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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": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc",
"installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"]
},
"bedtools/genomecov": {
"branch": "master",
"git_sha": "bfa8975eefb8df3e480a44ac9e594f23f52b2963",
"installed_by": ["modules"],
"patch": "modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff"
},
"bracken/bracken": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"cat/fastq": {
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"git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc",
"installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"],
"patch": "modules/nf-core/cat/fastq/cat-fastq.diff"
},
"custom/catadditionalfasta": {
"branch": "master",
"git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc",
"installed_by": ["modules"]
},
"custom/getchromsizes": {
"branch": "master",
"git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
"installed_by": ["modules"]
},
"custom/tx2gene": {
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"git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
"installed_by": ["modules", "quantify_pseudo_alignment"]
},
"dupradar": {
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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},
"fastp": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
},
"fastqc": {
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"installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"]
},
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},
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},
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},
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},
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"multiqc": {
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},
"picard/markduplicates": {
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"patch": "modules/nf-core/picard/markduplicates/picard-markduplicates.diff"
},
"preseq/lcextrap": {
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"rsem/calculateexpression": {
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"rseqc/tin": {
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},
"samtools/flagstat": {
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},
"samtools/idxstats": {
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"installed_by": [
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"bam_markduplicates_picard",
"bam_sort_stats_samtools"
]
},
"samtools/sort": {
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"installed_by": ["bam_sort_stats_samtools"]
},
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},
"sortmerna": {
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"patch": "modules/nf-core/sortmerna/sortmerna.diff"
},
"star/align": {
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"installed_by": ["modules"],
"patch": "modules/nf-core/star/align/star-align.diff"
},
"star/genomegenerate": {
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},
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},
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},
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},
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]
},
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}
}
}
}