| { |
| "format": "oscr-script-manifest/1", |
| "repository": "zenodo:16266612", |
| "url": "10.5281/zenodo.16266612", |
| "host": "zenodo.org", |
| "commit": "", |
| "license": "GPL-3.0", |
| "license_confirmed_by": "license file LICENSE", |
| "redistribution": "yes", |
| "files": [ |
| { |
| "path": "10_benchmarking/hmm_benchmarks.sh", |
| "sha256": "903f11f8e5983273d8de39caf8aef505709185a75718fa1db40962f9f9f05ed1", |
| "language": "Shell", |
| "lines": 24, |
| "truncated": false, |
| "block": 19, |
| "row": 15533 |
| }, |
| { |
| "path": "10_benchmarking/run_logregs.py", |
| "sha256": "875a2fb703b9c3b6de3aaa221ad90d3e41d7aee8f7e3b42c98bda5fbb88f8618", |
| "language": "Python", |
| "lines": 175, |
| "truncated": false, |
| "block": 19, |
| "row": 12541 |
| }, |
| { |
| "path": "1_srafetch/fasterqdump.sh", |
| "sha256": "f8137e797561eb90201bf7965205bf17da4b888d10538825107841107d48a80a", |
| "language": "Shell", |
| "lines": 11, |
| "truncated": false, |
| "block": 19, |
| "row": 15346 |
| }, |
| { |
| "path": "1_srafetch/sra_fetch.py", |
| "sha256": "af433a28cf23f19a14012b4b16e22f076c17ddb107e52f8ce292ca1a36eb9ea6", |
| "language": "Python", |
| "lines": 105, |
| "truncated": false, |
| "block": 19, |
| "row": 11076 |
| }, |
| { |
| "path": "2_qc_trimming/trim_zip.sh", |
| "sha256": "ab2b6a3e1a605ac3e2df7747f808742fab8c1655f4dbca110cb17a89c4aa8212", |
| "language": "Shell", |
| "lines": 102, |
| "truncated": false, |
| "block": 19, |
| "row": 15766 |
| }, |
| { |
| "path": "3_contigassembly/contig_assemble2.sh", |
| "sha256": "0fbb54fc272447f6576d119cb851a7e29604e21bfa99e6dcd0119af8c252f4da", |
| "language": "Shell", |
| "lines": 63, |
| "truncated": false, |
| "block": 19, |
| "row": 15733 |
| }, |
| { |
| "path": "3_contigassembly/repair_trimmed.sh", |
| "sha256": "d9c1c6af177877cefa882e58e05d88ebaec8dd4c3bb29b96ab75df18d80295ee", |
| "language": "Shell", |
| "lines": 37, |
| "truncated": false, |
| "block": 19, |
| "row": 15685 |
| }, |
| { |
| "path": "4_taxassignment/1_extract_info.sh", |
| "sha256": "b6ed1ddcc6cd077adcc7332bd08b813fce8508770e8b212b3e46949d5e961a39", |
| "language": "Shell", |
| "lines": 31, |
| "truncated": false, |
| "block": 19, |
| "row": 15492 |
| }, |
| { |
| "path": "4_taxassignment/2_tax_dump.sh", |
| "sha256": "87a6b416ae02a92e905ab48a5aebe825eb622c6ea6d328592ab6c58ff3450af0", |
| "language": "Shell", |
| "lines": 30, |
| "truncated": false, |
| "block": 19, |
| "row": 15455 |
| }, |
| { |
| "path": "4_taxassignment/kraken.sh", |
| "sha256": "d3ebc95519b2129cf4520edd347397729c887c9bc39b4cc71b31952844fe0d1c", |
| "language": "Shell", |
| "lines": 31, |
| "truncated": false, |
| "block": 19, |
| "row": 15540 |
| }, |
| { |
| "path": "4_taxassignment/mmseqs_assign.sh", |
| "sha256": "bfb2a6e0a5e07c37a97fa8f1cdd35e85293124e7b36a66d53ff5d558fb0f29b6", |
| "language": "Shell", |
| "lines": 13, |
| "truncated": false, |
| "block": 19, |
| "row": 15379 |
| }, |
| { |
| "path": "4_taxassignment/search_dict.py", |
| "sha256": "4003bc1b5df9bbd5f29d350c8bac2727729efd8954087793d18049b2e9c12328", |
| "language": "Python", |
| "lines": 27, |
| "truncated": false, |
| "block": 19, |
| "row": 9042 |
| }, |
| { |
| "path": "4_taxassignment/sort_kraken.R", |
| "sha256": "997b3823457f4b86bc9daeb0ae0a79f671eb27c98efb5ef64de610f687bff45c", |
| "language": "R", |
| "lines": 182, |
| "truncated": false, |
| "block": 19, |
| "row": 14970 |
| }, |
| { |
| "path": "4_taxassignment/sort_kraken.sh", |
| "sha256": "98aac670e3a9fb92551fbce0173fc87853e05b8c3335e05314b3db13edb5944e", |
| "language": "Shell", |
| "lines": 23, |
| "truncated": false, |
| "block": 19, |
| "row": 15475 |
| }, |
| { |
| "path": "4_taxassignment/tax_dict.py", |
| "sha256": "6ff4718c8c1bc25f58e72ebde8b2e3583a7d3d8f9bfec8bd7e64d9b1477798bd", |
| "language": "Python", |
| "lines": 57, |
| "truncated": false, |
| "block": 19, |
| "row": 9661 |
| }, |
| { |
| "path": "5_geneprediction/metaeuk_gm.sh", |
| "sha256": "e022c9731bfc86f0d04e3d98116cb9a3e3792603a9dfc82c2139f6a6578a7d32", |
| "language": "Shell", |
| "lines": 18, |
| "truncated": false, |
| "block": 19, |
| "row": 15396 |
| }, |
| { |
| "path": "5_geneprediction/prodigal_gm.sh", |
| "sha256": "486b9c61f6cef4f7cd5a84549bb7569400c389f617e3cca5bde534255286e356", |
| "language": "Shell", |
| "lines": 32, |
| "truncated": false, |
| "block": 19, |
| "row": 15594 |
| }, |
| { |
| "path": "6_pfamannotation/cat_pfams.sh", |
| "sha256": "fe97aee76089b061110385f39cadeff3a48ce1dacee1464bc2b34566b7465eda", |
| "language": "Shell", |
| "lines": 5, |
| "truncated": false, |
| "block": 19, |
| "row": 15288 |
| }, |
| { |
| "path": "6_pfamannotation/clean_hmmout.R", |
| "sha256": "9703fe4e17d893da1f722478768ba9da863690a1ea3caee036a59f4562236c8b", |
| "language": "R", |
| "lines": 55, |
| "truncated": false, |
| "block": 19, |
| "row": 14793 |
| }, |
| { |
| "path": "6_pfamannotation/extract_fasta_duf3494.py", |
| "sha256": "4e34edde4be1230fad21139560ddd94489684bf2dc05487ad0f87412bd2fd0f2", |
| "language": "Python", |
| "lines": 28, |
| "truncated": false, |
| "block": 19, |
| "row": 9281 |
| }, |
| { |
| "path": "6_pfamannotation/get_dufs_from_pfam.R", |
| "sha256": "c4e6418ebdf7c4638ebdb16e2ec50f44d47aac574816ea1878cdec25545869ad", |
| "language": "R", |
| "lines": 25, |
| "truncated": false, |
| "block": 19, |
| "row": 14707 |
| }, |
| { |
| "path": "6_pfamannotation/get_dufs_from_pfam.sh", |
| "sha256": "ddc3ee9a9898a9b7afd445d29c58ea0fa07db457decdf4f6fae412720ec09a64", |
| "language": "Shell", |
| "lines": 8, |
| "truncated": false, |
| "block": 19, |
| "row": 15308 |
| }, |
| { |
| "path": "6_pfamannotation/pfam_annotate.sh", |
| "sha256": "0ced83f33a3cb5cda6207d339c20e70f003b431fb7b4fdf789e32a4eb0bb8b73", |
| "language": "Shell", |
| "lines": 21, |
| "truncated": false, |
| "block": 19, |
| "row": 15447 |
| }, |
| { |
| "path": "7_alignseqs/align_magusehmm.sh", |
| "sha256": "6f7890123d03ff7aa5c21300335ce68e3599db51ff6c6b5f18f28292d1ac24c7", |
| "language": "Shell", |
| "lines": 15, |
| "truncated": false, |
| "block": 19, |
| "row": 15407 |
| }, |
| { |
| "path": "8_prepGA/clean_align.R", |
| "sha256": "74ddd5374e83a25559b869248ffcda76adf3b1481b1890f6c3e4ff8575d4b08a", |
| "language": "R", |
| "lines": 125, |
| "truncated": false, |
| "block": 19, |
| "row": 14912 |
| }, |
| { |
| "path": "8_prepGA/get_metadata.py", |
| "sha256": "4c08a1257af6980cad97733a0ed0b638fe7fe2e88986dfa8df6eecede500a0f0", |
| "language": "Python", |
| "lines": 123, |
| "truncated": false, |
| "block": 19, |
| "row": 11049 |
| }, |
| { |
| "path": "8_prepGA/id_conserved_regions.R", |
| "sha256": "d45551131cb8d916eca2308e4f55cd4b5e9b157fc19b024d632753b70a905be8", |
| "language": "R", |
| "lines": 78, |
| "truncated": false, |
| "block": 19, |
| "row": 14862 |
| }, |
| { |
| "path": "9_NN/run_esm_mod.py", |
| "sha256": "c0e053853c0de030378fd048519dfe4f55385ae6c666a04c8dc5f5a88235774f", |
| "language": "Python", |
| "lines": 67, |
| "truncated": false, |
| "block": 19, |
| "row": 10134 |
| }, |
| { |
| "path": "9_NN/run_nn.py", |
| "sha256": "cb3fe15af398125d043b1bebacdb362f4f80540a6eda0bd0d20f4e64352e424d", |
| "language": "Python", |
| "lines": 230, |
| "truncated": false, |
| "block": 19, |
| "row": 12976 |
| }, |
| { |
| "path": "LICENSE", |
| "sha256": "3972dc9744f6499f0f9b2dbf76696f2ae7ad8af9b23dde66d6af86c9dfb36986", |
| "language": "License", |
| "lines": 674, |
| "truncated": false, |
| "block": 1, |
| "row": 2235 |
| } |
| ] |
| } |
