From 86d5725186bfd546bdbaffda4b6d2c727ba7b592 Mon Sep 17 00:00:00 2001 From: hadley Date: Thu, 27 Jun 2019 10:10:26 -0400 Subject: [PATCH] schema update Schema update --- .DS_Store | Bin 0 -> 6148 bytes 10_SCA1/bcoexample_10.json | 28 +- 1_HCV1a/bcoexample_1.json | 266 +++++----- 2_Gut/bcoexample_2.json | 247 +++++----- 3_CAGrepeats/bcoexample_3.json | 24 +- 4_rnaSeqER-PR/bcoexample_4.json | 44 +- 5_viralScreening/bcoexample_5.json | 34 +- 6_clonalDisc/bcoexample_6.json | 329 +++++++------ 7_EGFR/bcoexample_7.json | 306 ++++++------ 8_gatk_Hemophilia/.DS_Store | Bin 0 -> 6148 bytes 8_gatk_Hemophilia/bcoexample_7.json | 360 -------------- 8_gatk_Hemophilia/bcoexample_8.json | 723 ++++++++++++++-------------- 9_WXSwf/bcoexample_9.json | 185 +++---- schema.v1.0/infered.json | 420 ++++++++++++++++ schema.v1.0/validate.py | 37 ++ 15 files changed, 1639 insertions(+), 1364 deletions(-) create mode 100644 .DS_Store create mode 100644 8_gatk_Hemophilia/.DS_Store delete mode 100644 8_gatk_Hemophilia/bcoexample_7.json create mode 100644 schema.v1.0/infered.json create mode 100755 schema.v1.0/validate.py diff --git a/.DS_Store b/.DS_Store new file mode 100644 index 0000000000000000000000000000000000000000..46387201a7c141efed4ccf0a8e8ec290a2f2e19e GIT binary patch literal 6148 zcmeHKy-ou$47Q=eNnJWJ<_Qq@2BA6z=Dt8_i|EkPRjOdlQ}7OqOw7C)pMOAi>UHRX z1hS?0b7DJ}e9|Q`5%K(aQxnaIs6rEDF-Am&M_m^lJOQ%K(b5B5(+kzme?w&LQ##O^ zw)9B-_22BC>czTi_q~mrh-|y2S?#(NBCGe0``5SS=k4iv+ir74^nQD^ir#|432F_*xceY41H4GgL1Ovgq4+C;OBs9V7SPb>(fYK5GD9>mW*iuVKPIAnS#Sk6{ zTPn~}*-H$zbc`pD%Z|m+(uuwJVE^)W@xuCb%%3!zI2(oz27-Yh1DDpF$^CzaUuLw( zAErbv7zhUb83R0N7R?-+^1JnDdvez%v?ZE|#1%0hum_I-bmSblQm6To*oe!H#ZYFE RaZLxtLqG`$6%70W17AhYFVFx0 literal 0 HcmV?d00001 diff --git a/10_SCA1/bcoexample_10.json b/10_SCA1/bcoexample_10.json index 4411c68..1e55f16 100644 --- a/10_SCA1/bcoexample_10.json +++ b/10_SCA1/bcoexample_10.json @@ -5,7 +5,11 @@ "version": "1.0", "createdby": "amandab2140@gwmail.gwu.edu", "created": "Feb 02, 2017 11:11:00", - "modified": "Feb 23, 2017 15:42:38", + "modified": "Feb 23, 2017 15:42:38", + "authors": [ + {"orcid": "0000-0003-1409-4549"}, + {"orcid": "0000-0002-9920-565X"} + ], "digital_signature": "", "verification_status": "unreviewed", "publication_status": "draft", @@ -18,10 +22,6 @@ "Full-penetrance: 39 and above CAG trinucleotide repeats." ], "description_domain": { - "authors": [ - {"orchid": "0000-0003-1409-4549"}, - {"orchid": "0000-0002-9920-565X"} - ], "xref":[ "taxID:9606", "DO:0050954", @@ -69,10 +69,24 @@ "pipeline_version": "0.2", "script": "https://hive.biochemistry.gwu.edu/workflows/antiviral_resistance_detection_hive.sh", "driver": "//hive.biochemistry.gwu.edu/hive-driver", - "prerequisites": [ + "software_prerequisites": [ {"name":"HIVE_hexagon","version":"1.3"}, {"name":"HIVE_heptagon","version":"1.3"} - ] + ], + "domain_prerequisites": [ + { + "url": "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/", + "name": "access to e-utils" + }, + { + "url": "ftp://:22/", + "name": "access to ftp" + } + ], + "env_parameters": [ + "HIVEv1.3" + ], + "script_type": "URI" }, "parametric_domain": { "trinucleotide_count_file": "36" diff --git a/1_HCV1a/bcoexample_1.json b/1_HCV1a/bcoexample_1.json index 1ae3492..be042f9 100644 --- a/1_HCV1a/bcoexample_1.json +++ b/1_HCV1a/bcoexample_1.json @@ -1,136 +1,132 @@ { - 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], - "authors": [ - { - "orcid": "0000-0003-1409-4549" - }, - { - "name": "Eric Donaldson" - } - ], - "description_domain": { - "keywords": [ - "HCV1a", - "Ledipasvir", - "antiviral resistance", - "SNP", - "amino acid substitutions" - "test2" - ], - "xref": [ - "SO:0000694", - "SO:0000667", - "SO:0000045", - "PubChem:67505836", - "SO:0000048", - "taxID:31646", - "PMID:25123381", - "PMID:26508693" - ], - "pipeline_steps": [ - { - "tool_name": "HIVE-hexagon", - "tool_desc": "The tool is used for alignment of reads to a set of references", - "tool_version": "1.3", - "tool_package": "HIVE", - "step_number": "1", - "input_uri_list": [ - "https://www.ncbi.nlm.nih.gov/nuccore/NC_004102.1", - "https://www.ncbi.nlm.nih.gov/nuccore/AJ238799.1", - "https://hive/nuc-read/557406", - "https://hive/nuc-read/557407" - ], - "output_uri_list": [ - "https://hive/data/557413/allCount-aligned.csv" - ] - }, - { - "tool_name": "HIVE-heptagon", - "tool_desc": "This tool is used for variant calling", - "tool_version": "1.3", - 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Based on a user-defined threshold, organisms identified are used for alignment in the Hexagon alignment." + ], + "authors": [ + { + "orcid": "0000-0003-1409-4549" + }, + { + "orcid": "0000-0002-8138-8312" + } + ], + "description_domain": { + "keywords": [ + "metagenome", + "metagenomic analysis", + "fecal" + ], + "xref": [ + "UBERON:0001988", + "taxID:9606" + ], + "pipeline_steps": [ + { + "tool_name": "HIVE_CensuScope", + "tool_desc": "Detect taxonomic composition of a metagenomic data set.", + "tool_version": "1.3", + "tool_package": "null", + "step_number": "1", + "input_uri_list": [ + "hive://nuc-read/514683", + "hive://nuc-read/514682", + "hive://genome/513957" + ], + "output_uri_list": [ + "hive:///data/524669/dnaAccessionBasedResult.csv" + ] + }, + { + "tool_name": "HIVE_hexagon", + "tool_desc": "Alignment of reads to a set of references", + "tool_version": "1.3", + "tool_package": "null", + "step_number": "2", + "input_uri_list": [ + "https://www.ncbi.nlm.nih.gov/nuccore/CP000139.1", + "https://www.ncbi.nlm.nih.gov/nuccore/FP929042.1", + "https://www.ncbi.nlm.nih.gov/nuccore/FP929046.1", + "https://www.ncbi.nlm.nih.gov/nuccore/FP929045.1", + "https://www.ncbi.nlm.nih.gov/nuccore/FP929043.1", + "https://www.ncbi.nlm.nih.gov/nuccore/FP929048.1", + "hive:///data/524669/dnaAccessionBasedResult.csv" + ], + "output_uri_list": [ + "hive://data/524569/alCount-Unalignedo524569-alCount--1.csv" + ] + } + ] + }, + "execution_domain": { + "script": "hive://workflows/human_gut_metagenomic_diversity.py", + "pipeline_version": "2.0", + "platform": "HIVE", + "driver": "python_v2.7.13", + "software_prerequisites": [ + { + "name": "HIVE_censuscope", + "version": "1.3" + }, + { + "name": "HIVE_hexagon", + "version": "1.3" + } + ], + "domain_prerequisites": [ + { + "url": "protocol://domain:port/application/path", + "name": "generic name" + }, + { + "url": "ftp://:22/", + "name": "access to ftp" + } + ], + "env_parameters": [ + "HIVEv1.3" + ], + "script_type": "URI" + }, + "parametric_domain": { + "complexityRefEntropy": "1.2 - 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] - }, + ], + "script_type": "CWL" + }, "parametric_domain": { "tophat_threads": "4", "tophat_no-coverage-search": "on", diff --git a/5_viralScreening/bcoexample_5.json b/5_viralScreening/bcoexample_5.json index 861bb14..8d13404 100644 --- a/5_viralScreening/bcoexample_5.json +++ b/5_viralScreening/bcoexample_5.json @@ -96,12 +96,34 @@ "pipeline_version": "2.0", "platform": "HIVE", "driver": "shell", - "prerequisites": [ - "HIVE-seq, version1.3", - "HIVE-IDBA-UD, version1.3", - "HIVE-hexagon, version 1.3", - "HIVE-heptagon, version 1.3" - ], + "software_prerequisites": [ + { + "name": "HIVE-seq", + "version": "1.3" + }, + { + "name": "HIVE-IDBA-UD", + "version": "1.3" + }, + { + "name": "HIVE-hexagon", + "version": "1.3" + }, + { + "name": "HIVE-heptagon", + "version": "1.3" + } + ], + "domain_prerequisites": [ + { + "url": "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/", + "name": "access to e-utils" + }, + { + "url": "ftp://:22/", + "name": "access to ftp" + } + ], "env_parameters": [ "HIVEv1.3" ], diff --git a/6_clonalDisc/bcoexample_6.json b/6_clonalDisc/bcoexample_6.json index 71964e3..e051b45 100644 --- a/6_clonalDisc/bcoexample_6.json +++ b/6_clonalDisc/bcoexample_6.json @@ -1,154 +1,179 @@ { - 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