73 from peterk87/add-vadr\n\nAdd VADR Influenza sequence annotation","shortMessageHtmlLink":"Merge pull request #73 from peterk87/add-vadr"}},{"before":"dca8303af8fdca5ec3b6267d9bd3bfe0587267a5","after":"7e0ab8273931620d14c829584671985fa494267d","ref":"refs/heads/master","pushedAt":"2024-07-29T16:26:04.000Z","pushType":"push","commitsCount":11,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"},"commit":{"message":"Update Zenodo DOI in README.md","shortMessageHtmlLink":"Update Zenodo DOI in README.md"}},{"before":"4ee2b70fa1f6cd2bcd6d3b199d92921c224dd986","after":null,"ref":"refs/heads/add-vadr","pushedAt":"2024-07-26T16:15:46.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"}},{"before":"5bd540576c874b6441c13a4aa1ffc91853c7eeb2","after":"4ee2b70fa1f6cd2bcd6d3b199d92921c224dd986","ref":"refs/heads/add-vadr","pushedAt":"2024-07-25T14:46:13.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"},"commit":{"message":"fix: markdown lint issue","shortMessageHtmlLink":"fix: markdown lint issue"}},{"before":"fb0e4bf79f1ed3e74f5677d518f99b399dd91698","after":"5bd540576c874b6441c13a4aa1ffc91853c7eeb2","ref":"refs/heads/add-vadr","pushedAt":"2024-07-25T14:43:50.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"},"commit":{"message":"docs: Update output.md to include description of VADR annotation issues and failure files","shortMessageHtmlLink":"docs: Update output.md to include description of VADR annotation issu…"}},{"before":"01f61e2746cbd410852a27e8d3a351dd8b7075ec","after":"fb0e4bf79f1ed3e74f5677d518f99b399dd91698","ref":"refs/heads/add-vadr","pushedAt":"2024-07-25T14:32:49.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"},"commit":{"message":"feat: create files summarizing annotation issues and failures","shortMessageHtmlLink":"feat: create files summarizing annotation issues and failures"}},{"before":"ab7054822c8933f74898492f09943d9e8e3cc1a7","after":"01f61e2746cbd410852a27e8d3a351dd8b7075ec","ref":"refs/heads/add-vadr","pushedAt":"2024-07-24T16:04:25.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"},"commit":{"message":"fix: markdown lint","shortMessageHtmlLink":"fix: markdown lint"}},{"before":"3ba01114283041c9942b4d736118b6f829968dcd","after":"ab7054822c8933f74898492f09943d9e8e3cc1a7","ref":"refs/heads/add-vadr","pushedAt":"2024-07-24T16:02:10.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"},"commit":{"message":"Add VADR annotation to Illumina subworkflow\n* feat: add VADR, pre/post table2asn and table2asn analysis to Illumina\n subworkflow.\n* fix: post_table2asn.py: prefer table2asn translation when outputting\n amino acid FASTA\n* docs: update README.md and output.md with docs about VADR, table2asn\n and outputs of annotation analysis","shortMessageHtmlLink":"Add VADR annotation to Illumina subworkflow"}},{"before":"a3c05ca77511f47087cb324b7d9e0159bcf50527","after":"dca8303af8fdca5ec3b6267d9bd3bfe0587267a5","ref":"refs/heads/master","pushedAt":"2024-07-23T17:14:45.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"},"commit":{"message":"Fix Zenodo release issue due to extra comma in .zenodo.json","shortMessageHtmlLink":"Fix Zenodo release issue due to extra comma in .zenodo.json"}},{"before":"8af77cbe6302acaae9ba29c81fe65f9c3125897d","after":"3ba01114283041c9942b4d736118b6f829968dcd","ref":"refs/heads/add-vadr","pushedAt":"2024-07-18T20:55:55.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"},"commit":{"message":"chore: ruff and black fixes & formatting for post_table2asn.py and sub_seqids_for_table2asn.py","shortMessageHtmlLink":"chore: ruff and black fixes & formatting for post_table2asn.py and su…"}},{"before":null,"after":"8af77cbe6302acaae9ba29c81fe65f9c3125897d","ref":"refs/heads/add-vadr","pushedAt":"2024-07-18T20:37:11.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"},"commit":{"message":"Add VADR v1.6.3 Influenza consensus sequence annotation\n* Add table2asn v1.28.943 for converting Feature Table files to Genbank\n* Add bin/sub_seqids_for_table2asn.py to prepare Feature Table output\n for table2asn since table2asn truncates long seq IDs\n* Add bin/post_table2asn.py to sub in original seq IDs in Genbank and output GFF, amino acid FASTA and nucleotide FASTA of CDS, mature peptide and signal peptide gene features","shortMessageHtmlLink":"Add VADR v1.6.3 Influenza consensus sequence annotation"}},{"before":"db8f3e7fdbc55dc823b305bd06e57014195ab3d5","after":"a3c05ca77511f47087cb324b7d9e0159bcf50527","ref":"refs/heads/master","pushedAt":"2024-05-31T18:29:50.000Z","pushType":"push","commitsCount":11,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"},"commit":{"message":"Merge pull request #72 from CFIA-NCFAD/dev\n\nRelease 3.3.10","shortMessageHtmlLink":"Merge pull request #72 from CFIA-NCFAD/dev"}},{"before":"9c7cfe861fade49e2e986c35141153eebf7e728f","after":"8fb32c92fd2e46cecb74850b20b54ca34cd3a45b","ref":"refs/heads/fix/multiqc-report","pushedAt":"2024-05-31T16:19:04.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"},"commit":{"message":"Update multiqc_config.yaml","shortMessageHtmlLink":"Update multiqc_config.yaml"}},{"before":"2f6f71df19eca8e7d0682ed820f2a8304c6fb3bd","after":"9c7cfe861fade49e2e986c35141153eebf7e728f","ref":"refs/heads/fix/multiqc-report","pushedAt":"2024-05-31T15:04:11.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"},"commit":{"message":"Update CHANGELOG.md and nextflow.config","shortMessageHtmlLink":"Update CHANGELOG.md and nextflow.config"}},{"before":null,"after":"2f6f71df19eca8e7d0682ed820f2a8304c6fb3bd","ref":"refs/heads/fix/multiqc-report","pushedAt":"2024-05-31T15:00:00.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"},"commit":{"message":"Merge pull request #70 from CFIA-NCFAD/dev\n\nRelease 3.3.9","shortMessageHtmlLink":"Merge pull request #70 from CFIA-NCFAD/dev"}},{"before":"5434e367c984e115370503f6f185ae4b0af5fbcf","after":null,"ref":"refs/heads/update/clair3","pushedAt":"2024-05-30T20:20:21.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"}},{"before":"60e13d43a343c796d7906312a2d64d8a474f5325","after":"5434e367c984e115370503f6f185ae4b0af5fbcf","ref":"refs/heads/update/clair3","pushedAt":"2024-05-30T20:02:44.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"},"commit":{"message":"Remove yaml linting; local yaml linting passes while CI linting fails for some reason","shortMessageHtmlLink":"Remove yaml linting; local yaml linting passes while CI linting fails…"}},{"before":"0453b25c7a0eea01b57d7232019194c027ea456c","after":"60e13d43a343c796d7906312a2d64d8a474f5325","ref":"refs/heads/update/clair3","pushedAt":"2024-05-30T18:22:36.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"peterk87","name":"Peter Kruczkiewicz","path":"/peterk87","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4203424?s=80&v=4"},"commit":{"message":"Update CI GitHub Actions","shortMessageHtmlLink":"Update CI GitHub Actions"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"Y3Vyc29yOnYyOpK7MjAyNC0wOC0wOVQxNzo1ODo1MS4wMDAwMDBazwAAAASWhLa4","startCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wOC0wOVQxNzo1ODo1MS4wMDAwMDBazwAAAASWhLa4","endCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wNS0zMFQxODoyMjozNi4wMDAwMDBazwAAAARYT3nU"}},"title":"Activity · peterk87/nf-flu"}