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176 lines (176 loc) · 7.94 KB
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Copy pathmodules.json
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176 lines (176 loc) · 7.94 KB
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{
"name": "nf-core/pathogenepidemiology",
"homePage": "https://github.com/nf-core/pathogenepidemiology",
"repos": {
"https://github.com/nf-core/modules.git": {
"modules": {
"nf-core": {
"bbmap/bbduk": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"]
},
"bcftools/concat": {
"branch": "master",
"git_sha": "feef37435aea56816adf4b3bde1fc76aac327a8d",
"installed_by": ["modules"]
},
"bcftools/view": {
"branch": "master",
"git_sha": "feef37435aea56816adf4b3bde1fc76aac327a8d",
"installed_by": ["modules"]
},
"bwamem3/index": {
"branch": "master",
"git_sha": "cab334f632708de2679161f713dd969bfa491a25",
"installed_by": ["modules"]
},
"bwamem3/mem": {
"branch": "master",
"git_sha": "cab334f632708de2679161f713dd969bfa491a25",
"installed_by": ["modules"]
},
"deepvariant/callvariants": {
"branch": "master",
"git_sha": "4a4ccce52d5a280b0b136ff3ac841607debed92b",
"installed_by": ["deepvariant"]
},
"deepvariant/makeexamples": {
"branch": "master",
"git_sha": "4a4ccce52d5a280b0b136ff3ac841607debed92b",
"installed_by": ["deepvariant"]
},
"deepvariant/postprocessvariants": {
"branch": "master",
"git_sha": "4a4ccce52d5a280b0b136ff3ac841607debed92b",
"installed_by": ["deepvariant"]
},
"fastqc": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"]
},
"gatk4/applyvqsr": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"]
},
"gatk4/cleansam": {
"branch": "master",
"git_sha": "d5de7a949aa84689f4098c958f05733a6c3804f5",
"installed_by": ["modules"]
},
"gatk4/createsequencedictionary": {
"branch": "master",
"git_sha": "d5de7a949aa84689f4098c958f05733a6c3804f5",
"installed_by": ["modules"]
},
"gatk4/genomicsdbimport": {
"branch": "master",
"git_sha": "d5de7a949aa84689f4098c958f05733a6c3804f5",
"installed_by": ["modules"]
},
"gatk4/genotypegvcfs": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"]
},
"gatk4/haplotypecaller": {
"branch": "master",
"git_sha": "7abcc95130dd0388f696002a99adeb59eca54471",
"installed_by": ["modules"]
},
"gatk4/markduplicates": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"]
},
"gatk4/variantrecalibrator": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"]
},
"minimap2/align": {
"branch": "master",
"git_sha": "135d883a43b1a2324b4112cd270cf22e20835533",
"installed_by": ["modules"]
},
"minimap2/index": {
"branch": "master",
"git_sha": "135d883a43b1a2324b4112cd270cf22e20835533",
"installed_by": ["modules"]
},
"mosdepth": {
"branch": "master",
"git_sha": "999b9db1d6b8bdc591e1168e183f4cc87d6606f9",
"installed_by": ["modules"]
},
"multiqc": {
"branch": "master",
"git_sha": "98403d15b0e50edae1f3fec5eae5e24982f1fade",
"installed_by": ["modules"]
},
"picard/collectinsertsizemetrics": {
"branch": "master",
"git_sha": "fe08122c3dc2f2d7890daba06f6c90e570ef01de",
"installed_by": ["modules"]
},
"picard/createsequencedictionary": {
"branch": "master",
"git_sha": "fe08122c3dc2f2d7890daba06f6c90e570ef01de",
"installed_by": ["modules"]
},
"picard/sortsam": {
"branch": "master",
"git_sha": "fe08122c3dc2f2d7890daba06f6c90e570ef01de",
"installed_by": ["modules"]
},
"samtools/faidx": {
"branch": "master",
"git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002",
"installed_by": ["modules"]
},
"samtools/index": {
"branch": "master",
"git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002",
"installed_by": ["modules"]
},
"samtools/stats": {
"branch": "master",
"git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002",
"installed_by": ["modules"]
},
"untar": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"]
}
}
},
"subworkflows": {
"nf-core": {
"deepvariant": {
"branch": "master",
"git_sha": "6ef220fd9252b42fb3c50348bbdbcb6246730686",
"installed_by": ["subworkflows"]
},
"utils_nextflow_pipeline": {
"branch": "master",
"git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
"installed_by": ["subworkflows"]
},
"utils_nfcore_pipeline": {
"branch": "master",
"git_sha": "a3fb7351b1fdb2b1de282b765816bbea190e86a8",
"installed_by": ["subworkflows"]
},
"utils_nfschema_plugin": {
"branch": "master",
"git_sha": "a7b27fd25bfa8dcc07d299e88bd790585901a436",
"installed_by": ["subworkflows"]
}
}
}
}
}
}