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Merge branch 'master' of github.com:databio/schema.databio.org
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‎public/bulker/schemas.json

+10-10
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@@ -1,26 +1,26 @@
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{
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"cdid": {
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"manifest": {
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"namespace": "bulker",
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"schema": "cdid",
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"url": "bulker/cdid.yaml",
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"description": "Two druids that describe the manifest"
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"schema": "manifest",
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"url": "bulker/manifest.yaml",
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"description": "Schema for bulker manifest"
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},
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"cmdlist": {
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"namespace": "bulker",
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"schema": "cmdlist",
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"url": "bulker/cmdlist.yaml",
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"description": "A list of commands and the containers that run them."
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},
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"manifest": {
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"namespace": "bulker",
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"schema": "manifest",
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"url": "bulker/manifest.yaml",
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"description": "Schema for bulker manifest"
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},
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"importlist": {
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"namespace": "bulker",
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"schema": "importlist",
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"url": "bulker/importlist.yaml",
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"description": "A priority list of bulker manifests that are imported."
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},
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"cdid": {
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"namespace": "bulker",
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"schema": "cdid",
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"url": "bulker/cdid.yaml",
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"description": "Two druids that describe the manifest"
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}
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}

‎public/list.json

+67-67
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@@ -1,23 +1,8 @@
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{
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"schemas/bulker/cdid": {
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"project": "bulker",
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"url": "bulker/cdid.yaml",
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"description": "Two druids that describe the manifest"
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},
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"schemas/bulker/cmdlist": {
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"project": "bulker",
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"url": "bulker/cmdlist.yaml",
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"description": "A list of commands and the containers that run them."
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},
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"schemas/bulker/manifest": {
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"project": "bulker",
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"url": "bulker/manifest.yaml",
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"description": "Schema for bulker manifest"
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},
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"schemas/bulker/importlist": {
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"project": "bulker",
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"url": "bulker/importlist.yaml",
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"description": "A priority list of bulker manifests that are imported."
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"schemas/refget/annotated_collection_digest": {
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"project": "refget",
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"url": "refget/annotated_collection_digest.yaml",
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"description": "Schema for an Annotated Collection Digest; this is analogous to a single fasta file with metadata."
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},
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"schemas/refget/SeqColArraySetInherent": {
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"project": "refget",
@@ -29,66 +14,81 @@
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"url": "refget/sequence.yaml",
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"description": "Schema for a single raw sequence"
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},
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"schemas/refget/annotated_collection_digest": {
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"schemas/refget/RawSeqCol": {
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"project": "refget",
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"url": "refget/annotated_collection_digest.yaml",
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"description": "Schema for an Annotated Collection Digest; this is analogous to a single fasta file with metadata."
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"url": "refget/RawSeqCol.yaml",
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"description": "Schema for List of ASDs"
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},
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"schemas/refget/ArrayedNestedSequenceCollection": {
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"schemas/refget/AnnotatedArrayedSequenceCollection": {
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"project": "refget",
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"url": "refget/ArrayedNestedSequenceCollection.yaml",
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"url": "refget/AnnotatedArrayedSequenceCollection.yaml",
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"description": "A collection of sequences"
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},
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"schemas/refget/ASDList": {
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"project": "refget",
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"url": "refget/ASDList.yaml",
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"description": "Schema for List of ASDs"
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},
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"schemas/refget/annotated_sequence_digest": {
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"schemas/refget/SeqColArraySet": {
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"project": "refget",
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"url": "refget/annotated_sequence_digest.yaml",
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"description": "Schema for an Annotated Sequence Digest; a digested Sequence plus metadata"
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"url": "refget/SeqColArraySet.yaml",
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"description": "SeqColArraySet"
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},
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"schemas/refget/ACDList": {
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"project": "refget",
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"url": "refget/ACDList.yaml",
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"description": "Schema for a list of ACDs; analogous to a collection of fasta files"
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},
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"schemas/refget/ArrayedSequenceCollection": {
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"project": "refget",
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"url": "refget/ArrayedSequenceCollection.yaml",
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"description": "A collection of sequences"
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},
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"schemas/refget/RawSeqCol": {
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"project": "refget",
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"url": "refget/RawSeqCol.yaml",
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"description": "Schema for List of ASDs"
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},
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"schemas/refget/TASeqCol": {
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"project": "refget",
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"url": "refget/TASeqCol.yaml",
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"description": "TAseqcol"
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},
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"schemas/refget/CustomAnnotatedArrayedSequenceCollection": {
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"schemas/refget/ArrayedNestedSequenceCollection": {
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"project": "refget",
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"url": "refget/CustomAnnotatedArrayedSequenceCollection.yaml",
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"url": "refget/ArrayedNestedSequenceCollection.yaml",
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"description": "A collection of sequences"
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},
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"schemas/refget/SeqColArraySet": {
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"schemas/refget/CustomAnnotatedArrayedSequenceCollection": {
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"project": "refget",
79-
"url": "refget/SeqColArraySet.yaml",
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"description": "SeqColArraySet"
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"url": "refget/CustomAnnotatedArrayedSequenceCollection.yaml",
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"description": "A collection of sequences"
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},
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"schemas/refget/AnnotatedArrayedSequenceCollection": {
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"schemas/refget/annotated_sequence_digest": {
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"project": "refget",
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"url": "refget/AnnotatedArrayedSequenceCollection.yaml",
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"description": "A collection of sequences"
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"url": "refget/annotated_sequence_digest.yaml",
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"description": "Schema for an Annotated Sequence Digest; a digested Sequence plus metadata"
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},
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"schemas/refget/AnnotatedSequenceList": {
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"project": "refget",
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"url": "refget/AnnotatedSequenceList.yaml",
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"description": "Schema for List of ASDs"
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},
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"schemas/refget/ASDList": {
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"project": "refget",
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"url": "refget/ASDList.yaml",
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"description": "Schema for List of ASDs"
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},
67+
"schemas/refget/ArrayedSequenceCollection": {
68+
"project": "refget",
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"url": "refget/ArrayedSequenceCollection.yaml",
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"description": "A collection of sequences"
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},
72+
"schemas/bulker/manifest": {
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"project": "bulker",
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"url": "bulker/manifest.yaml",
75+
"description": "Schema for bulker manifest"
76+
},
77+
"schemas/bulker/cmdlist": {
78+
"project": "bulker",
79+
"url": "bulker/cmdlist.yaml",
80+
"description": "A list of commands and the containers that run them."
81+
},
82+
"schemas/bulker/importlist": {
83+
"project": "bulker",
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"url": "bulker/importlist.yaml",
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"description": "A priority list of bulker manifests that are imported."
86+
},
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"schemas/bulker/cdid": {
88+
"project": "bulker",
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"url": "bulker/cdid.yaml",
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"description": "Two druids that describe the manifest"
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},
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"schemas/refgenie/refgenie_build": {
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"project": "refgenie",
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"url": "refgenie/refgenie_build.yaml",
@@ -104,6 +104,11 @@
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"url": "pep/2.0.0.yaml",
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"description": "Schema for a minimal PEP"
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},
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"schemas/pipelines/bedbuncher": {
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"project": "pipelines",
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"url": "pipelines/bedbuncher.yaml",
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"description": "bedbuncher PEP schema"
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},
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"schemas/pipelines/pipeline_interface": {
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"project": "pipelines",
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"url": "pipelines/pipeline_interface.yaml",
@@ -114,34 +119,29 @@
114119
"url": "pipelines/geofetch_sra_convert.yaml",
115120
"description": "A PEP for converting SRA files into fastq or bam format."
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},
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"schemas/pipelines/bedmaker": {
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"project": "pipelines",
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"url": "pipelines/bedmaker.yaml",
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"description": "bedmaker PEP schema"
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},
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"schemas/pipelines/bedbuncher": {
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"schemas/pipelines/bedboss": {
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"project": "pipelines",
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"url": "pipelines/bedbuncher.yaml",
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"description": "bedbuncher PEP schema"
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"url": "pipelines/bedboss.yaml",
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"description": "bedboss run-all pep schema"
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},
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"schemas/pipelines/pepatac": {
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"schemas/pipelines/bedstat": {
128128
"project": "pipelines",
129-
"url": "pipelines/pepatac.yaml",
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"description": "A PEP for ATAC-seq samples for the PEPATAC pipeline."
129+
"url": "pipelines/bedstat.yaml",
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"description": "bedstat PEP schema"
131131
},
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"schemas/pipelines/ProseqPEP": {
133133
"project": "pipelines",
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"url": "pipelines/ProseqPEP.yaml",
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"description": "A PEP for nascent RNA samples for the PEPPRO pipeline."
136136
},
137-
"schemas/pipelines/bedstat": {
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"schemas/pipelines/bedmaker": {
138138
"project": "pipelines",
139-
"url": "pipelines/bedstat.yaml",
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"description": "bedstat PEP schema"
139+
"url": "pipelines/bedmaker.yaml",
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"description": "bedmaker PEP schema"
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},
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"schemas/pipelines/bedboss": {
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"schemas/pipelines/pepatac": {
143143
"project": "pipelines",
144-
"url": "pipelines/bedboss.yaml",
145-
"description": "bedboss run-all pep schema"
144+
"url": "pipelines/pepatac.yaml",
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"description": "A PEP for ATAC-seq samples for the PEPATAC pipeline."
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}
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}

‎public/namespaces.json

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[
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"bulker",
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"refget",
3+
"bulker",
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"refgenie",
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"pep",
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"pipelines"

‎public/pipelines/schemas.json

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{
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"bedbuncher": {
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"namespace": "pipelines",
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"schema": "bedbuncher",
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"url": "pipelines/bedbuncher.yaml",
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"description": "bedbuncher PEP schema"
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},
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"pipeline_interface": {
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"namespace": "pipelines",
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"schema": "pipeline_interface",
@@ -11,40 +17,34 @@
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"url": "pipelines/geofetch_sra_convert.yaml",
1218
"description": "A PEP for converting SRA files into fastq or bam format."
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},
14-
"bedmaker": {
15-
"namespace": "pipelines",
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"schema": "bedmaker",
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"url": "pipelines/bedmaker.yaml",
18-
"description": "bedmaker PEP schema"
19-
},
20-
"bedbuncher": {
20+
"bedboss": {
2121
"namespace": "pipelines",
22-
"schema": "bedbuncher",
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"url": "pipelines/bedbuncher.yaml",
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"description": "bedbuncher PEP schema"
22+
"schema": "bedboss",
23+
"url": "pipelines/bedboss.yaml",
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"description": "bedboss run-all pep schema"
2525
},
26-
"pepatac": {
26+
"bedstat": {
2727
"namespace": "pipelines",
28-
"schema": "pepatac",
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"url": "pipelines/pepatac.yaml",
30-
"description": "A PEP for ATAC-seq samples for the PEPATAC pipeline."
28+
"schema": "bedstat",
29+
"url": "pipelines/bedstat.yaml",
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"description": "bedstat PEP schema"
3131
},
3232
"ProseqPEP": {
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"namespace": "pipelines",
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"schema": "ProseqPEP",
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"url": "pipelines/ProseqPEP.yaml",
3636
"description": "A PEP for nascent RNA samples for the PEPPRO pipeline."
3737
},
38-
"bedstat": {
38+
"bedmaker": {
3939
"namespace": "pipelines",
40-
"schema": "bedstat",
41-
"url": "pipelines/bedstat.yaml",
42-
"description": "bedstat PEP schema"
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"schema": "bedmaker",
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"url": "pipelines/bedmaker.yaml",
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"description": "bedmaker PEP schema"
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},
44-
"bedboss": {
44+
"pepatac": {
4545
"namespace": "pipelines",
46-
"schema": "bedboss",
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"url": "pipelines/bedboss.yaml",
48-
"description": "bedboss run-all pep schema"
46+
"schema": "pepatac",
47+
"url": "pipelines/pepatac.yaml",
48+
"description": "A PEP for ATAC-seq samples for the PEPATAC pipeline."
4949
}
5050
}

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