rebuild

databio · Jan 27, 2024 · d14e860 · d14e860
1 parent b34f476
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Showing 8 changed files with 152 additions and 153 deletions.
diff --git a/docs/CNAME b/docs/CNAME
diff --git a/docs/assets/index-U-7TVKIj.js → docs/assets/index-gWFMjtQe.js b/docs/assets/index-U-7TVKIj.js → docs/assets/index-gWFMjtQe.js
diff --git a/docs/bulker/schemas.json b/docs/bulker/schemas.json
@@ -1,26 +1,26 @@
 {
-    "cdid": {
+    "manifest": {
         "namespace": "bulker",
-        "schema": "cdid",
-        "url": "bulker/cdid.yaml",
-        "description": "Two druids that describe the manifest"
+        "schema": "manifest",
+        "url": "bulker/manifest.yaml",
+        "description": "Schema for bulker manifest"
     },
     "cmdlist": {
         "namespace": "bulker",
         "schema": "cmdlist",
         "url": "bulker/cmdlist.yaml",
         "description": "A list of commands and the containers that run them."
     },
-    "manifest": {
-        "namespace": "bulker",
-        "schema": "manifest",
-        "url": "bulker/manifest.yaml",
-        "description": "Schema for bulker manifest"
-    },
     "importlist": {
         "namespace": "bulker",
         "schema": "importlist",
         "url": "bulker/importlist.yaml",
         "description": "A priority list of bulker manifests that are imported."
+    },
+    "cdid": {
+        "namespace": "bulker",
+        "schema": "cdid",
+        "url": "bulker/cdid.yaml",
+        "description": "Two druids that describe the manifest"
     }
 }
diff --git a/docs/index.html b/docs/index.html
@@ -11,7 +11,7 @@
           href="//cdnjs.cloudflare.com/ajax/libs/highlight.js/11.6.0/styles/default.min.css">
 
     <title>Lab schemas</title>
-    <script type="module" crossorigin src="/assets/index-U-7TVKIj.js"></script>
+    <script type="module" crossorigin src="/assets/index-gWFMjtQe.js"></script>
   </head>
   <body>
     <nav class="navbar navbar-expand-lg py-2 mb-4 border-bottom navbar-light" aria-label="navbar" style="background-color: #EFF3F6;">

diff --git a/docs/list.json b/docs/list.json
@@ -1,23 +1,8 @@
 {
-    "schemas/bulker/cdid": {
-        "project": "bulker",
-        "url": "bulker/cdid.yaml",
-        "description": "Two druids that describe the manifest"
-    },
-    "schemas/bulker/cmdlist": {
-        "project": "bulker",
-        "url": "bulker/cmdlist.yaml",
-        "description": "A list of commands and the containers that run them."
-    },
-    "schemas/bulker/manifest": {
-        "project": "bulker",
-        "url": "bulker/manifest.yaml",
-        "description": "Schema for bulker manifest"
-    },
-    "schemas/bulker/importlist": {
-        "project": "bulker",
-        "url": "bulker/importlist.yaml",
-        "description": "A priority list of bulker manifests that are imported."
+    "schemas/refget/annotated_collection_digest": {
+        "project": "refget",
+        "url": "refget/annotated_collection_digest.yaml",
+        "description": "Schema for an Annotated Collection Digest; this is analogous to a single fasta file with metadata."
     },
     "schemas/refget/SeqColArraySetInherent": {
         "project": "refget",
@@ -29,66 +14,81 @@
         "url": "refget/sequence.yaml",
         "description": "Schema for a single raw sequence"
     },
-    "schemas/refget/annotated_collection_digest": {
+    "schemas/refget/RawSeqCol": {
         "project": "refget",
-        "url": "refget/annotated_collection_digest.yaml",
-        "description": "Schema for an Annotated Collection Digest; this is analogous to a single fasta file with metadata."
+        "url": "refget/RawSeqCol.yaml",
+        "description": "Schema for List of ASDs"
     },
-    "schemas/refget/ArrayedNestedSequenceCollection": {
+    "schemas/refget/AnnotatedArrayedSequenceCollection": {
         "project": "refget",
-        "url": "refget/ArrayedNestedSequenceCollection.yaml",
+        "url": "refget/AnnotatedArrayedSequenceCollection.yaml",
         "description": "A collection of sequences"
     },
-    "schemas/refget/ASDList": {
-        "project": "refget",
-        "url": "refget/ASDList.yaml",
-        "description": "Schema for List of ASDs"
-    },
-    "schemas/refget/annotated_sequence_digest": {
+    "schemas/refget/SeqColArraySet": {
         "project": "refget",
-        "url": "refget/annotated_sequence_digest.yaml",
-        "description": "Schema for an Annotated Sequence Digest; a digested Sequence plus metadata"
+        "url": "refget/SeqColArraySet.yaml",
+        "description": "SeqColArraySet"
     },
     "schemas/refget/ACDList": {
         "project": "refget",
         "url": "refget/ACDList.yaml",
         "description": "Schema for a list of ACDs; analogous to a collection of fasta files"
     },
-    "schemas/refget/ArrayedSequenceCollection": {
-        "project": "refget",
-        "url": "refget/ArrayedSequenceCollection.yaml",
-        "description": "A collection of sequences"
-    },
-    "schemas/refget/RawSeqCol": {
-        "project": "refget",
-        "url": "refget/RawSeqCol.yaml",
-        "description": "Schema for List of ASDs"
-    },
     "schemas/refget/TASeqCol": {
         "project": "refget",
         "url": "refget/TASeqCol.yaml",
         "description": "TAseqcol"
     },
-    "schemas/refget/CustomAnnotatedArrayedSequenceCollection": {
+    "schemas/refget/ArrayedNestedSequenceCollection": {
         "project": "refget",
-        "url": "refget/CustomAnnotatedArrayedSequenceCollection.yaml",
+        "url": "refget/ArrayedNestedSequenceCollection.yaml",
         "description": "A collection of sequences"
     },
-    "schemas/refget/SeqColArraySet": {
+    "schemas/refget/CustomAnnotatedArrayedSequenceCollection": {
         "project": "refget",
-        "url": "refget/SeqColArraySet.yaml",
-        "description": "SeqColArraySet"
+        "url": "refget/CustomAnnotatedArrayedSequenceCollection.yaml",
+        "description": "A collection of sequences"
     },
-    "schemas/refget/AnnotatedArrayedSequenceCollection": {
+    "schemas/refget/annotated_sequence_digest": {
         "project": "refget",
-        "url": "refget/AnnotatedArrayedSequenceCollection.yaml",
-        "description": "A collection of sequences"
+        "url": "refget/annotated_sequence_digest.yaml",
+        "description": "Schema for an Annotated Sequence Digest; a digested Sequence plus metadata"
     },
     "schemas/refget/AnnotatedSequenceList": {
         "project": "refget",
         "url": "refget/AnnotatedSequenceList.yaml",
         "description": "Schema for List of ASDs"
     },
+    "schemas/refget/ASDList": {
+        "project": "refget",
+        "url": "refget/ASDList.yaml",
+        "description": "Schema for List of ASDs"
+    },
+    "schemas/refget/ArrayedSequenceCollection": {
+        "project": "refget",
+        "url": "refget/ArrayedSequenceCollection.yaml",
+        "description": "A collection of sequences"
+    },
+    "schemas/bulker/manifest": {
+        "project": "bulker",
+        "url": "bulker/manifest.yaml",
+        "description": "Schema for bulker manifest"
+    },
+    "schemas/bulker/cmdlist": {
+        "project": "bulker",
+        "url": "bulker/cmdlist.yaml",
+        "description": "A list of commands and the containers that run them."
+    },
+    "schemas/bulker/importlist": {
+        "project": "bulker",
+        "url": "bulker/importlist.yaml",
+        "description": "A priority list of bulker manifests that are imported."
+    },
+    "schemas/bulker/cdid": {
+        "project": "bulker",
+        "url": "bulker/cdid.yaml",
+        "description": "Two druids that describe the manifest"
+    },
     "schemas/refgenie/refgenie_build": {
         "project": "refgenie",
         "url": "refgenie/refgenie_build.yaml",
@@ -104,6 +104,11 @@
         "url": "pep/2.0.0.yaml",
         "description": "Schema for a minimal PEP"
     },
+    "schemas/pipelines/bedbuncher": {
+        "project": "pipelines",
+        "url": "pipelines/bedbuncher.yaml",
+        "description": "bedbuncher PEP schema"
+    },
     "schemas/pipelines/pipeline_interface": {
         "project": "pipelines",
         "url": "pipelines/pipeline_interface.yaml",
@@ -114,34 +119,29 @@
         "url": "pipelines/geofetch_sra_convert.yaml",
         "description": "A PEP for converting SRA files into fastq or bam format."
     },
-    "schemas/pipelines/bedmaker": {
-        "project": "pipelines",
-        "url": "pipelines/bedmaker.yaml",
-        "description": "bedmaker PEP schema"
-    },
-    "schemas/pipelines/bedbuncher": {
+    "schemas/pipelines/bedboss": {
         "project": "pipelines",
-        "url": "pipelines/bedbuncher.yaml",
-        "description": "bedbuncher PEP schema"
+        "url": "pipelines/bedboss.yaml",
+        "description": "bedboss run-all pep schema"
     },
-    "schemas/pipelines/pepatac": {
+    "schemas/pipelines/bedstat": {
         "project": "pipelines",
-        "url": "pipelines/pepatac.yaml",
-        "description": "A PEP for ATAC-seq samples for the PEPATAC pipeline."
+        "url": "pipelines/bedstat.yaml",
+        "description": "bedstat PEP schema"
     },
     "schemas/pipelines/ProseqPEP": {
         "project": "pipelines",
         "url": "pipelines/ProseqPEP.yaml",
         "description": "A PEP for nascent RNA samples for the PEPPRO pipeline."
     },
-    "schemas/pipelines/bedstat": {
+    "schemas/pipelines/bedmaker": {
         "project": "pipelines",
-        "url": "pipelines/bedstat.yaml",
-        "description": "bedstat PEP schema"
+        "url": "pipelines/bedmaker.yaml",
+        "description": "bedmaker PEP schema"
     },
-    "schemas/pipelines/bedboss": {
+    "schemas/pipelines/pepatac": {
         "project": "pipelines",
-        "url": "pipelines/bedboss.yaml",
-        "description": "bedboss run-all pep schema"
+        "url": "pipelines/pepatac.yaml",
+        "description": "A PEP for ATAC-seq samples for the PEPATAC pipeline."
     }
 }
diff --git a/docs/namespaces.json b/docs/namespaces.json
@@ -1,6 +1,6 @@
 [
-    "bulker",
     "refget",
+    "bulker",
     "refgenie",
     "pep",
     "pipelines"

diff --git a/docs/pipelines/schemas.json b/docs/pipelines/schemas.json
@@ -1,4 +1,10 @@
 {
+    "bedbuncher": {
+        "namespace": "pipelines",
+        "schema": "bedbuncher",
+        "url": "pipelines/bedbuncher.yaml",
+        "description": "bedbuncher PEP schema"
+    },
     "pipeline_interface": {
         "namespace": "pipelines",
         "schema": "pipeline_interface",
@@ -11,40 +17,34 @@
         "url": "pipelines/geofetch_sra_convert.yaml",
         "description": "A PEP for converting SRA files into fastq or bam format."
     },
-    "bedmaker": {
-        "namespace": "pipelines",
-        "schema": "bedmaker",
-        "url": "pipelines/bedmaker.yaml",
-        "description": "bedmaker PEP schema"
-    },
-    "bedbuncher": {
+    "bedboss": {
         "namespace": "pipelines",
-        "schema": "bedbuncher",
-        "url": "pipelines/bedbuncher.yaml",
-        "description": "bedbuncher PEP schema"
+        "schema": "bedboss",
+        "url": "pipelines/bedboss.yaml",
+        "description": "bedboss run-all pep schema"
     },
-    "pepatac": {
+    "bedstat": {
         "namespace": "pipelines",
-        "schema": "pepatac",
-        "url": "pipelines/pepatac.yaml",
-        "description": "A PEP for ATAC-seq samples for the PEPATAC pipeline."
+        "schema": "bedstat",
+        "url": "pipelines/bedstat.yaml",
+        "description": "bedstat PEP schema"
     },
     "ProseqPEP": {
         "namespace": "pipelines",
         "schema": "ProseqPEP",
         "url": "pipelines/ProseqPEP.yaml",
         "description": "A PEP for nascent RNA samples for the PEPPRO pipeline."
     },
-    "bedstat": {
+    "bedmaker": {
         "namespace": "pipelines",
-        "schema": "bedstat",
-        "url": "pipelines/bedstat.yaml",
-        "description": "bedstat PEP schema"
+        "schema": "bedmaker",
+        "url": "pipelines/bedmaker.yaml",
+        "description": "bedmaker PEP schema"
     },
-    "bedboss": {
+    "pepatac": {
         "namespace": "pipelines",
-        "schema": "bedboss",
-        "url": "pipelines/bedboss.yaml",
-        "description": "bedboss run-all pep schema"
+        "schema": "pepatac",
+        "url": "pipelines/pepatac.yaml",
+        "description": "A PEP for ATAC-seq samples for the PEPATAC pipeline."
     }
 }