{
    "name": "nf-core/sarek",
    "homePage": "https://github.com/nf-core/sarek",
    "repos": {
        "https://github.com/nf-core/modules.git": {
            "modules": {
                "nf-core": {
                    "ascat": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "bcftools/annotate": {
                        "branch": "master",
                        "git_sha": "cb08035150685b11d890d90c9534d4f16869eaec",
                        "installed_by": ["modules"],
                        "patch": "modules/nf-core/bcftools/annotate/bcftools-annotate.diff"
                    },
                    "bcftools/concat": {
                        "branch": "master",
                        "git_sha": "d1e0ec7670fa77905a378627232566ce54c3c26d",
                        "installed_by": ["modules"]
                    },
                    "bcftools/mpileup": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["bam_ngscheckmate"]
                    },
                    "bcftools/sort": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "bcftools/stats": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "bwa/index": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "bwa/mem": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "bwamem2/index": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "bwamem2/mem": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "cat/cat": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "cat/fastq": {
                        "branch": "master",
                        "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc",
                        "installed_by": ["modules"]
                    },
                    "cnvkit/antitarget": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "cnvkit/batch": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "cnvkit/call": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "cnvkit/export": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "cnvkit/genemetrics": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "cnvkit/reference": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "controlfreec/assesssignificance": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"],
                        "patch": "modules/nf-core/controlfreec/assesssignificance/controlfreec-assesssignificance.diff"
                    },
                    "controlfreec/freec": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "controlfreec/freec2bed": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "controlfreec/freec2circos": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "controlfreec/makegraph2": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "deepvariant/rundeepvariant": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "dragmap/align": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"],
                        "patch": "modules/nf-core/dragmap/align/dragmap-align.diff"
                    },
                    "dragmap/hashtable": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"],
                        "patch": "modules/nf-core/dragmap/hashtable/dragmap-hashtable.diff"
                    },
                    "ensemblvep/download": {
                        "branch": "master",
                        "git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4",
                        "installed_by": ["modules"]
                    },
                    "ensemblvep/vep": {
                        "branch": "master",
                        "git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4",
                        "installed_by": ["modules", "vcf_annotate_ensemblvep"]
                    },
                    "fastp": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "fastqc": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "fgbio/callmolecularconsensusreads": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "fgbio/fastqtobam": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "fgbio/groupreadsbyumi": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "freebayes": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "gatk4/applybqsr": {
                        "branch": "master",
                        "git_sha": "6b3bf38285d94cc1ea3cd9fa93310d54b04c3819",
                        "installed_by": ["modules"]
                    },
                    "gatk4/applyvqsr": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "gatk4/baserecalibrator": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "gatk4/calculatecontamination": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "gatk4/cnnscorevariants": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "gatk4/createsequencedictionary": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "gatk4/estimatelibrarycomplexity": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "gatk4/filtermutectcalls": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "gatk4/filtervarianttranches": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "gatk4/gatherbqsrreports": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "gatk4/gatherpileupsummaries": {
                        "branch": "master",
                        "git_sha": "679f45cae4f603f12d7c38c042afee11150574a0",
                        "installed_by": ["modules"]
                    },
                    "gatk4/genomicsdbimport": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "gatk4/genotypegvcfs": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "gatk4/getpileupsummaries": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "gatk4/haplotypecaller": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "gatk4/intervallisttobed": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"],
                        "patch": "modules/nf-core/gatk4/intervallisttobed/gatk4-intervallisttobed.diff"
                    },
                    "gatk4/learnreadorientationmodel": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "gatk4/markduplicates": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "gatk4/mergemutectstats": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "gatk4/mergevcfs": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "gatk4/mutect2": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "gatk4/variantrecalibrator": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "gatk4spark/applybqsr": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "gatk4spark/baserecalibrator": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "gatk4spark/markduplicates": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "gawk": {
                        "branch": "master",
                        "git_sha": "97321eded31a12598837a476d3615300af413bb7",
                        "installed_by": ["modules"]
                    },
                    "goleft/indexcov": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "lofreq/callparallel": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "manta/germline": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "manta/somatic": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "manta/tumoronly": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "mosdepth": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "msisensorpro/msisomatic": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "msisensorpro/scan": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "multiqc": {
                        "branch": "master",
                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                        "installed_by": ["modules"]
                    },
                    "ngscheckmate/ncm": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["bam_ngscheckmate"]
                    },
                    "samblaster": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "samtools/bam2fq": {
                        "branch": "master",
                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                        "installed_by": ["modules"]
                    },
                    "samtools/collatefastq": {
                        "branch": "master",
                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                        "installed_by": ["modules"]
                    },
                    "samtools/convert": {
                        "branch": "master",
                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                        "installed_by": ["modules"]
                    },
                    "samtools/faidx": {
                        "branch": "master",
                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                        "installed_by": ["modules"]
                    },
                    "samtools/index": {
                        "branch": "master",
                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                        "installed_by": ["modules"]
                    },
                    "samtools/merge": {
                        "branch": "master",
                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                        "installed_by": ["modules"]
                    },
                    "samtools/mpileup": {
                        "branch": "master",
                        "git_sha": "13e7d1046922381df90cd8fe9bee8c3e57ae8457",
                        "installed_by": ["modules"]
                    },
                    "samtools/stats": {
                        "branch": "master",
                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                        "installed_by": ["modules"]
                    },
                    "samtools/view": {
                        "branch": "master",
                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                        "installed_by": ["modules"]
                    },
                    "sentieon/applyvarcal": {
                        "branch": "master",
                        "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d",
                        "installed_by": ["modules"]
                    },
                    "sentieon/bwamem": {
                        "branch": "master",
                        "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d",
                        "installed_by": ["modules"]
                    },
                    "sentieon/dedup": {
                        "branch": "master",
                        "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d",
                        "installed_by": ["modules"]
                    },
                    "sentieon/dnamodelapply": {
                        "branch": "master",
                        "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d",
                        "installed_by": ["modules"]
                    },
                    "sentieon/dnascope": {
                        "branch": "master",
                        "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d",
                        "installed_by": ["modules"]
                    },
                    "sentieon/gvcftyper": {
                        "branch": "master",
                        "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d",
                        "installed_by": ["modules"]
                    },
                    "sentieon/haplotyper": {
                        "branch": "master",
                        "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d",
                        "installed_by": ["modules"]
                    },
                    "sentieon/varcal": {
                        "branch": "master",
                        "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d",
                        "installed_by": ["modules"]
                    },
                    "snpeff/download": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "snpeff/snpeff": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules", "vcf_annotate_snpeff"]
                    },
                    "spring/decompress": {
                        "branch": "master",
                        "git_sha": "d7462e71f9129083ce10c3fe953ed401781e0ebd",
                        "installed_by": ["modules"]
                    },
                    "strelka/germline": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "strelka/somatic": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "svdb/merge": {
                        "branch": "master",
                        "git_sha": "eb2c3f7ee2c938ab1a49764bdb1319adaa35492c",
                        "installed_by": ["modules"]
                    },
                    "tabix/bgziptabix": {
                        "branch": "master",
                        "git_sha": "f448e846bdadd80fc8be31fbbc78d9f5b5131a45",
                        "installed_by": ["modules", "vcf_annotate_snpeff"]
                    },
                    "tabix/tabix": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules", "vcf_annotate_ensemblvep"]
                    },
                    "tiddit/sv": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "untar": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "unzip": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    },
                    "vcftools": {
                        "branch": "master",
                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                        "installed_by": ["modules"]
                    }
                }
            },
            "subworkflows": {
                "nf-core": {
                    "bam_ngscheckmate": {
                        "branch": "master",
                        "git_sha": "c60c14b285b89bdd0607e371417dadb80385ad6e",
                        "installed_by": ["subworkflows"]
                    },
                    "utils_nextflow_pipeline": {
                        "branch": "master",
                        "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",
                        "installed_by": ["subworkflows"]
                    },
                    "utils_nfcore_pipeline": {
                        "branch": "master",
                        "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba",
                        "installed_by": ["subworkflows"]
                    },
                    "utils_nfschema_plugin": {
                        "branch": "master",
                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
                        "installed_by": ["subworkflows"]
                    },
                    "vcf_annotate_ensemblvep": {
                        "branch": "master",
                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
                        "installed_by": ["subworkflows"]
                    },
                    "vcf_annotate_snpeff": {
                        "branch": "master",
                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
                        "installed_by": ["subworkflows"]
                    }
                }
            }
        }
    }
}
