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modules.json
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{
"name": "nf-core/riboseq",
"homePage": "/~https://github.com/nf-core/riboseq",
"repos": {
"/~https://github.com/nf-core/modules.git": {
"modules": {
"nf-core": {
"anota2seq/anota2seqrun": {
"branch": "master",
"git_sha": "916b5fb9713d6f1a02e9a7c565e430ae0d647b9f",
"installed_by": ["modules"]
},
"bbmap/bbsplit": {
"branch": "master",
"git_sha": "ecc2139bc014be1d0117d6c69458d82fbfa3328f",
"installed_by": ["preprocess_rnaseq"]
},
"cat/fastq": {
"branch": "master",
"git_sha": "0997b47c93c06b49aa7b3fefda87e728312cf2ca",
"installed_by": ["preprocess_rnaseq"]
},
"custom/catadditionalfasta": {
"branch": "master",
"git_sha": "ba6ec49354837595649acd84e7a867d59bf11ad0",
"installed_by": ["modules"]
},
"custom/getchromsizes": {
"branch": "master",
"git_sha": "1b0ffa4e5aed5b7e3cd4311af31bd3b2c8345051",
"installed_by": ["modules"]
},
"custom/tx2gene": {
"branch": "master",
"git_sha": "ec155021a9104441bf6a9bae3b55d1b5b0bfdb3a",
"installed_by": ["quantify_pseudo_alignment"]
},
"cutadapt": {
"branch": "master",
"git_sha": "6618151ed69274863dc6fe6d2920afa90abaca1f",
"installed_by": ["modules"]
},
"fastp": {
"branch": "master",
"git_sha": "95cf5fe0194c7bf5cb0e3027a2eb7e7c89385080",
"installed_by": ["fastq_fastqc_umitools_fastp"]
},
"fastqc": {
"branch": "master",
"git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
"installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"]
},
"fq/subsample": {
"branch": "master",
"git_sha": "59d1faf07ace4f7a00f7fa7778bce4e1f1dcdd63",
"installed_by": ["fastq_subsample_fq_salmon"]
},
"gffread": {
"branch": "master",
"git_sha": "b1b959609bda44341120aed1766329909f54b8d0",
"installed_by": ["modules"]
},
"gunzip": {
"branch": "master",
"git_sha": "3a5fef109d113b4997c9822198664ca5f2716208",
"installed_by": ["modules"]
},
"kallisto/index": {
"branch": "master",
"git_sha": "de5811dd9ca15af1e131806001bcaae909e42021",
"installed_by": ["modules"]
},
"kallisto/quant": {
"branch": "master",
"git_sha": "de5811dd9ca15af1e131806001bcaae909e42021",
"installed_by": ["quantify_pseudo_alignment"]
},
"multiqc": {
"branch": "master",
"git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
"installed_by": ["modules"]
},
"ribotish/predict": {
"branch": "master",
"git_sha": "d3039382e6943ee8e80016a1e8d7c0f79e21e31e",
"installed_by": ["modules"]
},
"ribotish/quality": {
"branch": "master",
"git_sha": "d3039382e6943ee8e80016a1e8d7c0f79e21e31e",
"installed_by": ["modules"]
},
"ribotricer/detectorfs": {
"branch": "master",
"git_sha": "eef39ece87292a7e11d7f52eec165dbb6e5b696a",
"installed_by": ["modules"]
},
"ribotricer/prepareorfs": {
"branch": "master",
"git_sha": "db0c1159f2d90a0e0ee6753f7299b4ec68439c39",
"installed_by": ["modules"]
},
"rsem/preparereference": {
"branch": "master",
"git_sha": "301b088c7e9e00c4c80686411383f07173b54d69",
"installed_by": ["modules"]
},
"salmon/index": {
"branch": "master",
"git_sha": "ffc101e1b84ef3df2e4e4a966e84b3c513ae5693",
"installed_by": ["fastq_subsample_fq_salmon"]
},
"salmon/quant": {
"branch": "master",
"git_sha": "03a8562231d575c313266c193a980594b941e3ea",
"installed_by": ["fastq_subsample_fq_salmon", "quantify_pseudo_alignment"]
},
"samtools/flagstat": {
"branch": "master",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["bam_stats_samtools"]
},
"samtools/idxstats": {
"branch": "master",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["bam_stats_samtools"]
},
"samtools/index": {
"branch": "master",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["bam_dedup_stats_samtools_umitools", "bam_sort_stats_samtools"]
},
"samtools/sort": {
"branch": "master",
"git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26",
"installed_by": ["bam_sort_stats_samtools"]
},
"samtools/stats": {
"branch": "master",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["bam_stats_samtools"]
},
"sortmerna": {
"branch": "master",
"git_sha": "df05c8db5195867c0bc7b92c1788115b66f0d17d",
"installed_by": ["preprocess_rnaseq"]
},
"star/align": {
"branch": "master",
"git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9",
"installed_by": ["fastq_align_star"]
},
"star/genomegenerate": {
"branch": "master",
"git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9",
"installed_by": ["modules"]
},
"summarizedexperiment/summarizedexperiment": {
"branch": "master",
"git_sha": "31751460f9ce9552846e13fdeec6953dcb47132d",
"installed_by": ["quantify_pseudo_alignment"]
},
"trimgalore": {
"branch": "master",
"git_sha": "a98418419ae6c9df3cf6cf108d1e1aba71037d5a",
"installed_by": ["fastq_fastqc_umitools_trimgalore"]
},
"tximeta/tximport": {
"branch": "master",
"git_sha": "c275c3baac6df8f0c7c500760a0cf014ce7b525d",
"installed_by": ["quantify_pseudo_alignment"]
},
"umitools/dedup": {
"branch": "master",
"git_sha": "3bd4f34e3093c2a16e6a8eefc22242b9b94641db",
"installed_by": ["bam_dedup_stats_samtools_umitools"]
},
"umitools/extract": {
"branch": "master",
"git_sha": "d2c5e76f291379f3dd403e48e46ed7e6ba5da744",
"installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"]
},
"umitools/prepareforrsem": {
"branch": "master",
"git_sha": "fac6cc9b2bc4042225bd9247ec03b413f764b47f",
"installed_by": ["modules"]
},
"untar": {
"branch": "master",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
"installed_by": ["modules"]
}
}
},
"subworkflows": {
"nf-core": {
"bam_dedup_stats_samtools_umitools": {
"branch": "master",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["subworkflows"]
},
"bam_sort_stats_samtools": {
"branch": "master",
"git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26",
"installed_by": ["fastq_align_star"]
},
"bam_stats_samtools": {
"branch": "master",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["bam_dedup_stats_samtools_umitools", "bam_sort_stats_samtools"]
},
"fastq_align_star": {
"branch": "master",
"git_sha": "1d1d7df613ff53223259c14185858cd742cd4743",
"installed_by": ["subworkflows"]
},
"fastq_fastqc_umitools_fastp": {
"branch": "master",
"git_sha": "cabcc0dadf8366aa7a9930066a7b3dd90d9825d5",
"installed_by": ["preprocess_rnaseq"]
},
"fastq_fastqc_umitools_trimgalore": {
"branch": "master",
"git_sha": "cb6defa0834eda9d6d3f967e981c819fc3e257bf",
"installed_by": ["preprocess_rnaseq"]
},
"fastq_subsample_fq_salmon": {
"branch": "master",
"git_sha": "003920c7f9a8ae19b69a97171922880220bedf56",
"installed_by": ["preprocess_rnaseq"]
},
"preprocess_rnaseq": {
"branch": "master",
"git_sha": "8aa7040ca55a511ee4bc079803a8446db00f34c8",
"installed_by": ["subworkflows"]
},
"quantify_pseudo_alignment": {
"branch": "master",
"git_sha": "bca4985339b3ba879f457565806deb2377873b83",
"installed_by": ["subworkflows"]
},
"utils_nextflow_pipeline": {
"branch": "master",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
"installed_by": ["subworkflows"]
},
"utils_nfcore_pipeline": {
"branch": "master",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
"installed_by": ["subworkflows"]
},
"utils_nfvalidation_plugin": {
"branch": "master",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
"installed_by": ["subworkflows"]
}
}
}
}
}
}