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Copy pathmodules.json
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266 lines (266 loc) · 12.7 KB
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{
"name": "nf-core/rnafusion",
"homePage": "https://github.com/nf-core/rnafusion",
"repos": {
"https://github.com/nf-core/modules.git": {
"modules": {
"nf-core": {
"agat/convertgff2bed": {
"branch": "master",
"git_sha": "b785bb0b56bb518ab40c41f41d0e8749fb638257",
"installed_by": ["modules"]
},
"agat/convertspgff2tsv": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"arriba/arriba": {
"branch": "master",
"git_sha": "025a6f75e1f72e4ab60abb4bd65b3f289d4ad910",
"installed_by": ["modules"]
},
"arriba/visualisation": {
"branch": "master",
"git_sha": "025a6f75e1f72e4ab60abb4bd65b3f289d4ad910",
"installed_by": ["modules"]
},
"bioawk": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"cat/cat": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"cat/fastq": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"ctatsplicing/prepgenomelib": {
"branch": "master",
"git_sha": "8476d6a2adf7fb2e2f23229344aeabcd94a14b0b",
"installed_by": ["modules"],
"patch": "modules/nf-core/ctatsplicing/prepgenomelib/ctatsplicing-prepgenomelib.diff"
},
"ctatsplicing/startocancerintrons": {
"branch": "master",
"git_sha": "8476d6a2adf7fb2e2f23229344aeabcd94a14b0b",
"installed_by": ["modules"],
"patch": "modules/nf-core/ctatsplicing/startocancerintrons/ctatsplicing-startocancerintrons.diff"
},
"fastp": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
},
"fastqc": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
},
"fusioncatcher/fusioncatcher": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"],
"patch": "modules/nf-core/fusioncatcher/fusioncatcher/fusioncatcher-fusioncatcher.diff"
},
"fusioninspector": {
"branch": "master",
"git_sha": "eb5d65fc9a77b039dd95b11135ded338783747c7",
"installed_by": ["modules"]
},
"fusionreport/detect": {
"branch": "master",
"git_sha": "6ed53ffdb0d6be9a34de52b9472693397994e6d0",
"installed_by": ["modules"]
},
"fusionreport/download": {
"branch": "master",
"git_sha": "b871d05e5c8aab73132a41ede89c40910726df74",
"installed_by": ["modules"]
},
"gatk4/bedtointervallist": {
"branch": "master",
"git_sha": "a57253204b8f4022edfeaa3ae2f5e2abecd8858b",
"installed_by": ["modules"]
},
"gatk4/createsequencedictionary": {
"branch": "master",
"git_sha": "a57253204b8f4022edfeaa3ae2f5e2abecd8858b",
"installed_by": ["modules"]
},
"gatk4/markduplicates": {
"branch": "master",
"git_sha": "a57253204b8f4022edfeaa3ae2f5e2abecd8858b",
"installed_by": ["modules"]
},
"gffread": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"multiqc": {
"branch": "master",
"git_sha": "9656d955b700a8707c4a67821ab056f8c1095675",
"installed_by": ["modules"]
},
"picard/collectinsertsizemetrics": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"picard/collectrnaseqmetrics": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"picard/collectwgsmetrics": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"salmon/index": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"salmon/quant": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"samtools/collatefastq": {
"branch": "master",
"git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
"installed_by": ["modules"]
},
"samtools/convert": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"samtools/faidx": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"samtools/flagstat": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["bam_stats_samtools"]
},
"samtools/idxstats": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["bam_stats_samtools"]
},
"samtools/index": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["bam_sort_stats_samtools"]
},
"samtools/sort": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["bam_sort_stats_samtools"]
},
"samtools/stats": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["bam_stats_samtools"]
},
"star/align": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["fastq_align_star"],
"patch": "modules/nf-core/star/align/star-align.diff"
},
"star/genomegenerate": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"starfusion/build": {
"branch": "master",
"git_sha": "310a7a59c7f2362d25070e5928f3139f92377eaf",
"installed_by": ["modules"]
},
"starfusion/detect": {
"branch": "master",
"git_sha": "b0f38d0ea7515484442edc96046858924fc477dc",
"installed_by": ["modules"]
},
"stringtie/merge": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["bam_stringtie_merge", "modules"]
},
"stringtie/stringtie": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["bam_stringtie_merge", "modules"]
},
"ucsc/gtftogenepred": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"umitools/extract": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["fastq_fastqc_umitools_fastp"]
}
}
},
"subworkflows": {
"nf-core": {
"bam_sort_stats_samtools": {
"branch": "master",
"git_sha": "156feda0cb6589cd29c04902004fa3b53bc00205",
"installed_by": ["fastq_align_star"]
},
"bam_stats_samtools": {
"branch": "master",
"git_sha": "156feda0cb6589cd29c04902004fa3b53bc00205",
"installed_by": ["bam_sort_stats_samtools"]
},
"bam_stringtie_merge": {
"branch": "master",
"git_sha": "5ce6cef7d4a100409aa30bca79b5020b6738767c",
"installed_by": ["subworkflows"]
},
"fastq_align_star": {
"branch": "master",
"git_sha": "4e3e10e502ec6ab6b1c4b4fecd923ff1fa287338",
"installed_by": ["subworkflows"],
"patch": "subworkflows/nf-core/fastq_align_star/fastq_align_star.diff"
},
"fastq_fastqc_umitools_fastp": {
"branch": "master",
"git_sha": "8f2ec534d0418bf724cfd5f053176a9c500fae78",
"installed_by": ["subworkflows"]
},
"utils_nextflow_pipeline": {
"branch": "master",
"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
"installed_by": ["subworkflows"]
},
"utils_nfcore_pipeline": {
"branch": "master",
"git_sha": "a3fb7351b1fdb2b1de282b765816bbea190e86a8",
"installed_by": ["subworkflows"]
},
"utils_nfschema_plugin": {
"branch": "master",
"git_sha": "ce3424257de288c0ca25f097a68d3a289da23f12",
"installed_by": ["subworkflows"]
}
}
}
}
}
}