| { |
| "format": "oscr-script-manifest/1", |
| "repository": "gitlab.mpcdf.mpg.de/mpibr/laur/cuttlefishomics/soffgenome", |
| "url": "https://archive.softwareheritage.org/swh:1:dir:55d0af83f088bd734c66ca681fe48855e35eae83;origin=https://gitlab.mpcdf.mpg.de/mpibr/laur/cuttlefishomics/soffgenome;visit=swh:1:snp:ef236282e660b36085bf722edd6916303f50ce33;anchor=swh:1:rev:efe218e0bf3c8318c5c729cbab94478dbf5b5502", |
| "host": "gitlab.mpcdf.mpg.de", |
| "commit": "efe218e0bf3c8318c5c729cbab94478dbf5b5502", |
| "license": "MIT", |
| "license_confirmed_by": "license file LICENSE", |
| "redistribution": "yes", |
| "files": [ |
| { |
| "path": "LICENSE", |
| "sha256": "024259309641f522f50544a41dce0025bf0935d5706549023b32c7fab2722ae8", |
| "language": "License", |
| "lines": 21, |
| "truncated": false, |
| "block": 6, |
| "row": 1580 |
| }, |
| { |
| "path": "README.md", |
| "sha256": "67d5e76b37e38c0baa8d4882a4720653016f234535f1fdb621d4da763219ac4a", |
| "language": "Text", |
| "lines": 68, |
| "truncated": false, |
| "block": 8, |
| "row": 10301 |
| }, |
| { |
| "path": "alignment/starJS_to_bed6.pl", |
| "sha256": "4ee547a5ff93a03b16eaa596eda78719a0911174dce76bf1e694826eacf3a938", |
| "language": "Perl", |
| "lines": 42, |
| "truncated": false, |
| "block": 6, |
| "row": 20028 |
| }, |
| { |
| "path": "alignment/task_countreads.sh", |
| "sha256": "3550a2b3637d8d117eff416552e3f9d5bb553d27a0da3fd899b9988f30ba6d6d", |
| "language": "Shell", |
| "lines": 46, |
| "truncated": false, |
| "block": 8, |
| "row": 8045 |
| }, |
| { |
| "path": "alignment/task_graphbed.sh", |
| "sha256": "35a6040d6d8adee7879a9f0a88055223f97e4a33660a5c779c7b1916691f0f6a", |
| "language": "Shell", |
| "lines": 45, |
| "truncated": false, |
| "block": 8, |
| "row": 7754 |
| }, |
| { |
| "path": "alignment/task_minimap.sh", |
| "sha256": "13a1c4ea2a58dcc12552d9b24d4af1afe2004611e887b33eb93a460efa42d09f", |
| "language": "Shell", |
| "lines": 81, |
| "truncated": false, |
| "block": 8, |
| "row": 8614 |
| }, |
| { |
| "path": "alignment/task_minimap_sanger.sh", |
| "sha256": "f168269d893d81c3efae9f136c49e39349b6bb1934fd6d12b57d34dd676f167e", |
| "language": "Shell", |
| "lines": 37, |
| "truncated": false, |
| "block": 8, |
| "row": 7737 |
| }, |
| { |
| "path": "alignment/task_minimap_species.sh", |
| "sha256": "430a6f4fa500bd74741b65827e4b5f5ff97e95254a2633a69089b2d70f1ebfea", |
| "language": "Shell", |
| "lines": 44, |
| "truncated": false, |
| "block": 8, |
| "row": 7899 |
| }, |
| { |
| "path": "alignment/task_mkref_species.sh", |
| "sha256": "591ff4c0d16e76a3adf2b35119137287165a65c6697074e2eb9febb593d2734a", |
| "language": "Shell", |
| "lines": 33, |
| "truncated": false, |
| "block": 8, |
| "row": 7518 |
| }, |
| { |
| "path": "alignment/task_mkrefs.sh", |
| "sha256": "3b874592547108cd1ca18a791133b9160a6d70b0c1f836cd0af499c71d1e4741", |
| "language": "Shell", |
| "lines": 67, |
| "truncated": false, |
| "block": 8, |
| "row": 8171 |
| }, |
| { |
| "path": "alignment/task_star_count_braker.sh", |
| "sha256": "da70a596a069b3b2008e9056fed2a6c3b191d5d45f507cd01f1b933c7c92e3b5", |
| "language": "Shell", |
| "lines": 94, |
| "truncated": false, |
| "block": 8, |
| "row": 8718 |
| }, |
| { |
| "path": "alignment/task_star_dna.sh", |
| "sha256": "f17a399e69afe7cf4de24dbc8847b5337a069f3cef0a02b050af548a0c44a2a6", |
| "language": "Shell", |
| "lines": 61, |
| "truncated": false, |
| "block": 8, |
| "row": 8373 |
| }, |
| { |
| "path": "alignment/task_star_dna_species.sh", |
| "sha256": "3e0f0958965977156d74a74239bde92c03426cf3f82beccde6eafc271821b3c7", |
| "language": "Shell", |
| "lines": 54, |
| "truncated": false, |
| "block": 8, |
| "row": 8274 |
| }, |
| { |
| "path": "alignment/task_star_rna.sh", |
| "sha256": "c8b5405d070640c19c5e7200386ee8b1f93e21d5b4e890982c2dc0450fb0cf5f", |
| "language": "Shell", |
| "lines": 89, |
| "truncated": false, |
| "block": 8, |
| "row": 8692 |
| }, |
| { |
| "path": "alignment/task_star_scell.sh", |
| "sha256": "b709cc27c08c0f1412fddfb07f504eed95ebafcd33f228597600e40083111951", |
| "language": "Shell", |
| "lines": 93, |
| "truncated": false, |
| "block": 8, |
| "row": 8702 |
| }, |
| { |
| "path": "analysis/gene_families/cafe5/cafe5_top_families_heatmap.R", |
| "sha256": "db3362c2fbfbc471aff586a60d49da72956182448cd744172cf2fe7d809ef841", |
| "language": "R", |
| "lines": 461, |
| "truncated": false, |
| "block": 8, |
| "row": 4670 |
| }, |
| { |
| "path": "analysis/gene_families/cafe5/gene_repeat_overlap.py", |
| "sha256": "0e3a68ec18b1357c4ee4b05532409527352669f3706d97495a0ebb1fc3d6d951", |
| "language": "Python", |
| "lines": 533, |
| "truncated": false, |
| "block": 7, |
| "row": 9071 |
| }, |
| { |
| "path": "analysis/gene_families/cafe5/large_families_heatmap.R", |
| "sha256": "1168fb32cc204bd23a94812a5b70a4d34b68f4e1155d55ee39ce0643ba984bdc", |
| "language": "R", |
| "lines": 507, |
| "truncated": false, |
| "block": 8, |
| "row": 4715 |
| }, |
| { |
| "path": "analysis/gene_families/cafe5/run_cafe5.sh", |
| "sha256": "344c8efd9dd300b363ea54d7baf7c178c69d8bb6cd2d2d924daec23e26247d20", |
| "language": "Shell", |
| "lines": 100, |
| "truncated": false, |
| "block": 8, |
| "row": 9022 |
| }, |
| { |
| "path": "analysis/gene_families/gene_family_expression_analysis.Rmd", |
| "sha256": "30e79baaa3e13f9ad8363f662299f436f6b8952475c074c2129ba58880d5be7b", |
| "language": "R", |
| "lines": 1354, |
| "truncated": false, |
| "block": 8, |
| "row": 5120 |
| }, |
| { |
| "path": "analysis/gene_families/orthofinder/orthofinder_to_cafe.R", |
| "sha256": "cc9c92ad1ed54acd8b6c28beab24d662f18235f8f0585ef3303338f4dc31f462", |
| "language": "R", |
| "lines": 70, |
| "truncated": false, |
| "block": 8, |
| "row": 2365 |
| }, |
| { |
| "path": "analysis/genome_alignments/breakpoints/breakpoint_analysis.ipynb", |
| "sha256": "1341300ae18cdd19ed3591d08f877adee8c8ba24b686e10d1e8c5e1a1cd07d61", |
| "language": "Jupyter", |
| "lines": 1598, |
| "truncated": false, |
| "block": 6, |
| "row": 1247 |
| }, |
| { |
| "path": "analysis/genome_alignments/breakpoints/count_hic_trans_background.sh", |
| "sha256": "0269d85480b734559143fda2bc34511f19b92ddb9a95dbc33e3c94190e4d805a", |
| "language": "Shell", |
| "lines": 198, |
| "truncated": false, |
| "block": 8, |
| "row": 9164 |
| }, |
| { |
| "path": "analysis/genome_alignments/breakpoints/extract_hic_trans_pairs.sh", |
| "sha256": "fdd1fed624c3cfd31dad651ae682fbfd05737af92ea7ba12d88a53fdaecb9937", |
| "language": "Shell", |
| "lines": 166, |
| "truncated": false, |
| "block": 8, |
| "row": 9157 |
| }, |
| { |
| "path": "analysis/genome_alignments/breakpoints/extract_spanning_reads.py", |
| "sha256": "4133de1e345b48624f2d79b606b4afa5901f505de3a99e96b58f9a0d2c1ac952", |
| "language": "Python", |
| "lines": 322, |
| "truncated": false, |
| "block": 7, |
| "row": 4620 |
| }, |
| { |
| "path": "analysis/genome_alignments/breakpoints/generate_scaffold_beds.sh", |
| "sha256": "4607dfc190d672d6285782a4801b469bf8f8a174b0a2b9e8120c1fa7f04ef8ee", |
| "language": "Shell", |
| "lines": 47, |
| "truncated": false, |
| "block": 8, |
| "row": 8232 |
| }, |
| { |
| "path": "analysis/genome_alignments/breakpoints/run_map_hic_scaffolds.sh", |
| "sha256": "43291be032ad694bfb456ec509112af6bfba0b57de2da943db4a6c5644e81cba", |
| "language": "Shell", |
| "lines": 129, |
| "truncated": false, |
| "block": 8, |
| "row": 9080 |
| }, |
| { |
| "path": "analysis/genome_alignments/breakpoints/run_map_hifi_scaffolds.sh", |
| "sha256": "a15053f67166667e1d6079237f1692bbbcd556a5c8a970c4471975232e12d64c", |
| "language": "Shell", |
| "lines": 107, |
| "truncated": false, |
| "block": 8, |
| "row": 8952 |
| }, |
| { |
| "path": "analysis/genome_alignments/breakpoints/run_repeatmasker_junctions.sh", |
| "sha256": "534bee3c15a65aff90ffd18cac3ff4ad92ac2fd42c93e2e8387cd63feb134ac5", |
| "language": "Shell", |
| "lines": 198, |
| "truncated": false, |
| "block": 8, |
| "row": 9186 |
| }, |
| { |
| "path": "analysis/genome_alignments/wga/assembly_comparison.R", |
| "sha256": "224f2134950b2f4631c29a3db268d60d144e2ba9516275ce65f2dd6a2052933d", |
| "language": "R", |
| "lines": 352, |
| "truncated": false, |
| "block": 8, |
| "row": 4488 |
| }, |
| { |
| "path": "analysis/genome_alignments/wga/run_winnowmap.sh", |
| "sha256": "5bcb45cb8864547684290b158e762211acc9de24cc43330c029a74dc68858784", |
| "language": "Shell", |
| "lines": 65, |
| "truncated": false, |
| "block": 8, |
| "row": 8556 |
| }, |
| { |
| "path": "analysis/rna_seq/bulkRNA_Deseq2_braker.Rmd", |
| "sha256": "0f8f33e673547af672d257c96d286624367fc65a77d389554e64f1f1e5d264e9", |
| "language": "R", |
| "lines": 428, |
| "truncated": false, |
| "block": 8, |
| "row": 4415 |
| }, |
| { |
| "path": "analysis/rna_seq/emapper_interproscan_LUT.R", |
| "sha256": "016e5d9b347a48d88926aaba582756c1eb27da4606da37164f5da0971cd2ca7a", |
| "language": "R", |
| "lines": 33, |
| "truncated": false, |
| "block": 8, |
| "row": 1971 |
| }, |
| { |
| "path": "analysis/rna_seq/parse_interproscan_go.R", |
| "sha256": "b2965ff26ee7bd20f477ee10bf2c3913aa4da76eaa630b36ba30beb24629f68c", |
| "language": "R", |
| "lines": 409, |
| "truncated": false, |
| "block": 8, |
| "row": 4617 |
| }, |
| { |
| "path": "annotation/stringtieGTF2BED12.pl", |
| "sha256": "37d90b0f51c7c9034cd4481781f200d06e69dcc3d67a55ed032f45e83ee2be9f", |
| "language": "Perl", |
| "lines": 133, |
| "truncated": false, |
| "block": 6, |
| "row": 20059 |
| }, |
| { |
| "path": "annotation/task_braker_softmasked.sh", |
| "sha256": "7f200284aa0e2545358dd0732c4d315fd220d3daac0f5024963d263da1ce4027", |
| "language": "Shell", |
| "lines": 67, |
| "truncated": false, |
| "block": 8, |
| "row": 8520 |
| }, |
| { |
| "path": "annotation/task_repeatmasker.sh", |
| "sha256": "eaf3012d8086b8406b1117554411a0000b2f5d82eb79b84e564e79eeeddc488d", |
| "language": "Shell", |
| "lines": 38, |
| "truncated": false, |
| "block": 8, |
| "row": 7572 |
| }, |
| { |
| "path": "annotation/task_repeatmasker_custom.sh", |
| "sha256": "c31d91dc5cf34c775fc048eeef44e52c9ed5c53b564a275663cbabdb844fcd36", |
| "language": "Shell", |
| "lines": 79, |
| "truncated": false, |
| "block": 8, |
| "row": 8580 |
| }, |
| { |
| "path": "annotation/task_repeatmasker_custom_softmask.sh", |
| "sha256": "ae64b15f7e627356c45e503fc9b937b40ac48a7a321a9f3643dd160423615352", |
| "language": "Shell", |
| "lines": 77, |
| "truncated": false, |
| "block": 8, |
| "row": 8549 |
| }, |
| { |
| "path": "annotation/task_repeatmodeler.sh", |
| "sha256": "02df4f9a61d694155f4500a47e18565dff94585093b46810dc6207e34d958423", |
| "language": "Shell", |
| "lines": 82, |
| "truncated": false, |
| "block": 8, |
| "row": 8582 |
| }, |
| { |
| "path": "annotation/task_stringtie_long.sh", |
| "sha256": "bdcd6b43d6d0f23636e376dee3371702b9c83468ff8b0e3cd24d715d1f7495e4", |
| "language": "Shell", |
| "lines": 38, |
| "truncated": false, |
| "block": 8, |
| "row": 7726 |
| }, |
| { |
| "path": "annotation/task_stringtie_merged.sh", |
| "sha256": "d2c33f971c67d5f0329a906166d3ea06d9454e7928ddbff9602106f63d714662", |
| "language": "Shell", |
| "lines": 46, |
| "truncated": false, |
| "block": 8, |
| "row": 7827 |
| }, |
| { |
| "path": "annotation/task_stringtie_mixed.sh", |
| "sha256": "cac2054aae5687ffcb4dc1b6c06ccb2d66e7d1c7bf9f0e163f6e3ac3d16d7b51", |
| "language": "Shell", |
| "lines": 55, |
| "truncated": false, |
| "block": 8, |
| "row": 8193 |
| }, |
| { |
| "path": "annotation/task_trinity.sh", |
| "sha256": "110456859bf3bf6758da42e862e675165c9dc45467c029dee491462613853c34", |
| "language": "Shell", |
| "lines": 53, |
| "truncated": false, |
| "block": 8, |
| "row": 8280 |
| }, |
| { |
| "path": "archive/old_pipeline/filterFastqWithWhitelist.pl", |
| "sha256": "1c60c4a88aaba8f062af0390a297b389a5ce21beeebbd0eb4c48f32a6a1d23a7", |
| "language": "Perl", |
| "lines": 56, |
| "truncated": false, |
| "block": 6, |
| "row": 20031 |
| }, |
| { |
| "path": "archive/old_pipeline/getVecScreenCategories.pl", |
| "sha256": "d3582ac9a939497aa3a8e3c51cd78170c229bc90ef0a5bbc19d74ee912cf0a9e", |
| "language": "Perl", |
| "lines": 103, |
| "truncated": false, |
| "block": 6, |
| "row": 20051 |
| }, |
| { |
| "path": "archive/old_pipeline/pipeline.sh", |
| "sha256": "5334ae62fb15e54be557713771b1dc7d374ca9b13191001e9922d822cf094dce", |
| "language": "Shell", |
| "lines": 427, |
| "truncated": false, |
| "block": 8, |
| "row": 9364 |
| }, |
| { |
| "path": "archive/old_pipeline/run_busco.sh", |
| "sha256": "7aeb37e3b36e05ab094cd762d0e587410e9d2c3418ba352f9321cc7af32a2a2d", |
| "language": "Shell", |
| "lines": 39, |
| "truncated": false, |
| "block": 8, |
| "row": 7508 |
| }, |
| { |
| "path": "archive/old_pipeline/run_canu.sh", |
| "sha256": "635d6deeecc1a256feb1aad5b3bd234087815caf19aac9950b47ccc4437f0a16", |
| "language": "Shell", |
| "lines": 50, |
| "truncated": false, |
| "block": 8, |
| "row": 7860 |
| }, |
| { |
| "path": "archive/old_pipeline/run_maphic.sh", |
| "sha256": "a36b3f4f29d2b64765d719d8a160be34cb195aca5062a82e65d2276eabed4be3", |
| "language": "Shell", |
| "lines": 74, |
| "truncated": false, |
| "block": 8, |
| "row": 8275 |
| }, |
| { |
| "path": "archive/old_pipeline/run_purge.sh", |
| "sha256": "60948d74ce9619a1897ec0cb052335ef7ce77d27870dd0ea31ded8ed6ba29698", |
| "language": "Shell", |
| "lines": 70, |
| "truncated": false, |
| "block": 8, |
| "row": 8436 |
| }, |
| { |
| "path": "archive/old_pipeline/run_scaffolding.sh", |
| "sha256": "97ebaf5950fd4cedb6f36fb3885a34da4cc2bc8afe5d3d5901b8d6749b7b4793", |
| "language": "Shell", |
| "lines": 78, |
| "truncated": false, |
| "block": 8, |
| "row": 8694 |
| }, |
| { |
| "path": "archive/old_pipeline/run_sortbam.sh", |
| "sha256": "a0cb8289d8a69fd6675bd2b48c8795ab845a8cdc53094affa57d50a04d9dcfec", |
| "language": "Shell", |
| "lines": 42, |
| "truncated": false, |
| "block": 8, |
| "row": 7432 |
| }, |
| { |
| "path": "archive/utils/assemblyStats.pl", |
| "sha256": "2b5d1908e8bf25a9cf62a0b679456ef4f430f0936e4c4dd5366ea6806ba7f88b", |
| "language": "Perl", |
| "lines": 124, |
| "truncated": false, |
| "block": 6, |
| "row": 20050 |
| }, |
| { |
| "path": "assembly/config/biotools.sh", |
| "sha256": "8cf87fd30a7be5b9732348312def00eaf091d5a533b31da8b71db16fd1a3a2ad", |
| "language": "Shell", |
| "lines": 15, |
| "truncated": false, |
| "block": 8, |
| "row": 7331 |
| }, |
| { |
| "path": "assembly/config/data.sh", |
| "sha256": "bc49cef81bfa474af04d589d77deb6941a193bc2ae593a51a56fb5d5f9c85cbb", |
| "language": "Shell", |
| "lines": 11, |
| "truncated": false, |
| "block": 8, |
| "row": 7241 |
| }, |
| { |
| "path": "assembly/run_busco.sh", |
| "sha256": "181cd3f68ce8d647a4f0ad09153696c93ff574a85dfce1c7a58bb6a642ee0a5f", |
| "language": "Shell", |
| "lines": 75, |
| "truncated": false, |
| "block": 8, |
| "row": 8752 |
| }, |
| { |
| "path": "assembly/run_clean_hic.sh", |
| "sha256": "38115f314cfd7b607a9841b90843a61136b126a329d84e18a381611135e619c7", |
| "language": "Shell", |
| "lines": 87, |
| "truncated": false, |
| "block": 8, |
| "row": 8794 |
| }, |
| { |
| "path": "assembly/run_clean_hifi.sh", |
| "sha256": "7c3446935688d9d1207889fab6b68fdf821a9780338ed1c89a69746ca36af4df", |
| "language": "Shell", |
| "lines": 93, |
| "truncated": false, |
| "block": 8, |
| "row": 8832 |
| }, |
| { |
| "path": "assembly/run_clean_mito.sh", |
| "sha256": "a5bc3a35985e60fe298898089a7a1936dad2d0fd0df40196262a86b40357358f", |
| "language": "Shell", |
| "lines": 56, |
| "truncated": false, |
| "block": 8, |
| "row": 8385 |
| }, |
| { |
| "path": "assembly/run_filter_hifi.sh", |
| "sha256": "6392ca775d5415fe11a6d5a46bef3d70855f6d34b4703e155cc40ac32c5133cf", |
| "language": "Shell", |
| "lines": 86, |
| "truncated": false, |
| "block": 8, |
| "row": 8785 |
| }, |
| { |
| "path": "assembly/run_hifiasm_mpibr.sh", |
| "sha256": "5fbd8a594ddde044c8df30f3d51b1f1a99b7ef14cabe72b730e1dd9fbbe8c3bc", |
| "language": "Shell", |
| "lines": 46, |
| "truncated": false, |
| "block": 8, |
| "row": 7901 |
| }, |
| { |
| "path": "assembly/run_hifiasm_sanger.sh", |
| "sha256": "c50dc1e0c2a30a2af535a096c935d5b2624a615841fa152538d63612a69655f8", |
| "language": "Shell", |
| "lines": 44, |
| "truncated": false, |
| "block": 8, |
| "row": 7931 |
| }, |
| { |
| "path": "assembly/run_map_hic.sh", |
| "sha256": "cb91284ad0575a66a27f1fe5ae7677c5fb1df6712e5a807726f074dfceb95cd7", |
| "language": "Shell", |
| "lines": 118, |
| "truncated": false, |
| "block": 8, |
| "row": 9035 |
| }, |
| { |
| "path": "assembly/run_map_ilmn.sh", |
| "sha256": "ac3880214411b497a46d3d2a91557e775c7c94853283410807d4cc78ee84e90d", |
| "language": "Shell", |
| "lines": 79, |
| "truncated": false, |
| "block": 8, |
| "row": 8817 |
| }, |
| { |
| "path": "assembly/run_minimap.sh", |
| "sha256": "1f6cdc0fc02e6d751f86d2cab71553bfa1fce968cb716f2b286aa03f26f19c2d", |
| "language": "Shell", |
| "lines": 57, |
| "truncated": false, |
| "block": 8, |
| "row": 8460 |
| }, |
| { |
| "path": "assembly/run_scaffolding.sh", |
| "sha256": "6d991b24e5a55de518dfc76d09d48600e360c1d8341e0e7c00ed5d1ff220991b", |
| "language": "Shell", |
| "lines": 101, |
| "truncated": false, |
| "block": 8, |
| "row": 9005 |
| }, |
| { |
| "path": "assembly/utils/validators.sh", |
| "sha256": "0074389a1722d3c97508f0e6c219a65d80db20988ebc81c713b6b4fa62e5a235", |
| "language": "Shell", |
| "lines": 47, |
| "truncated": false, |
| "block": 8, |
| "row": 7787 |
| } |
| ] |
| } |
