Skip to content

Commit

Permalink
Create bcoexample_8.json
Browse files Browse the repository at this point in the history
  • Loading branch information
HadleyKing committed Jun 27, 2019
1 parent 6650510 commit 2bde021
Showing 1 changed file with 374 additions and 0 deletions.
374 changes: 374 additions & 0 deletions 8_gatk_Hemophilia/bcoexample_8.json
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"
]
}
}

0 comments on commit 2bde021

Please sign in to comment.