From 79cdd12fdf841176ed013e166592d15a282c5d9c Mon Sep 17 00:00:00 2001 From: Jennifer Jou Date: Thu, 26 Aug 2021 12:56:24 -0700 Subject: [PATCH] ENCD-6111 Add compartments output_type --- src/encoded/schemas/analysis_step.json | 2 ++ src/encoded/schemas/changelogs/analysis_step.md | 1 + src/encoded/schemas/changelogs/file.md | 1 + src/encoded/schemas/file.json | 2 ++ src/encoded/tests/data/inserts/file.json | 17 +++++++++++++++++ 5 files changed, 23 insertions(+) diff --git a/src/encoded/schemas/analysis_step.json b/src/encoded/schemas/analysis_step.json index aa3f1146a37..74185e45a7d 100644 --- a/src/encoded/schemas/analysis_step.json +++ b/src/encoded/schemas/analysis_step.json @@ -121,6 +121,7 @@ "chromatin interactions", "chromosomes reference", "chromosome sizes", + "compartments", "consensus DNase hypersensitivity sites", "conservative IDR thresholded peaks", "control normalized signal", @@ -311,6 +312,7 @@ "chromatin interactions", "chromosomes reference", "chromosome sizes", + "compartments", "consensus DNase hypersensitivity sites", "conservative IDR thresholded peaks", "control normalized signal", diff --git a/src/encoded/schemas/changelogs/analysis_step.md b/src/encoded/schemas/changelogs/analysis_step.md index 6f5d406be2d..cee9f273eff 100644 --- a/src/encoded/schemas/changelogs/analysis_step.md +++ b/src/encoded/schemas/changelogs/analysis_step.md @@ -16,6 +16,7 @@ * Added *genome compartment identification* to the enum list for *analysis_step_types* * Added *sparse peak count matrix* to the enum lists for *input_file_types* and *output_file_types* * Added *functional conservation quantifications* to the enum lists for *input_file_types* and *output_file_types* +* Added *compartments* to the enum lists for *input_file_types* and *output_file_types* ### Schema version 15 * *input_file_types*, *output_file_types* enums *blacklisted regions* and *mitochondria blacklisted regions* were replaced by *exclusion list regions* and *mitochondrial exclusion list regions* respectively diff --git a/src/encoded/schemas/changelogs/file.md b/src/encoded/schemas/changelogs/file.md index 8daa20c784c..46993e9fb0b 100644 --- a/src/encoded/schemas/changelogs/file.md +++ b/src/encoded/schemas/changelogs/file.md @@ -8,6 +8,7 @@ * Added *fragments* to the enum list for *output_type*, the new output type is to be submitted as tar.gz only * Added *sparse peak count matrix* to the enum list for *output_type* * Added *functional conservation quantifications* to the enum list for *output_type* +* Added *compartments* to the enum list for *output_type* ### Schema version 29 * Added Ultima Genomics platform to dependency that enforces that *read_length* property should not be specified for FASTQ files produced by Oxford Nanopore and PacBio platforms. diff --git a/src/encoded/schemas/file.json b/src/encoded/schemas/file.json index 94def647032..ff4880ca788 100644 --- a/src/encoded/schemas/file.json +++ b/src/encoded/schemas/file.json @@ -1598,6 +1598,7 @@ "chromatin interactions", "chromosomes reference", "chromosome sizes", + "compartments", "consensus DNase hypersensitivity sites", "curated binding sites", "curated SNVs", @@ -2359,6 +2360,7 @@ "unidirectional peaks": "annotation", "polyA sites": "annotation", "functional conservation quantifications": "annotation", + "compartments": "annotation", "transcriptome reference": "reference", "transcriptome index": "reference", diff --git a/src/encoded/tests/data/inserts/file.json b/src/encoded/tests/data/inserts/file.json index a761581dfaf..b870ea14b41 100644 --- a/src/encoded/tests/data/inserts/file.json +++ b/src/encoded/tests/data/inserts/file.json @@ -4745,5 +4745,22 @@ "output_type": "functional conservation quantifications", "lab": "/labs/richard-myers/", "aliases": ["hongkai-ji:human_elements_scored_file"] + }, + { + "_test": "Hi-C compartments", + "status": "in progress", + "submitted_file_name": "hi-c_compartments.bed.gz", + "uuid": "9ddfc5b8-2e9c-4ba2-a8b4-e5a0897a32cc", + "submitted_by": "facilisi.tristique@potenti.vivamus", + "md5sum": "9ddfc5b806a832272e691bd4e2bb622a", + "accession": "ENCFF333HIC", + "file_format": "bigWig", + "award": "/awards/U54HG006998/", + "assembly": "GRCh38", + "dataset": "/experiments/ENCSR000AJK/", + "file_size": 18000000, + "output_type": "compartments", + "lab": "/labs/richard-myers/", + "aliases": ["erez-aiden:hi-c_compartments"] } ]