PIPE-56-genophase-reference-update (#150)

ENCODE-DCC · Mar 10, 2022 · 504cda7 · 504cda7
1 parent 681a0ea
commit 504cda7
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Showing 5 changed files with 19 additions and 19 deletions.
diff --git a/genophase.wdl b/genophase.wdl
@@ -4,9 +4,9 @@ import "./hic.wdl"
 
 workflow genophase {
     meta {
-        version: "1.12.1"
-        caper_docker: "encodedcc/hic-pipeline:1.12.1"
-        caper_singularity: "docker://encodedcc/hic-pipeline:1.12.1"
+        version: "1.12.2"
+        caper_docker: "encodedcc/hic-pipeline:1.12.2"
+        caper_singularity: "docker://encodedcc/hic-pipeline:1.12.2"
         croo_out_def: "https://raw.githubusercontent.com/ENCODE-DCC/hic-pipeline/dev/croo_out_def.json"
     }
 
@@ -25,8 +25,8 @@ workflow genophase {
         Int? run_3d_dna_ram_gb
         Boolean no_phasing = false
 
-        String docker = "encodedcc/hic-pipeline:1.12.1"
-        String singularity = "docker://encodedcc/hic-pipeline:1.12.1"
+        String docker = "encodedcc/hic-pipeline:1.12.2"
+        String singularity = "docker://encodedcc/hic-pipeline:1.12.2"
     }
 
     RuntimeEnvironment runtime_environment = {

diff --git a/hic.wdl b/hic.wdl
@@ -19,9 +19,9 @@ struct RuntimeEnvironment {
 
 workflow hic {
     meta {
-        version: "1.12.1"
-        caper_docker: "encodedcc/hic-pipeline:1.12.1"
-        caper_singularity: "docker://encodedcc/hic-pipeline:1.12.1"
+        version: "1.12.2"
+        caper_docker: "encodedcc/hic-pipeline:1.12.2"
+        caper_singularity: "docker://encodedcc/hic-pipeline:1.12.2"
         croo_out_def: "https://raw.githubusercontent.com/ENCODE-DCC/hic-pipeline/dev/croo_out_def.json"
         description: "ENCODE Hi-C pipeline, see https://github.com/ENCODE-DCC/hic-pipeline for details."
     }
@@ -65,10 +65,10 @@ workflow hic {
         Int? create_accessibility_track_disk_size_gb
         String assembly_name = "undefined"
 
-        String docker = "encodedcc/hic-pipeline:1.12.1"
-        String singularity = "docker://encodedcc/hic-pipeline:1.12.1"
-        String delta_docker = "encodedcc/hic-pipeline:1.12.1_delta"
-        String hiccups_docker = "encodedcc/hic-pipeline:1.12.1_hiccups"
+        String docker = "encodedcc/hic-pipeline:1.12.2"
+        String singularity = "docker://encodedcc/hic-pipeline:1.12.2"
+        String delta_docker = "encodedcc/hic-pipeline:1.12.2_delta"
+        String hiccups_docker = "encodedcc/hic-pipeline:1.12.2_hiccups"
     }
 
     RuntimeEnvironment runtime_environment = {

diff --git a/hic_pipeline/__init__.py b/hic_pipeline/__init__.py
@@ -1,5 +1,5 @@
 __title__ = "hic-pipeline"
-__version__ = "1.12.1"
+__version__ = "1.12.2"
 __description__ = "ENCODE Hi-C uniform processing pipeline."
 __url__ = "https://github.com/ENCODE-DCC/hic-pipeline"
 __uri__ = __url__

diff --git a/make_restriction_site_locations.wdl b/make_restriction_site_locations.wdl
@@ -7,9 +7,9 @@ struct RuntimeEnvironment {
 
 workflow make_restriction_site_locations {
     meta {
-        version: "1.12.1"
-        caper_docker: "encodedcc/hic-pipeline:1.12.1"
-        caper_singularity: "docker://encodedcc/hic-pipeline:1.12.1"
+        version: "1.12.2"
+        caper_docker: "encodedcc/hic-pipeline:1.12.2"
+        caper_singularity: "docker://encodedcc/hic-pipeline:1.12.2"
     }
 
     parameter_meta {
@@ -22,8 +22,8 @@ workflow make_restriction_site_locations {
         File reference_fasta
         String assembly_name
         String restriction_enzyme
-        String docker = "encodedcc/hic-pipeline:1.12.1"
-        String singularity = "docker://encodedcc/hic-pipeline:1.12.1"
+        String docker = "encodedcc/hic-pipeline:1.12.2"
+        String singularity = "docker://encodedcc/hic-pipeline:1.12.2"
     }
 
 

diff --git a/scripts/make_genophase_input_json_from_portal.py b/scripts/make_genophase_input_json_from_portal.py
@@ -12,7 +12,7 @@
         _PORTAL_URL,
         "/files/GRCh38_no_alt_analysis_set_GCA_000001405.15/@@download/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.gz",
     ),
-    "gatk_bundle_tar": "https://test.encodedcc.org/files/TSTFF044741/@@download/TSTFF044741.tar.gz",
+    "gatk_bundle_tar": "https://www.encodeproject.org/files/ENCFF975DYE/@@download/ENCFF975DYE.tar.gz",
 }