-
Notifications
You must be signed in to change notification settings - Fork 12
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
6650510
commit 2bde021
Showing
1 changed file
with
374 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,374 @@ | ||
{ | ||
"id": "obj.1298", | ||
"name": "Identification of recombinant antihemophilic factor VII [UniProt:P00451] inhibitor SNPs [SO:0000694] in human [taxID:9606] blood [UBERON:0000178] extracted from patients with hemophilia A [DOID:12134]", | ||
"title": "Identification of recombinant antihemophilic factor", | ||
"version": "1.0", | ||
"createdby": "[email protected]", | ||
"created": "Mar 12, 2017 16:50:32", | ||
"modified": "Jun 15, 2017 11:43:35", | ||
"digital_signature": "as243hgdfbvsh345354jnjhjfdf", | ||
"verification_status": "unreviewed", | ||
"publication_status": "draft", | ||
"usability_domain": [ | ||
"Identify SNPs [SO:0000694] that correlate with the development of an inhibitory response to recombinant antihemophilic factor VII [UniProt:P00451] in patients with hemophilia A [DOID:12134]" | ||
], | ||
"authors": [ | ||
{ | ||
"orcid": "0000-0003-1409-4549" | ||
}, | ||
{ | ||
"name": "Joe Mcgill" | ||
} | ||
], | ||
"description_domain": { | ||
"keywords": [ | ||
"hemophilia A", | ||
"recombinant antihemophilic factor VII", | ||
"SNPs" | ||
], | ||
"xref": [ | ||
"taxID:9606 ", | ||
"UBERON:0000178 ", | ||
"DB:00025 ", | ||
"SO:0000694", | ||
"UniProt:P00451" | ||
], | ||
"pipeline_steps": [ | ||
{ | ||
"tool_name": "samtools_faidx", | ||
"tool_desc": "Index reference sequence in the FASTA format", | ||
"tool_version": "0.1.19-96b5f2294a", | ||
"tool_package": "", | ||
"step_number": "1", | ||
"input_uri_list": [ | ||
"ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/technical/reference/human_g1k_v37.fasta.gz" | ||
], | ||
"output_uri_list": [ | ||
"./biocompute/human_g1k_v37.fasta" | ||
] | ||
}, | ||
{ | ||
"tool_name": "picard_CreateSequenceDictionary", | ||
"tool_desc": "Creates a sequence dictionary for a reference sequence", | ||
"tool_version": "v2.6.0", | ||
"tool_package": "", | ||
"step_number": "2", | ||
"input_uri_list": [ | ||
"ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/technical/reference/human_g1k_v37.fasta.gz" | ||
], | ||
"output_uri_list": [ | ||
"home/jmcgill/Desktop/biocompute/human_g1k_v37.dict" | ||
] | ||
}, | ||
{ | ||
"tool_name": "samtools_sort", | ||
"tool_desc": "Sort alignments by leftmost coordinates", | ||
"tool_version": "", | ||
"tool_package": "", | ||
"step_number": "3", | ||
"input_uri_list": [ | ||
"./bam_files/biocompute/B_S30.bam", | ||
"./bam_files/biocompute/C_S31.bam", | ||
"./bam_files/biocompute/D_S32.bam", | ||
"./bam_files/biocompute/Hai003_S3.bam", | ||
"./bam_files/biocompute/Hai004_S4.bam", | ||
"./bam_files/biocompute/Hai006_S6.bam", | ||
"./bam_files/biocompute/Hai007_S7.bam", | ||
"./bam_files/biocompute/Hai012_S41.bam", | ||
"./bam_files/biocompute/Hawi010_S16.bam", | ||
"./bam_files/biocompute/Hawi015_S21.bam", | ||
"./bam_files/biocompute/Hawi028_S35.bam", | ||
"./bam_files/biocompute/Hawi032_S39.bam" | ||
], | ||
"output_uri_list": [ | ||
"/home/biocompute/B_S30.bam_sorted", | ||
"/home/biocompute/C_S31.bam_sorted", | ||
"/home/biocompute/D_S32.bam_sorted", | ||
"/home/biocompute/Hai003_S3.bam_sorted", | ||
"/home/biocompute/Hai004_S4.bam_sorted", | ||
"/home/biocompute/Hai006_S6.bam_sorted", | ||
"/home/biocompute/Hai007_S7.bam_sorted", | ||
"/home/biocompute/Hai012_S41.bam_sorted", | ||
"/home/biocompute/Hawi010_S16.bam_sorted", | ||
"/home/biocompute/Hawi015_S21.bam_sorted", | ||
"/home/biocompute/Hawi028_S35.bam_sorted", | ||
"/home/biocompute/Hawi032_S39.bam_so" | ||
] | ||
}, | ||
{ | ||
"tool_name": "picard_MarkDuplicates", | ||
"tool_desc": "This tool locates and tags duplicate reads in a BAM or SAM file", | ||
"tool_version": "0.1.19-96b5f2294a", | ||
"tool_package": "", | ||
"step_number": "4", | ||
"input_uri_list": [ | ||
"B_sorted.bam", | ||
"C_sorted.bam", | ||
"D_sorted.bam", | ||
"Hai003_sorted.bam", | ||
"Hai004_sorted.bam", | ||
"Hai006_sorted.bam", | ||
"Hai007_sorted.bam", | ||
"Hai012_sorted.bam", | ||
"Hawi010_sorted.bam", | ||
"Hawi015_sorted.bam", | ||
"Hawi028_sorted.bam", | ||
"Hawi032_sorted.bam" | ||
], | ||
"output_uri_list": [ | ||
"new_B_mark_duplicates.bam", | ||
"new_C_mark_duplicates.bam", | ||
"new_D_mark_duplicates.bam", | ||
"new_Hai003_mark_duplicates.bam", | ||
"new_Hai004_mark_duplicates.bam", | ||
"new_Hai006_mark_duplicates.bam", | ||
"new_Hai007_mark_duplicates.bam", | ||
"new_Hai012_mark_duplicates.bam", | ||
"new_Hawi010_mark_duplicates.bam", | ||
"new_Hawi015_mark_duplicates.bam", | ||
"new_Hawi028_mark_duplicates.bam", | ||
"new_Hawi032_mark_duplicates.bam", | ||
"B.txt", | ||
"C.txt", | ||
"D.txt", | ||
"Hai003.txt", | ||
"Hai004.txt", | ||
"Hai006.txt", | ||
"Hai007.txt", | ||
"Hai012.txt", | ||
"Hawi010.txt", | ||
"Hawi015.txt", | ||
"Hawi028.txt", | ||
"Hawi032.txt" | ||
] | ||
}, | ||
{ | ||
"tool_name": "picard_AddOrReplaceReadGroups", | ||
"tool_desc": "Replace read groups in a BAM file", | ||
"tool_version": "0.1.19-96b5f2294a", | ||
"tool_package": "", | ||
"step_number": "5", | ||
"input_uri_list": [ | ||
"new_B_mark_duplicates.bam", | ||
"new_C_mark_duplicates.bam", | ||
"new_D_mark_duplicates.bam", | ||
"new_Hai003_mark_duplicates.bam", | ||
"new_Hai004_mark_duplicates.bam", | ||
"new_Hai006_mark_duplicates.bam", | ||
"new_Hai007_mark_duplicates.bam", | ||
"new_Hai012_mark_duplicates.bam", | ||
"new_Hawi010_mark_duplicates.bam", | ||
"new_Hawi015_mark_duplicates.bam", | ||
"new_Hawi028_mark_duplicates.bam", | ||
"new_Hawi032_mark_duplicates.bam" | ||
], | ||
"output_uri_list": [ | ||
"with_header_new_B_mark_duplicates.bam", | ||
"with_header_new_C_mark_duplicates.bam", | ||
"with_header_new_D_mark_duplicates.bam", | ||
"with_header_new_Hai003_mark_duplicates.bam", | ||
"with_header_new_Hai004_mark_duplicates.bam", | ||
"with_header_new_Hai006_mark_duplicates.bam", | ||
"with_header_new_Hai007_mark_duplicates.bam", | ||
"with_header_new_Hai012_mark_duplicates.bam", | ||
"with_header_new_Hawi010_mark_duplicates.bam", | ||
"with_header_new_Hawi015_mark_duplicates.bam", | ||
"with_header_new_Hawi028_mark_duplicates.bam", | ||
"with_header_new_Hawi032_mark_duplicates.bam" | ||
] | ||
}, | ||
{ | ||
"tool_name": "GenomeAnalysisTK_RealignerTargetCreator", | ||
"tool_desc": "Determining (small) suspicious intervals which are likely in need of realignment", | ||
"tool_version": "3.7-0-gcfedb67", | ||
"tool_package": "", | ||
"step_number": "6", | ||
"input_uri_list": [ | ||
"./biocompute/human_g1k_v37.fasta", | ||
"with_header_new_B_mark_duplicates.bam", | ||
"with_header_new_C_mark_duplicates.bam", | ||
"with_header_new_D_mark_duplicates.bam", | ||
"with_header_new_Hai003_mark_duplicates.bam", | ||
"with_header_new_Hai004_mark_duplicates.bam", | ||
"with_header_new_Hai006_mark_duplicates.bam", | ||
"with_header_new_Hai007_mark_duplicates.bam", | ||
"with_header_new_Hai012_mark_duplicates.bam", | ||
"with_header_new_Hawi010_mark_duplicates.bam", | ||
"with_header_new_Hawi015_mark_duplicates.bam", | ||
"with_header_new_Hawi028_mark_duplicates.bam", | ||
"with_header_new_Hawi032_mark_duplicates.bam" | ||
], | ||
"output_uri_list": [ | ||
"realignedB.list", | ||
"realignedC.list", | ||
"realignedD.list", | ||
"realignedHai003.list", | ||
"realignedHai004.list", | ||
"realignedHai006.list", | ||
"realignedHai007.list", | ||
"realignedHai012.list", | ||
"realignedHawi010.list", | ||
"realignedHawi015.list", | ||
"realignedHawi028.list", | ||
"realignedHawi032.list" | ||
] | ||
}, | ||
{ | ||
"tool_name": "GenomeAnalysisTK_IndelRealigner", | ||
"tool_desc": "Perform local realignment of reads around indels", | ||
"tool_version": "3.7-0-gcfedb67", | ||
"tool_package": "", | ||
"step_number": "7", | ||
"input_uri_list": [ | ||
"./biocompute/human_g1k_v37.fasta", | ||
"with_header_new_B_mark_duplicates.bam-targetIntervals", | ||
"with_header_new_C_mark_duplicates.bam-targetIntervals", | ||
"with_header_new_D_mark_duplicates.bam-targetIntervals", | ||
"with_header_new_Hai003_mark_duplicates.bam-targetIntervals", | ||
"with_header_new_Hai004_mark_duplicates.bam-targetIntervals", | ||
"with_header_new_Hai006_mark_duplicates.bam-targetIntervals", | ||
"with_header_new_Hai007_mark_duplicates.bam-targetIntervals", | ||
"with_header_new_Hai012_mark_duplicates.bam-targetIntervals", | ||
"with_header_new_Hawi010_mark_duplicates.bam-targetIntervals", | ||
"with_header_new_Hawi015_mark_duplicates.bam-targetIntervals", | ||
"with_header_new_Hawi028_mark_duplicates.bam-targetIntervals", | ||
"with_header_new_Hawi032_mark_duplicates.bam-targetIntervals", | ||
"realignedB.list", | ||
"realignedC.list", | ||
"realignedD.list", | ||
"realignedHai003.list", | ||
"realignedHai004.list", | ||
"realignedHai006.list", | ||
"realignedHai007.list", | ||
"realignedHai012.list", | ||
"realignedHawi010.list", | ||
"realignedHawi015.list", | ||
"realignedHawi028.list", | ||
"realignedHawi032.list" | ||
], | ||
"output_uri_list": [ | ||
"B_realigned_reads.bam", | ||
"C_realigned_reads.bam", | ||
"D_realigned_reads.bam", | ||
"Hai003_realigned_reads.bam", | ||
"Hai004_realigned_reads.bam", | ||
"Hai006_realigned_reads.bam", | ||
"Hai007_realigned_reads.bam", | ||
"Hai012_realigned_reads.bam", | ||
"Hawi010_realigned_reads.bam", | ||
"Hawi015_realigned_reads.bam", | ||
"Hawi028_realigned_reads.bam", | ||
"Hawi032_realigned_reads.bam" | ||
] | ||
}, | ||
{ | ||
"tool_name": "GenomeAnalysisTK_HaplotypeCaller", | ||
"tool_desc": "Perform local realignment of reads around indels", | ||
"tool_version": "3.7-0-gcfedb67", | ||
"tool_package": "", | ||
"step_number": "8", | ||
"input_uri_list": [ | ||
"B_realigned_reads.bam", | ||
"C_realigned_reads.bam", | ||
"D_realigned_reads.bam", | ||
"Hai003_realigned_reads.bam", | ||
"Hai004_realigned_reads.bam", | ||
"Hai006_realigned_reads.bam", | ||
"Hai007_realigned_reads.bam", | ||
"Hai012_realigned_reads.bam", | ||
"Hawi010_realigned_reads.bam", | ||
"Hawi015_realigned_reads.bam", | ||
"Hawi028_realigned_reads.bam", | ||
"Hawi032_realigned_reads.bam" | ||
], | ||
"output_uri_list": [ | ||
"B_gatk_raw_snps.vcf", | ||
"C_gatk_raw_snps.vcf", | ||
"D_gatk_raw_snps.vcf", | ||
"Hai003_gatk_raw_snps.vcf", | ||
"Hai004_gatk_raw_snps.vcf", | ||
"Hai006_gatk_raw_snps.vcf", | ||
"Hai007_gatk_raw_snps.vcf", | ||
"Hai012_gatk_raw_snps.vcf", | ||
"Hawi010_gatk_raw_snps.vcf", | ||
"Hawi015_gatk_raw_snps.vcf", | ||
"Hawi028_gatk_raw_snps.vcf", | ||
"Hawi032_gatk_raw_snps.vcf" | ||
] | ||
} | ||
] | ||
}, | ||
"execution_domain": { | ||
"script": "https://github.com/biocompute-objects//HTS-CSRS/tree/master/8_gatk_Hemophilia/make_vcfs.py", | ||
"pipeline_version": "1.0", | ||
"platform": "linux", | ||
"driver": "Python 2.7.10", | ||
"software_prerequisites": [ | ||
{ | ||
"name": "GenomAnalysisToolKit", | ||
"version": "3.6" | ||
}, | ||
{ | ||
"name": "Picard", | ||
"version": "v2.6.0" | ||
}, | ||
{ | ||
"name": "samtools", | ||
"version": "v0.1.19-96b5f2294a" | ||
}, | ||
{ | ||
"name": "Python", | ||
"version": "2.7.10" | ||
} | ||
], | ||
"domain_prerequisites": [ | ||
{ | ||
"url": "ftp://:22/", | ||
"name": "access to ftp" | ||
} | ||
], | ||
"env_parameters": [ | ||
"10 GB memory required" | ||
], | ||
"script_type": "URI" | ||
}, | ||
"parametric_domain": { | ||
"picard_MarkDuplicates_REMOVE_DUPLICATES": "no", | ||
"picard_AddOrReplaceReadGroups_ReadGroupPlatform": "illumina", | ||
"GenomeAnalysisTK_HaplotypeCaller_Intervals": "X", | ||
"GenomeAnalysisTK_RealignerTargetCreator_Num_threads": "22" | ||
}, | ||
"io_domain": { | ||
"reference_uri_list": [ | ||
"ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/technical/reference/human_g1k_v37.fasta.gz" | ||
], | ||
"input_uri_list": [ | ||
"B_gatk_raw_snps.vcf", | ||
"C_gatk_raw_snps.vcf", | ||
"D_gatk_raw_snps.vcf", | ||
"Hai003_gatk_raw_snps.vcf", | ||
"Hai004_gatk_raw_snps.vcf", | ||
"Hai006_gatk_raw_snps.vcf", | ||
"Hai007_gatk_raw_snps.vcf", | ||
"Hai012_gatk_raw_snps.vcf", | ||
"Hawi010_gatk_raw_snps.vcf", | ||
"Hawi015_gatk_raw_snps.vcf", | ||
"Hawi028_gatk_raw_snps.vcf", | ||
"Hawi032_gatk_raw_snps.vcf" | ||
], | ||
"output_uri_list": [ | ||
"./B_S30.bam", | ||
"./C_S31.bam", | ||
"./D_S32.bam", | ||
"./Hai003_S3.bam", | ||
"./Hai004_S4.bam", | ||
"./Hai006_S6.bam", | ||
"./Hai007_S7.bam", | ||
"./Hai012_S41.bam", | ||
"./Hawi010_S16.bam", | ||
"./Hawi015_S21.bam", | ||
"./Hawi028_S35.bam", | ||
"./Hawi032_S39.bam" | ||
] | ||
} | ||
} |