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Copy pathmodules.json
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285 lines (285 loc) · 13.8 KB
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{
"name": "nf-core/methylseq",
"homePage": "https://github.com/nf-core/methylseq",
"repos": {
"https://github.com/nf-core/modules.git": {
"modules": {
"nf-core": {
"bedtools/intersect": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"bismark/align": {
"branch": "master",
"git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
"installed_by": ["fastq_align_dedup_bismark"]
},
"bismark/coverage2cytosine": {
"branch": "master",
"git_sha": "107a3fb196ca4a174614d50d928739156a3c0f6c",
"installed_by": ["fastq_align_dedup_bismark"]
},
"bismark/deduplicate": {
"branch": "master",
"git_sha": "107a3fb196ca4a174614d50d928739156a3c0f6c",
"installed_by": ["fastq_align_dedup_bismark"]
},
"bismark/genomepreparation": {
"branch": "master",
"git_sha": "107a3fb196ca4a174614d50d928739156a3c0f6c",
"installed_by": ["fasta_index_bismark_bwameth", "fasta_index_methylseq"]
},
"bismark/methylationextractor": {
"branch": "master",
"git_sha": "107a3fb196ca4a174614d50d928739156a3c0f6c",
"installed_by": ["fastq_align_dedup_bismark"]
},
"bismark/report": {
"branch": "master",
"git_sha": "107a3fb196ca4a174614d50d928739156a3c0f6c",
"installed_by": ["fastq_align_dedup_bismark"]
},
"bismark/summary": {
"branch": "master",
"git_sha": "107a3fb196ca4a174614d50d928739156a3c0f6c",
"installed_by": ["fastq_align_dedup_bismark"]
},
"bwa/index": {
"branch": "master",
"git_sha": "1c46359c837ef768b004519f535c30378e8289fc",
"installed_by": ["fasta_index_methylseq"]
},
"bwa/mem": {
"branch": "master",
"git_sha": "1c46359c837ef768b004519f535c30378e8289fc",
"installed_by": ["fastq_align_bwa"]
},
"bwameth/align": {
"branch": "master",
"git_sha": "96d9a187355d26f9a5e0380f8b59c7005d073268",
"installed_by": ["fastq_align_dedup_bwameth"]
},
"bwameth/index": {
"branch": "master",
"git_sha": "79f1c3e487520405be6dd47ed7f196efd1e3b63e",
"installed_by": ["fasta_index_bismark_bwameth", "fasta_index_methylseq"]
},
"cat/fastq": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"fastqc": {
"branch": "master",
"git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
"installed_by": ["modules"]
},
"gunzip": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["fasta_index_bismark_bwameth", "fasta_index_methylseq"]
},
"methyldackel/extract": {
"branch": "master",
"git_sha": "c8df5757c72362907a43de49a6b20bd4998907a0",
"installed_by": ["bam_methyldackel", "fastq_align_dedup_bwameth"]
},
"methyldackel/mbias": {
"branch": "master",
"git_sha": "c8df5757c72362907a43de49a6b20bd4998907a0",
"installed_by": ["bam_methyldackel", "fastq_align_dedup_bwameth"]
},
"multiqc": {
"branch": "master",
"git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
"installed_by": ["modules"]
},
"parabricks/fq2bammeth": {
"branch": "master",
"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
"installed_by": ["fastq_align_dedup_bwameth"]
},
"picard/addorreplacereadgroups": {
"branch": "master",
"git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
"installed_by": ["fastq_align_dedup_bwamem"]
},
"picard/bedtointervallist": {
"branch": "master",
"git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
"installed_by": ["modules"]
},
"picard/collecthsmetrics": {
"branch": "master",
"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
"installed_by": ["modules"]
},
"picard/createsequencedictionary": {
"branch": "master",
"git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
"installed_by": ["modules"]
},
"picard/markduplicates": {
"branch": "master",
"git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
"installed_by": ["fastq_align_dedup_bwamem", "fastq_align_dedup_bwameth"]
},
"preseq/lcextrap": {
"branch": "master",
"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
"installed_by": ["modules"]
},
"qualimap/bamqc": {
"branch": "master",
"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
"installed_by": ["modules"]
},
"qualimap/bamqccram": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"rastair/call": {
"branch": "master",
"git_sha": "20ff6c8d298d29bc00d3ef11cda614dac5f77ce8",
"installed_by": ["bam_taps_conversion"]
},
"rastair/mbias": {
"branch": "master",
"git_sha": "20ff6c8d298d29bc00d3ef11cda614dac5f77ce8",
"installed_by": ["bam_taps_conversion"]
},
"rastair/mbiasparser": {
"branch": "master",
"git_sha": "a4f1768a3026017b92a7e5d1c8b0fb9ac3efa3a9",
"installed_by": ["bam_taps_conversion"]
},
"rastair/methylkit": {
"branch": "master",
"git_sha": "0dca361fb441760fb333467b3f5800d34490fb86",
"installed_by": ["bam_taps_conversion"]
},
"samtools/faidx": {
"branch": "master",
"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
"installed_by": ["fasta_index_bismark_bwameth", "fasta_index_methylseq"]
},
"samtools/flagstat": {
"branch": "master",
"git_sha": "e334e12a1e985adc5ffc3fc78a68be1de711de45",
"installed_by": ["bam_stats_samtools", "fastq_align_dedup_bwameth"]
},
"samtools/idxstats": {
"branch": "master",
"git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
"installed_by": ["bam_stats_samtools"]
},
"samtools/index": {
"branch": "master",
"git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
"installed_by": [
"bam_sort_stats_samtools",
"fastq_align_dedup_bismark",
"fastq_align_dedup_bwamem",
"fastq_align_dedup_bwameth"
]
},
"samtools/sort": {
"branch": "master",
"git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
"installed_by": [
"bam_sort_stats_samtools",
"fastq_align_dedup_bismark",
"fastq_align_dedup_bwameth"
]
},
"samtools/stats": {
"branch": "master",
"git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
"installed_by": ["bam_stats_samtools", "fastq_align_dedup_bwameth"]
},
"trimgalore": {
"branch": "master",
"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
"installed_by": ["modules"]
},
"untar": {
"branch": "master",
"git_sha": "00ee87ebb541af0008596400ce6d5f66d79d5408",
"installed_by": ["fasta_index_bismark_bwameth", "fasta_index_methylseq"]
}
}
},
"subworkflows": {
"nf-core": {
"bam_methyldackel": {
"branch": "master",
"git_sha": "c8df5757c72362907a43de49a6b20bd4998907a0",
"installed_by": ["subworkflows"]
},
"bam_sort_stats_samtools": {
"branch": "master",
"git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
"installed_by": ["fastq_align_bwa"]
},
"bam_stats_samtools": {
"branch": "master",
"git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
"installed_by": ["bam_sort_stats_samtools"]
},
"bam_taps_conversion": {
"branch": "master",
"git_sha": "a4f1768a3026017b92a7e5d1c8b0fb9ac3efa3a9",
"installed_by": ["subworkflows"]
},
"fasta_index_bismark_bwameth": {
"branch": "master",
"git_sha": "107a3fb196ca4a174614d50d928739156a3c0f6c",
"installed_by": ["subworkflows"]
},
"fasta_index_methylseq": {
"branch": "master",
"git_sha": "654daca6c7d8a17479d1c56fb5fb8d1663f11428",
"installed_by": ["subworkflows"]
},
"fastq_align_bwa": {
"branch": "master",
"git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
"installed_by": ["fastq_align_dedup_bwamem"]
},
"fastq_align_dedup_bismark": {
"branch": "master",
"git_sha": "654daca6c7d8a17479d1c56fb5fb8d1663f11428",
"installed_by": ["subworkflows"]
},
"fastq_align_dedup_bwamem": {
"branch": "master",
"git_sha": "654daca6c7d8a17479d1c56fb5fb8d1663f11428",
"installed_by": ["subworkflows"]
},
"fastq_align_dedup_bwameth": {
"branch": "master",
"git_sha": "654daca6c7d8a17479d1c56fb5fb8d1663f11428",
"installed_by": ["subworkflows"]
},
"utils_nextflow_pipeline": {
"branch": "master",
"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
"installed_by": ["subworkflows"]
},
"utils_nfcore_pipeline": {
"branch": "master",
"git_sha": "df4d1c8cdee98a1bbbed8fc51e82296568e0f9c1",
"installed_by": ["subworkflows"]
},
"utils_nfschema_plugin": {
"branch": "master",
"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
"installed_by": ["subworkflows"]
}
}
}
}
}
}