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modules.json
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modules.json
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{
"name": "mskcc/forte",
"homePage": "https://github.com/mskcc/forte",
"repos": {
"[email protected]:mskcc-omics-workflows/modules.git": {
"modules": {
"msk": {
"gbcms": {
"branch": "develop",
"git_sha": "e70681357ccd39e7a10d328ca696c074750d8163",
"installed_by": ["modules"]
}
}
}
},
"https://github.com/nf-core/modules.git": {
"modules": {
"nf-core": {
"agat/spaddintrons": {
"branch": "master",
"git_sha": "6898156da3604a6bdf26c36036053a970050fea0",
"installed_by": ["modules"]
},
"arriba": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"cat/cat": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"cat/fastq": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"custom/dumpsoftwareversions": {
"branch": "master",
"git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e",
"installed_by": ["modules"]
},
"fastp": {
"branch": "master",
"git_sha": "20a508676f40d0fd3f911ac595af91ec845704c4",
"installed_by": ["modules"]
},
"gatk4/bedtointervallist": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"gatk4/createsequencedictionary": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"gunzip": {
"branch": "master",
"git_sha": "3a5fef109d113b4997c9822198664ca5f2716208",
"installed_by": ["modules"]
},
"kallisto/index": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"kallisto/quant": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"multiqc": {
"branch": "master",
"git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",
"installed_by": ["modules"],
"patch": "modules/nf-core/multiqc/multiqc.diff"
},
"picard/collecthsmetrics": {
"branch": "master",
"git_sha": "0ce3ab0ac301f160225b22254fa238478b4389f2",
"installed_by": ["modules"]
},
"picard/collectrnaseqmetrics": {
"branch": "master",
"git_sha": "54f28e020daf9215ab000da7af3b273e85639855",
"installed_by": ["modules"]
},
"rseqc/bamstat": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["bam_rseqc", "modules"]
},
"rseqc/inferexperiment": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["bam_rseqc", "modules"]
},
"rseqc/innerdistance": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["bam_rseqc", "modules"]
},
"rseqc/junctionannotation": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules", "bam_rseqc"]
},
"rseqc/junctionsaturation": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["bam_rseqc", "modules"]
},
"rseqc/readdistribution": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["bam_rseqc", "modules"]
},
"rseqc/readduplication": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["bam_rseqc", "modules"]
},
"rseqc/tin": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["bam_rseqc", "modules"]
},
"samtools/bam2fq": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"samtools/faidx": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"samtools/index": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"samtools/merge": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"star/align": {
"branch": "master",
"git_sha": "57d75dbac06812c59798a48585032f6e50bb1914",
"installed_by": ["modules"]
},
"star/genomegenerate": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
},
"subread/featurecounts": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"],
"patch": "modules/nf-core/subread/featurecounts/subread-featurecounts.diff"
},
"ucsc/gtftogenepred": {
"branch": "master",
"git_sha": "511909dedab2a9955f2c3eae88abd3733edfd349",
"installed_by": ["modules"]
},
"umitools/dedup": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
},
"umitools/extract": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"],
"patch": "modules/nf-core/umitools/extract/umitools-extract.diff"
}
}
},
"subworkflows": {
"nf-core": {
"bam_rseqc": {
"branch": "master",
"git_sha": "b8f7bdc6f0e37f2946c84c5ac676c6030ebbf8c4",
"installed_by": ["subworkflows"]
}
}
}
}
}
}