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modules.json
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234 lines (234 loc) · 11.2 KB
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{
"name": "dincalcilab/samurai",
"homePage": "https://github.com/dincalcilab/samurai",
"repos": {
"https://github.com/nf-core/modules.git": {
"modules": {
"nf-core": {
"bowtie2/align": {
"branch": "master",
"git_sha": "ecf739de71e6abe5690616b48a9cba924170e8f6",
"installed_by": ["fastq_align_dna"]
},
"bowtie2/build": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["fasta_index_dna"]
},
"bwa/index": {
"branch": "master",
"git_sha": "1c46359c837ef768b004519f535c30378e8289fc",
"installed_by": ["fasta_index_dna", "modules"]
},
"bwa/mem": {
"branch": "master",
"git_sha": "1c46359c837ef768b004519f535c30378e8289fc",
"installed_by": ["fastq_align_bwa", "fastq_align_dna", "modules"]
},
"bwamem2/index": {
"branch": "master",
"git_sha": "d86336f3e7ae0d5f76c67b0859409769cfeb2af2",
"installed_by": ["fasta_index_dna", "modules"]
},
"bwamem2/mem": {
"branch": "master",
"git_sha": "d86336f3e7ae0d5f76c67b0859409769cfeb2af2",
"installed_by": ["fastq_align_dna", "modules"]
},
"dragmap/align": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["fastq_align_dna"]
},
"dragmap/hashtable": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["fasta_index_dna"]
},
"fastp": {
"branch": "master",
"git_sha": "d9ec4ef289ad39b8a662a7a12be50409b11df84b",
"installed_by": ["fastq_trim_fastp_fastqc", "modules"]
},
"fastqc": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["fastq_trim_fastp_fastqc", "modules"]
},
"hmmcopy/readcounter": {
"branch": "master",
"git_sha": "3db80bad01d58d9977654212253a30af42c9fd48",
"installed_by": ["modules"]
},
"ichorcna/createpon": {
"branch": "master",
"git_sha": "a507bfc61c00fc9881f408c3fb1b375bb8078a81",
"installed_by": ["modules"]
},
"ichorcna/run": {
"branch": "master",
"git_sha": "a507bfc61c00fc9881f408c3fb1b375bb8078a81",
"installed_by": ["modules"]
},
"multiqc": {
"branch": "master",
"git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49",
"installed_by": ["modules"]
},
"picard/collecthsmetrics": {
"branch": "master",
"git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
"installed_by": ["bam_qc_picard"]
},
"picard/collectmultiplemetrics": {
"branch": "master",
"git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
"installed_by": ["bam_qc_picard"]
},
"picard/collectwgsmetrics": {
"branch": "master",
"git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
"installed_by": ["bam_qc_picard"]
},
"picard/markduplicates": {
"branch": "master",
"git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
"installed_by": ["bam_markduplicates_picard", "modules"]
},
"samtools/faidx": {
"branch": "master",
"git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
"installed_by": ["modules"]
},
"samtools/flagstat": {
"branch": "master",
"git_sha": "e334e12a1e985adc5ffc3fc78a68be1de711de45",
"installed_by": ["bam_stats_samtools", "modules"]
},
"samtools/idxstats": {
"branch": "master",
"git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
"installed_by": ["bam_stats_samtools", "modules"]
},
"samtools/index": {
"branch": "master",
"git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
"installed_by": ["bam_markduplicates_picard", "bam_sort_stats_samtools", "modules"]
},
"samtools/sort": {
"branch": "master",
"git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
"installed_by": ["bam_sort_stats_samtools", "modules"]
},
"samtools/stats": {
"branch": "master",
"git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
"installed_by": ["bam_stats_samtools", "modules"]
},
"samtools/view": {
"branch": "master",
"git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
"installed_by": ["modules"]
},
"snapaligner/align": {
"branch": "master",
"git_sha": "9a2df1234c202637503b0a3626ad5d118fa6a7ef",
"installed_by": ["fastq_align_dna"]
},
"snapaligner/index": {
"branch": "master",
"git_sha": "804078353d4a3c519411639d424853d046927d85",
"installed_by": ["fasta_index_dna"]
},
"strobealign": {
"branch": "master",
"git_sha": "c698799db60819ff8769000e429defad1cb432af",
"installed_by": ["fastq_align_dna"],
"patch": "modules/nf-core/strobealign/strobealign.diff"
},
"wisecondorx/convert": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["bam_cnv_wisecondorx", "modules"]
},
"wisecondorx/newref": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"wisecondorx/predict": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["bam_cnv_wisecondorx", "modules"],
"patch": "modules/nf-core/wisecondorx/predict/wisecondorx-predict.diff"
}
}
},
"subworkflows": {
"nf-core": {
"bam_cnv_wisecondorx": {
"branch": "master",
"git_sha": "1b63503190c38f85e8b041894ebaaf7ac3d22df6",
"installed_by": ["subworkflows"]
},
"bam_markduplicates_picard": {
"branch": "master",
"git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
"installed_by": ["subworkflows"]
},
"bam_qc_picard": {
"branch": "master",
"git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
"installed_by": ["subworkflows"]
},
"bam_sort_stats_samtools": {
"branch": "master",
"git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
"installed_by": ["fastq_align_bwa"]
},
"bam_stats_samtools": {
"branch": "master",
"git_sha": "e334e12a1e985adc5ffc3fc78a68be1de711de45",
"installed_by": ["bam_markduplicates_picard", "bam_sort_stats_samtools"]
},
"fasta_index_dna": {
"branch": "master",
"git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
"installed_by": ["subworkflows"],
"patch": "subworkflows/nf-core/fasta_index_dna/fasta_index_dna.diff"
},
"fastq_align_bwa": {
"branch": "master",
"git_sha": "1c46359c837ef768b004519f535c30378e8289fc",
"installed_by": ["subworkflows"]
},
"fastq_align_dna": {
"branch": "master",
"git_sha": "070ddae7fb59384d3d85bf69eb9a1d71ab33ada9",
"installed_by": ["subworkflows"]
},
"fastq_trim_fastp_fastqc": {
"branch": "master",
"git_sha": "d9ec4ef289ad39b8a662a7a12be50409b11df84b",
"installed_by": ["subworkflows"]
},
"utils_nextflow_pipeline": {
"branch": "master",
"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
"installed_by": ["subworkflows"]
},
"utils_nfcore_pipeline": {
"branch": "master",
"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
"installed_by": ["subworkflows"]
},
"utils_nfschema_plugin": {
"branch": "master",
"git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd",
"installed_by": ["subworkflows"]
}
}
}
}
}
}