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modules.json
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modules.json
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{
"name": "nf-core/rnaseq",
"homePage": "https://github.com/nf-core/rnaseq",
"repos": {
"https://github.com/nf-core/modules.git": {
"modules": {
"nf-core": {
"bbmap/bbsplit": {
"branch": "master",
"git_sha": "e228790f2957152ad2534e39abd7b3878963e89d",
"installed_by": ["modules"]
},
"cat/fastq": {
"branch": "master",
"git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
"installed_by": ["modules"]
},
"custom/dumpsoftwareversions": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"custom/getchromsizes": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"fastp": {
"branch": "master",
"git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd",
"installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
},
"fastqc": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["fastq_fastqc_umitools_trimgalore", "fastq_fastqc_umitools_fastp"]
},
"fq/subsample": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules", "fastq_subsample_fq_salmon"]
},
"gffread": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"gunzip": {
"branch": "master",
"git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
"installed_by": ["modules"]
},
"hisat2/align": {
"branch": "master",
"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
"installed_by": ["fastq_align_hisat2"]
},
"hisat2/build": {
"branch": "master",
"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
"installed_by": ["modules"]
},
"hisat2/extractsplicesites": {
"branch": "master",
"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
"installed_by": ["modules"]
},
"picard/markduplicates": {
"branch": "master",
"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
"installed_by": ["bam_markduplicates_picard"]
},
"preseq/lcextrap": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"qualimap/rnaseq": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"rsem/calculateexpression": {
"branch": "master",
"git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
"installed_by": ["modules"]
},
"rsem/preparereference": {
"branch": "master",
"git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
"installed_by": ["modules"]
},
"rseqc/bamstat": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["bam_rseqc"]
},
"rseqc/inferexperiment": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["bam_rseqc"]
},
"rseqc/innerdistance": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["bam_rseqc"]
},
"rseqc/junctionannotation": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["bam_rseqc"]
},
"rseqc/junctionsaturation": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["bam_rseqc"]
},
"rseqc/readdistribution": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["bam_rseqc"]
},
"rseqc/readduplication": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["bam_rseqc"]
},
"rseqc/tin": {
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["bam_rseqc"]
},
"salmon/index": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["fastq_subsample_fq_salmon"]
},
"salmon/quant": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules", "fastq_subsample_fq_salmon"]
},
"samtools/flagstat": {
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["bam_stats_samtools"]
},
"samtools/idxstats": {
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"installed_by": ["bam_stats_samtools"]
},
"samtools/index": {
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": [
"bam_markduplicates_picard",
"bam_sort_stats_samtools",
"bam_dedup_stats_samtools_umitools"
]
},
"samtools/sort": {
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"git_sha": "a0f7be95788366c1923171e358da7d049eb440f9",
"installed_by": ["bam_sort_stats_samtools"]
},
"samtools/stats": {
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"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
"installed_by": ["bam_stats_samtools"]
},
"sortmerna": {
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"star/align": {
"branch": "master",
"git_sha": "57d75dbac06812c59798a48585032f6e50bb1914",
"installed_by": ["modules"]
},
"star/genomegenerate": {
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},
"stringtie/stringtie": {
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"installed_by": ["modules"]
},
"subread/featurecounts": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"trimgalore": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["fastq_fastqc_umitools_trimgalore"]
},
"ucsc/bedclip": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["bedgraph_bedclip_bedgraphtobigwig"]
},
"ucsc/bedgraphtobigwig": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["bedgraph_bedclip_bedgraphtobigwig"]
},
"umitools/dedup": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["bam_dedup_stats_samtools_umitools"]
},
"umitools/extract": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"]
},
"untar": {
"branch": "master",
"git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
"installed_by": ["modules"]
}
}
},
"subworkflows": {
"nf-core": {
"bam_dedup_stats_samtools_umitools": {
"branch": "master",
"git_sha": "e228790f2957152ad2534e39abd7b3878963e89d",
"installed_by": ["subworkflows"]
},
"bam_markduplicates_picard": {
"branch": "master",
"git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
"installed_by": ["subworkflows"]
},
"bam_rseqc": {
"branch": "master",
"git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
"installed_by": ["subworkflows"]
},
"bam_sort_stats_samtools": {
"branch": "master",
"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
"installed_by": ["fastq_align_hisat2"]
},
"bam_stats_samtools": {
"branch": "master",
"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
"installed_by": [
"bam_markduplicates_picard",
"bam_sort_stats_samtools",
"bam_dedup_stats_samtools_umitools"
]
},
"bedgraph_bedclip_bedgraphtobigwig": {
"branch": "master",
"git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
"installed_by": ["subworkflows"]
},
"fastq_align_hisat2": {
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"installed_by": ["subworkflows"]
},
"fastq_fastqc_umitools_fastp": {
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"git_sha": "48dbb403fb2849b3d2c6c2e3eaaedbcca799428d",
"installed_by": ["subworkflows"]
},
"fastq_fastqc_umitools_trimgalore": {
"branch": "master",
"git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
"installed_by": ["subworkflows"]
},
"fastq_subsample_fq_salmon": {
"branch": "master",
"git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
"installed_by": ["subworkflows"]
}
}
}
}
}
}