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"integrity": "sha512-tVGE0mVJPGb0chKhqmsoosjsS+qUnJVGJpZgsHYQcGoPlG3B51R3PouqTgEGH2Dc9jjFyOqOpix6ZHNMXp1FZg==", + "version": "0.3.1", + "resolved": "https://registry.npmjs.org/tinyexec/-/tinyexec-0.3.1.tgz", + "integrity": "sha512-WiCJLEECkO18gwqIp6+hJg0//p23HXp4S+gGtAKu3mI2F2/sXC4FvHvXvB0zJVVaTPhx1/tOwdbRsa1sOBIKqQ==", "license": "MIT" }, "node_modules/to-fast-properties": { @@ -12855,9 +12870,9 @@ "license": "Apache-2.0" }, "node_modules/tsconfck": { - "version": "3.1.3", - "resolved": "https://registry.npmjs.org/tsconfck/-/tsconfck-3.1.3.tgz", - "integrity": "sha512-ulNZP1SVpRDesxeMLON/LtWM8HIgAJEIVpVVhBM6gsmvQ8+Rh+ZG7FWGvHh7Ah3pRABwVJWklWCr/BTZSv0xnQ==", + "version": "3.1.4", + "resolved": "https://registry.npmjs.org/tsconfck/-/tsconfck-3.1.4.tgz", + "integrity": "sha512-kdqWFGVJqe+KGYvlSO9NIaWn9jT1Ny4oKVzAJsKii5eoE9snzTJzL4+MMVOMn+fikWGFmKEylcXL710V/kIPJQ==", "license": "MIT", "bin": { "tsconfck": "bin/tsconfck.js" @@ -13292,9 +13307,9 @@ } }, "node_modules/vite": { - "version": "5.4.8", - "resolved": "https://registry.npmjs.org/vite/-/vite-5.4.8.tgz", - "integrity": "sha512-FqrItQ4DT1NC4zCUqMB4c4AZORMKIa0m8/URVCZ77OZ/QSNeJ54bU1vrFADbDsuwfIPcgknRkmqakQcgnL4GiQ==", + "version": "5.4.9", + "resolved": "https://registry.npmjs.org/vite/-/vite-5.4.9.tgz", + "integrity": "sha512-20OVpJHh0PAM0oSOELa5GaZNWeDjcAvQjGXy2Uyr+Tp+/D2/Hdz6NLgpJLsarPTA2QJ6v8mX2P1ZfbsSKvdMkg==", "license": "MIT", "dependencies": { "esbuild": "^0.21.3", @@ -13764,7 +13779,7 @@ "kleur": "^4.1.5", "leaflet": "^1.9.4", "lite-youtube-embed": "^0.3.2", - "mermaid": "^10.9.1", + "mermaid": "^10.9.3", "nanostores": "^0.10.3", "octokit": "^4.0.2", "party-js": "^2.2.0", diff --git a/public/components.json b/public/components.json index 540c6366fe..adcb10417e 100644 --- a/public/components.json +++ b/public/components.json @@ -7784,6 +7784,18 @@ "name": "rnafusion", "version": "3.0.2" }, + { + "name": "rnafusion", + "version": "3.0.2" + }, + { + "name": "rnafusion", + "version": "3.0.2" + }, + { + "name": "rnafusion", + "version": "3.0.2" + }, { "name": "rnafusion", "version": "3.0.2" @@ -25626,6 +25638,30 @@ "name": "genomeassembler", "version": "dev" }, + { + "name": "pathogensurveillance", + "version": "dev" + }, + { + "name": "genomeassembler", + "version": "dev" + }, + { + "name": "pathogensurveillance", + "version": "dev" + }, + { + "name": "genomeassembler", + "version": "dev" + }, + { + "name": "pathogensurveillance", + "version": "dev" + }, + { + "name": "genomeassembler", + "version": "dev" + }, { "name": "pathogensurveillance", "version": "dev" @@ -48463,25 +48499,50 @@ "description": "Input SAM/BAM file", "pattern": "*.{bam,sam}" } - } - ], - [ + }, { - "run_haplotypecaller": { - "type": "boolean", - "description": "Run variant calling on the input files. Needed to generate gvcf output." + "bai": { + "type": "file", + "description": "Input BAM file index", + "pattern": "*.bai" } - } - ], - [ + }, { - "run_bqsr": { - "type": "boolean", - "description": "Run BQSR on the input files. Needed to generate recall metrics." + "target_regions_bed": { + "type": "file", + "description": "Optional BED file containing target regions for BQSR and variant calling.", + "pattern": "*.bed" + } + }, + { + "filter_regions_bed": { + "type": "file", + "description": "Optional BED file containing regions to filter.", + "pattern": "*.bed" + } + }, + { + "intermediate_bqsr_tables": { + "type": "file", + "description": "Optional list of BQSR tables, used when parsing files created by `elprep split`", + "pattern": "*.table" + } + }, + { + "recall_file": { + "type": "file", + "description": "Recall file with intermediate results for bqsr", + "pattern": "*.recall" } } ], [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, { "reference_sequences": { "type": "file", @@ -48492,14 +48553,11 @@ ], [ { - "filter_regions_bed": { - "type": "file", - "description": "Optional BED file containing regions to filter.", - "pattern": "*.bed" + "meta3": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" } - } - ], - [ + }, { "reference_elfasta": { "type": "file", @@ -48509,6 +48567,12 @@ } ], [ + { + "meta4": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, { "known_sites_elsites": { "type": "file", @@ -48519,19 +48583,17 @@ ], [ { - "target_regions_bed": { - "type": "file", - "description": "Optional BED file containing target regions for BQSR and variant calling.", - "pattern": "*.bed" + "run_haplotypecaller": { + "type": "boolean", + "description": "Run variant calling on the input files. Needed to generate gvcf output." } } ], [ { - "intermediate_bqsr_tables": { - "type": "file", - "description": "Optional list of BQSR tables, used when parsing files created by `elprep split`", - "pattern": "*.table" + "run_bqsr": { + "type": "boolean", + "description": "Run BQSR on the input files. Needed to generate recall metrics." } } ], @@ -48566,13 +48628,14 @@ { "meta": { "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.{bam,sam}" } }, { - "output/**.{bam,sam}": { - "type": "file", - "description": "Sorted, markdup, optionally BQSR BAM/SAM file", + "*.{bam,sam}": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", "pattern": "*.{bam,sam}" } } @@ -48583,13 +48646,14 @@ { "meta": { "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "elprep-*.log" } }, { - "logs/elprep/elprep*": { - "type": "list", - "description": "Runtime log files", + "*.log": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", "pattern": "elprep-*.log" } } @@ -48600,13 +48664,14 @@ { "meta": { "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.{metrics.txt}" } }, { "*.metrics.txt": { - "type": "file", - "description": "Optional duplicate metrics file generated by elprep", + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", "pattern": "*.{metrics.txt}" } } @@ -48617,13 +48682,14 @@ { "meta": { "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.{recall}" } }, { "*.recall": { - "type": "file", - "description": "Optional recall metrics file generated by elprep", + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", "pattern": "*.{recall}" } } @@ -48634,13 +48700,14 @@ { "meta": { "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.{vcf.gz}" } }, { "*.vcf.gz": { - "type": "file", - "description": "Optional GVCF output file", + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", "pattern": "*.{vcf.gz}" } } @@ -48651,13 +48718,14 @@ { "meta": { "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.{table}" } }, { "*.table": { - "type": "file", - "description": "Optional intermediate BQSR table output file", + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", "pattern": "*.{table}" } } @@ -48668,13 +48736,14 @@ { "meta": { "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.{activity_profile.igv}" } }, { "*.activity_profile.igv": { - "type": "file", - "description": "Optional activity profile output file", + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", "pattern": "*.{activity_profile.igv}" } } @@ -48685,13 +48754,14 @@ { "meta": { "type": "map", - "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", + "pattern": "*.{assembly_regions.igv}" } }, { "*.assembly_regions.igv": { - "type": "file", - "description": "Optional activity regions output file", + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n", "pattern": "*.{assembly_regions.igv}" } } @@ -107702,6 +107772,18 @@ "name": "genomeassembler", "version": "dev" }, + { + "name": "genomeassembler", + "version": "dev" + }, + { + "name": "genomeassembler", + "version": "dev" + }, + { + "name": "genomeassembler", + "version": "dev" + }, { "name": "genomeassembler", "version": "dev" @@ -126230,6 +126312,177 @@ ] } }, + { + "name": "parabricks_fq2bammeth", + "path": "modules/nf-core/parabricks/fq2bammeth/meta.yml", + "type": "module", + "meta": { + "name": "parabricks_fq2bammeth", + "description": "VIDIA Clara Parabricks GPU-accelerated fast, accurate algorithm for mapping methylated DNA sequence reads to a reference genome, performing local alignment, and producing alignment for different parts of the query sequence", + "keywords": [ + "align", + "sort", + "bqsr", + "duplicates", + "bwameth" + ], + "tools": [ + { + "parabricks": { + "description": "NVIDIA Clara Parabricks GPU-accelerated genomics tools", + "homepage": "https://www.nvidia.com/en-us/clara/genomics/", + "documentation": "https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/man_fq2bam_meth.html#fq2bam-meth-reference", + "licence": [ + "custom" + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "fastq.gz files", + "pattern": "*.fastq.gz" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta information\n" + } + }, + { + "fasta": { + "type": "file", + "description": "reference fasta file - must be unzipped", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing index information\n" + } + }, + { + "index": { + "type": "file", + "description": "reference BWA index", + "pattern": "*.{amb,ann,bwt,pac,sa}" + } + } + ], + [ + { + "known_sites": { + "type": "file", + "description": "(optional) known sites file(s) for calculating BQSR. markdups must be true to perform BQSR.", + "pattern": "*.vcf.gz" + } + } + ] + ], + "output": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.bam" + } + } + ] + }, + { + "bai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "index corresponding to sorted BAM file", + "pattern": "*.bai" + } + } + ] + }, + { + "qc_metrics": [ + { + "qc_metrics": { + "type": "directory", + "description": "(optional) optional directory of qc metrics", + "pattern": "qc_metrics" + } + } + ] + }, + { + "bqsr_table": [ + { + "*.table": { + "type": "file", + "description": "(optional) table from base quality score recalibration calculation, to be used with parabricks/applybqsr", + "pattern": "*.table" + } + } + ] + }, + { + "duplicate_metrics": [ + { + "duplicate-metrics.txt": { + "type": "file", + "description": "(optional) metrics calculated from marking duplcates in the bam file", + "pattern": "*-duplicate-metrics.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + } + ], + "authors": [ + "@sateeshperi" + ], + "maintainers": [ + "@sateeshperi" + ] + } + }, { "name": "parabricks_genotypegvcf", "path": "modules/nf-core/parabricks/genotypegvcf/meta.yml", @@ -142458,6 +142711,13 @@ "pattern": "*.{bai}" } }, + { + "bamlist": { + "type": "file", + "description": "(Optional) File with list of BAM/CRAM files to impute. One file per line.", + "pattern": "*.{txt}" + } + }, { "reference_haplotype_file": { "type": "file", @@ -198969,6 +199229,10 @@ "name": "datasync", "version": "dev" }, + { + "name": "deepmodeloptim", + "version": "dev" + }, { "name": "demo", "version": "1.0.1" @@ -199230,6 +199494,10 @@ "name": "datasync", "version": "dev" }, + { + "name": "deepmodeloptim", + "version": "dev" + }, { "name": "demo", "version": "1.0.1" @@ -199479,6 +199747,10 @@ "name": "createtaxdb", "version": "dev" }, + { + "name": "deepmodeloptim", + "version": "dev" + }, { "name": "demo", "version": "1.0.1" diff --git a/public/pipeline_names.json b/public/pipeline_names.json index 6c3e319496..0387d10388 100644 --- a/public/pipeline_names.json +++ b/public/pipeline_names.json @@ -1 +1 @@ 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\ No newline at end of file +{"pipeline":["airrflow","ampliseq","atacseq","bacass","bactmap","bamtofastq","cageseq","callingcards","chipseq","circdna","circrna","clipseq","coproid","createpanelrefs","createtaxdb","crisprseq","cutandrun","datasync","deepmodeloptim","demo","demultiplex","denovotranscript","detaxizer","diaproteomics","differentialabundance","drugresponseeval","dualrnaseq","eager","epitopeprediction","fastquorum","fetchngs","funcscan","genomeannotator","genomeassembler","genomeskim","gwas","hgtseq","hic","hicar","hlatyping","imcyto","isoseq","lncpipe","mag","magmap","marsseq","mcmicro","meerpipe","metaboigniter","metapep","metatdenovo","methylarray","methylseq","mhcquant","mnaseseq","molkart","multiplesequencealign","nanoseq","nanostring","nascent","omicsgenetraitassociation","oncoanalyser","pairgenomealign","pangenome","pathogensurveillance","pgdb","phageannotator","phaseimpute","phyloplace","pixelator","proteinfold","proteomicslfq","radseq","rangeland","raredisease","readsimulator","reportho","riboseq","rnadnavar","rnafusion","rnaseq","rnasplice","rnavar","sammyseq","sarek","scdownstream","scnanoseq","scrnaseq","seqinspector","slamseq","smrnaseq","spatialvi","spinningjenny","taxprofiler","tbanalyzer","tfactivity","troughgraph","variantbenchmarking","variantcatalogue","viralintegration","viralrecon"]} 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"temp_clone_token": "", @@ -3674,7 +3674,7 @@ "status": "disabled" } }, - "network_count": 147, + "network_count": 148, "subscribers_count": 142, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, @@ -5469,9 +5469,9 @@ "url": "https://api.github.com/repos/nf-core/createtaxdb", "created_at": "2023-10-24T08:41:35Z", "updated_at": "2024-10-12T13:36:35Z", - "pushed_at": "2024-10-21T10:54:23Z", + "pushed_at": "2024-10-22T11:11:21Z", "homepage": "https://nf-co.re/createtaxdb", - "size": 3223, + "size": 3224, "stargazers_count": 7, "watchers_count": 7, "language": "Nextflow", @@ -7510,6 +7510,184 @@ } ] }, + { + "id": 766922895, + "node_id": "R_kgDOLbZQjw", + "name": "deepmodeloptim", + "full_name": "nf-core/deepmodeloptim", + "private": false, + "description": "Stochastic Testing and Input Manipulation for Unbiased Learning Systems", + "fork": false, + "url": "https://api.github.com/repos/nf-core/deepmodeloptim", + "created_at": "2024-03-04T11:37:13Z", + 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"archived": false, "disabled": false, - "open_issues_count": 37, + "open_issues_count": 36, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -28431,7 +28632,7 @@ ], "visibility": "public", "forks": 34, - "open_issues": 37, + "open_issues": 36, "watchers": 85, "default_branch": "master", "temp_clone_token": "", @@ -28559,7 +28760,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": true, - "open_pr_count": 3, + "open_pr_count": 1, "repository_url": "https://github.com/nf-core/raredisease", "contributors": [ { @@ -29443,8 +29644,8 @@ }, { "tag_name": "dev", - "published_at": "2024-10-21T14:21:38Z", - "tag_sha": "a45198b90db27672ae1b766adfcc4a20c891d5a0", + "published_at": "2024-10-22T16:50:20Z", + "tag_sha": "610c0238536a07d962dfa50c57b051cf7e338190", "has_schema": true, "doc_files": [ "docs/output.md", @@ -30404,10 +30605,10 @@ "fork": false, "url": 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"contributors": [ { @@ -31415,9 +31616,9 @@ "url": "https://api.github.com/repos/nf-core/rnaseq", "created_at": "2018-03-29T13:10:58Z", "updated_at": "2024-10-21T03:05:06Z", - "pushed_at": "2024-10-21T20:45:50Z", + "pushed_at": "2024-10-23T09:42:54Z", "homepage": "https://nf-co.re/rnaseq", - "size": 72156, + "size": 72243, "stargazers_count": 886, "watchers_count": 886, "language": "Nextflow", @@ -31545,7 +31746,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": true, - "open_pr_count": 12, + "open_pr_count": 11, "repository_url": "https://github.com/nf-core/rnaseq", "contributors": [ { @@ -33544,8 +33745,8 @@ }, { "tag_name": "dev", - "published_at": "2024-10-21T18:23:18Z", - "tag_sha": "a97256b9151c26d1684ad1142d3a47865bde2be1", + "published_at": "2024-10-22T12:53:13Z", + "tag_sha": "3671d5967ab13c31152884eab47856e13c4ad32f", "has_schema": true, "doc_files": [ "docs/output.md", @@ -34629,12 +34830,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/sarek", "created_at": "2019-04-30T15:43:00Z", - "updated_at": "2024-10-19T08:06:05Z", + "updated_at": "2024-10-23T06:21:40Z", "pushed_at": "2024-10-15T11:41:33Z", "homepage": "https://nf-co.re/sarek", "size": 92155, - "stargazers_count": 400, - "watchers_count": 400, + "stargazers_count": 402, + "watchers_count": 402, "language": "Nextflow", "has_issues": true, "has_projects": false, @@ -34665,7 +34866,7 @@ "visibility": "public", "forks": 404, "open_issues": 284, - "watchers": 400, + "watchers": 402, "default_branch": "master", "temp_clone_token": "", "allow_squash_merge": true, @@ -37157,12 +37358,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/scdownstream", "created_at": "2024-06-11T06:38:31Z", - "updated_at": "2024-10-21T06:27:12Z", + "updated_at": "2024-10-22T03:22:24Z", "pushed_at": "2024-10-18T06:02:39Z", "homepage": "https://nf-co.re/scdownstream", "size": 1910, - "stargazers_count": 34, - "watchers_count": 34, + "stargazers_count": 35, + "watchers_count": 35, "language": "Nextflow", "has_issues": true, "has_projects": false, @@ -37188,7 +37389,7 @@ "visibility": "public", "forks": 9, "open_issues": 19, - "watchers": 34, + "watchers": 35, "default_branch": "dev", "temp_clone_token": "", "allow_squash_merge": true, @@ -39823,12 +40024,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/smrnaseq", "created_at": "2018-07-11T14:56:59Z", - "updated_at": "2024-10-14T09:58:05Z", + "updated_at": "2024-10-23T07:36:24Z", "pushed_at": "2024-10-16T18:06:26Z", "homepage": "https://nf-co.re/smrnaseq", "size": 8758, - "stargazers_count": 73, - "watchers_count": 73, + "stargazers_count": 74, + "watchers_count": 74, "language": "Nextflow", "has_issues": true, "has_projects": false, @@ -39850,7 +40051,7 @@ "visibility": "public", "forks": 125, "open_issues": 13, - "watchers": 73, + "watchers": 74, "default_branch": "master", "temp_clone_token": "", "allow_squash_merge": false, @@ -40524,9 +40725,9 @@ "url": "https://api.github.com/repos/nf-core/spatialvi", "created_at": "2022-02-23T20:44:38Z", "updated_at": "2024-10-14T00:59:32Z", - "pushed_at": "2024-10-11T13:55:49Z", + "pushed_at": "2024-10-23T08:20:25Z", "homepage": "https://nf-co.re/spatialvi", - "size": 7220, + "size": 7231, "stargazers_count": 50, "watchers_count": 50, "language": "Nextflow", @@ -40539,7 +40740,7 @@ "forks_count": 18, "archived": false, "disabled": false, - "open_issues_count": 6, + "open_issues_count": 7, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -40558,7 +40759,7 @@ ], "visibility": "public", "forks": 18, - "open_issues": 6, + "open_issues": 7, "watchers": 50, "default_branch": "dev", "temp_clone_token": "", @@ -40661,7 +40862,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": true, - "open_pr_count": 2, + "open_pr_count": 3, "repository_url": "https://github.com/nf-core/spatialvi", "contributors": [ { @@ -41133,9 +41334,9 @@ "url": "https://api.github.com/repos/nf-core/taxprofiler", "created_at": "2022-02-18T06:56:10Z", "updated_at": "2024-10-03T16:54:18Z", - "pushed_at": "2024-10-18T13:55:39Z", + "pushed_at": "2024-10-22T12:36:15Z", "homepage": "https://nf-co.re/taxprofiler", - "size": 14730, + "size": 14756, "stargazers_count": 127, "watchers_count": 127, "language": "Nextflow", @@ -42941,7 +43142,7 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/variantbenchmarking", "created_at": "2023-12-07T10:56:32Z", - "updated_at": "2024-10-17T06:51:53Z", + "updated_at": "2024-10-22T13:31:52Z", "pushed_at": "2024-10-21T14:57:44Z", "homepage": "https://nf-co.re/variantbenchmarking", "size": 3832, @@ -42957,7 +43158,7 @@ "forks_count": 6, "archived": false, "disabled": false, - "open_issues_count": 13, + "open_issues_count": 17, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -42969,7 +43170,7 @@ ], "visibility": "public", "forks": 6, - "open_issues": 13, + "open_issues": 17, "watchers": 11, "default_branch": "dev", "temp_clone_token": "", diff --git a/sites/configs/netlify.toml b/sites/configs/netlify.toml index abafcd9218..77728f7b02 100644 --- a/sites/configs/netlify.toml +++ b/sites/configs/netlify.toml @@ -4,7 +4,7 @@ node_bundler = "esbuild" [build] environment = { NODE_VERSION = "20.4.0" } command = "npm run build -w sites/configs" -ignore = "git diff --quiet $CACHED_COMMIT_REF $COMMIT_REF sites/main-site/src/components sites/main-site/src/layouts sites/configs" +ignore = "git diff --quiet $CACHED_COMMIT_REF $COMMIT_REF sites/main-site/src/components sites/main-site/src/layouts sites/configs public/pipelines.json" [[headers]] for = "/_astro/*" [headers.values] diff --git a/sites/configs/src/pages/configs/[configslug].astro b/sites/configs/src/pages/configs/[configslug].astro index b951bc0daf..2d39480bc5 100644 --- a/sites/configs/src/pages/configs/[configslug].astro +++ b/sites/configs/src/pages/configs/[configslug].astro @@ -113,7 +113,9 @@ content = content?.replace(/nf-core\/configs(:)?\s*/g, ''); //wrap raw_config as markdown code-block raw_config = '```groovy title="' + path.split('/').pop() + '"\n' + raw_config + '\n```'; -const contact = config.config_profile_contact.match(/@(\w+)/) ? config.config_profile_contact.match(/@(\w+)/)[1] : ''; +const contact = config.config_profile_contact.match(/@([A-Za-z0-9-]+)/) + ? config.config_profile_contact.match(/@([A-Za-z0-9-]+)/)[1] + : ''; const gh_url = 'https://github.com/nf-core/configs/blob/master/docs/' + configslug + '.md'; --- diff --git a/sites/main-site/package.json b/sites/main-site/package.json index ecca63d6f7..15bcdaf809 100644 --- a/sites/main-site/package.json +++ b/sites/main-site/package.json @@ -63,7 +63,7 @@ "kleur": "^4.1.5", "leaflet": "^1.9.4", "lite-youtube-embed": "^0.3.2", - "mermaid": "^10.9.1", + "mermaid": "^10.9.3", "nanostores": "^0.10.3", "octokit": "^4.0.2", "party-js": "^2.2.0", diff --git a/sites/main-site/src/content/events/2024/hackathon-barcelona.mdx b/sites/main-site/src/content/events/2024/hackathon-barcelona.mdx index 97df7015b4..57e1478b8b 100644 --- a/sites/main-site/src/content/events/2024/hackathon-barcelona.mdx +++ b/sites/main-site/src/content/events/2024/hackathon-barcelona.mdx @@ -318,18 +318,16 @@ You can move freely between projects throughout the event. -## Components - This is a pipeline for downstream gene expression analysis, with a main focus on differential expression analysis. Currently, we are working on a new branch `dev-ratio` with two objectives: @@ -337,15 +335,17 @@ You can move freely between projects throughout the event. - convert the pipeline into a modular and unified framework that allocates different ways of performing differential analysis. By joining this group you will help with: - 1) Implement and add nf-core modules that wrap other methods that can be used to perform differential analysis. Some modules (ie. propr) were already created but need to be updated (beginner friendly). + 1) Implement and add nf-core modules that wrap other methods that can be used to perform differential analysis. Some modules (ie. propd) were already created but need to be updated (beginner friendly). 2) Add these new modules to the pipeline and update the pipeline parameters correspondingly (beginner friendly). 3) Add the existing modules to the new modular subworkflow in a way that will reproduce the original pipeline’s behaviour (beginner - intermediate level). 4) Update the code required to generate the plots and reports (beginner - intermediate level). - 5) Help in the restructuring of the pipeline architecture (intermediate level). + 5) Restructure the pipeline architecture (intermediate level). 6) Update documentation (beginner friendly). +## Components +