PIPE-90-juicer218

ENCODE-DCC · Nov 2, 2022 · d606fc7 · d606fc7
1 parent 511636c
commit d606fc7
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Showing 3 changed files with 11 additions and 10 deletions.
diff --git a/docker/hic-pipeline/Dockerfile b/docker/hic-pipeline/Dockerfile
@@ -115,7 +115,7 @@ RUN git clone --branch encode https://github.com/theaidenlab/juicer.git && \
     chmod +x CPU/* CPU/common/* misc/* && \
     find -mindepth 1 -maxdepth 1  -type d -not -name "CPU" -not -name ".git" -not -name "misc" | xargs rm -rf
 
-# Install Juicer tools 2.13 and 2.17
+# Install Juicer tools 2.13 and 2.20
 RUN curl \
         -L \
         https://github.com/aidenlab/Juicebox/releases/download/v2.13.06/juicer_tools_2.13.06.jar \
@@ -127,9 +127,9 @@ RUN curl \
 
 RUN curl \
         -L \
-        https://github.com/aidenlab/Juicebox/releases/download/v2.17.00/juicer_tools_2.17.00.jar \
-        -o /opt/juicer/CPU/juicer_tools_2.17.00.jar && \
-    chmod 666 /opt/juicer/CPU/juicer_tools_2.17.00.jar
+        https://github.com/aidenlab/Juicebox/releases/download/v2.20.00/juicer_tools.2.20.00.jar \
+        -o /opt/juicer/CPU/juicer_tools.2.20.00.jar && \
+    chmod 666 /opt/juicer/CPU/juicer_tools.2.20.00.jar
 
 RUN curl \
         -LO \

diff --git a/hic.wdl b/hic.wdl
@@ -1117,8 +1117,8 @@ task localizer {
             ~{hic} \
             $LOOPS_FILE \
             localized
-        gzip -n localized/localizedList_primary_100.bedpe
-        mv localized/localizedList_primary_100.bedpe.gz localized_loops_~{quality}.bedpe.gz
+        gzip -n localized/localizedList_primary_~{localizer_resolution}.bedpe
+        mv localized/localizedList_primary_~{localizer_resolution}.bedpe.gz localized_loops_~{quality}.bedpe.gz
     }
 
     output {

diff --git a/megamap.wdl b/megamap.wdl
@@ -19,6 +19,7 @@ workflow megamap {
         Array[Int] create_hic_in_situ_resolutions = [2500000, 1000000, 500000, 250000, 100000, 50000, 25000, 10000, 5000, 2000, 1000, 500, 200, 100]
         Array[Int] create_hic_intact_resolutions = [2500000, 1000000, 500000, 250000, 100000, 50000, 25000, 10000, 5000, 2000, 1000, 500, 200, 100, 50, 20, 10]
         Boolean intact = true
+        Int localizer_resolution = 100
 
         # Resource parameters
         Int? add_norm_mthreads
@@ -75,7 +76,7 @@ workflow megamap {
         mthreads = add_norm_mthreads,
         save_ram = add_norm_save_ram,
         quality = quality,
-        juicer_tools_jar = "/opt/juicer/CPU/juicer_tools_2.17.00.jar",
+        juicer_tools_jar = "/opt/juicer/CPU/juicer_tools.2.20.00.jar",
         normalization_command = "addnorm2",
         num_cpus = add_norm_num_cpus,
         ram_gb = add_norm_ram_gb,
@@ -107,7 +108,7 @@ workflow megamap {
         call hic.localizer as localizer_intact { input:
             hic = add_norm.output_hic,
             loops = hiccups_2.merged_loops,
-            localizer_resolution = 10,
+            localizer_resolution = localizer_resolution,
             localizer_window = 10,
             quality = quality,
             runtime_environment = runtime_environment,
@@ -139,7 +140,7 @@ workflow megamap {
     call hic.localizer as localizer_delta { input:
         hic = add_norm.output_hic,
         loops = delta.loops,
-        localizer_resolution = 10,
+        localizer_resolution = localizer_resolution,
         localizer_window = 10,
         runtime_environment = runtime_environment,
     }
@@ -242,7 +243,7 @@ task sum_hic_files {
         set -euo pipefail
         java \
             -jar \
-            /opt/juicer/CPU/juicer_tools_2.17.00.jar \
+            /opt/juicer/CPU/juicer_tools.2.20.00.jar \
             sum \
             --threads ~{num_cpus} \
             summed.hic \