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Copy pathmodules.json
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executable file
·245 lines (245 loc) · 11.8 KB
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{
"name": "nf-core/rnavar",
"homePage": "https://github.com/nf-core/rnavar",
"repos": {
"https://github.com/nf-core/modules.git": {
"modules": {
"nf-core": {
"bcftools/annotate": {
"branch": "master",
"git_sha": "feef37435aea56816adf4b3bde1fc76aac327a8d",
"installed_by": ["modules"]
},
"cat/fastq": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"]
},
"ensemblvep/download": {
"branch": "master",
"git_sha": "251885fdb29eca03523d326aca5c827d1f6bdfeb",
"installed_by": ["cache_download_ensemblvep_snpeff"]
},
"ensemblvep/vep": {
"branch": "master",
"git_sha": "251885fdb29eca03523d326aca5c827d1f6bdfeb",
"installed_by": ["vcf_annotate_ensemblvep"]
},
"fastqc": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"],
"patch": "modules/nf-core/fastqc/fastqc.diff"
},
"gatk4/applybqsr": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"]
},
"gatk4/baserecalibrator": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"],
"patch": "modules/nf-core/gatk4/baserecalibrator/gatk4-baserecalibrator.diff"
},
"gatk4/bedtointervallist": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"]
},
"gatk4/combinegvcfs": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"]
},
"gatk4/createsequencedictionary": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"]
},
"gatk4/haplotypecaller": {
"branch": "master",
"git_sha": "b73338eca19d798eb0ef6ed112ef4d27a30d2871",
"installed_by": ["modules"]
},
"gatk4/intervallisttools": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"]
},
"gatk4/mergevcfs": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"]
},
"gatk4/splitncigarreads": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"]
},
"gatk4/variantfiltration": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"]
},
"gffread": {
"branch": "master",
"git_sha": "c9ad4d691aa339e478a77847e3ef854ccd21778b",
"installed_by": ["modules"]
},
"gunzip": {
"branch": "master",
"git_sha": "0902eac3012baaf4f9ab6513c8c55acc9353c96c",
"installed_by": ["modules"]
},
"htslib/bgziptabix": {
"branch": "master",
"git_sha": "54e41f4ed3aead45054380a9befeb927612ffc91",
"installed_by": ["vcf_annotate_snpeff"]
},
"mosdepth": {
"branch": "master",
"git_sha": "999b9db1d6b8bdc591e1168e183f4cc87d6606f9",
"installed_by": ["modules"],
"patch": "modules/nf-core/mosdepth/mosdepth.diff"
},
"multiqc": {
"branch": "master",
"git_sha": "98403d15b0e50edae1f3fec5eae5e24982f1fade",
"installed_by": ["modules"]
},
"picard/markduplicates": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["bam_markduplicates_picard"],
"patch": "modules/nf-core/picard/markduplicates/picard-markduplicates.diff"
},
"samtools/faidx": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"]
},
"samtools/flagstat": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["bam_stats_samtools"],
"patch": "modules/nf-core/samtools/flagstat/samtools-flagstat.diff"
},
"samtools/idxstats": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["bam_stats_samtools"],
"patch": "modules/nf-core/samtools/idxstats/samtools-idxstats.diff"
},
"samtools/index": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["bam_markduplicates_picard", "bam_sort_stats_samtools", "modules"]
},
"samtools/merge": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"]
},
"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", "modules"],
"patch": "modules/nf-core/samtools/stats/samtools-stats.diff"
},
"seq2hla": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"]
},
"snpeff/download": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["cache_download_ensemblvep_snpeff"]
},
"snpeff/snpeff": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules", "vcf_annotate_snpeff"]
},
"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": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"]
},
"star/indexversion": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"]
},
"umitools/extract": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"],
"patch": "modules/nf-core/umitools/extract/umitools-extract.diff"
},
"untar": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"]
}
}
},
"subworkflows": {
"nf-core": {
"bam_markduplicates_picard": {
"branch": "master",
"git_sha": "1298fbd2004c2913d6682ce4a419647d97a8fc3f",
"installed_by": ["subworkflows"]
},
"bam_sort_stats_samtools": {
"branch": "master",
"git_sha": "156feda0cb6589cd29c04902004fa3b53bc00205",
"installed_by": ["fastq_align_star", "subworkflows"]
},
"bam_stats_samtools": {
"branch": "master",
"git_sha": "156feda0cb6589cd29c04902004fa3b53bc00205",
"installed_by": ["bam_markduplicates_picard", "bam_sort_stats_samtools"]
},
"cache_download_ensemblvep_snpeff": {
"branch": "master",
"git_sha": "09bae0b3db772c2d763e3cc1834c1370d0db1289",
"installed_by": ["subworkflows"]
},
"fastq_align_star": {
"branch": "master",
"git_sha": "4e3e10e502ec6ab6b1c4b4fecd923ff1fa287338",
"installed_by": ["subworkflows"]
},
"utils_annotation_cache": {
"branch": "master",
"git_sha": "4068160bf33db57f33793989e08cda44ba1fefbf",
"installed_by": ["subworkflows"]
},
"vcf_annotate_ensemblvep": {
"branch": "master",
"git_sha": "251885fdb29eca03523d326aca5c827d1f6bdfeb",
"installed_by": ["subworkflows"]
},
"vcf_annotate_snpeff": {
"branch": "master",
"git_sha": "54e41f4ed3aead45054380a9befeb927612ffc91",
"installed_by": ["subworkflows"]
}
}
}
}
}
}