PIP-1580-slice-subcompartments (#126)

docker/hic-pipeline/Dockerfile

@@ -113,6 +113,12 @@ RUN curl \
     chmod 666 /opt/juicer/CPU/common/juicer_tools.jar && \
     ln -s juicer/CPU scripts
 
+RUN curl \
+        -LO \
+        https://github.com/sa501428/mixer-tools/releases/download/v4.07.08/MixerTools.4.7.8.jar && \
+    chmod 666 /opt/MixerTools.4.7.8.jar && \
+    ln -s /opt/MixerTools.4.7.8.jar /opt/MixerTools.jar
+
 # For sorting, LC_ALL is C
 ENV LC_ALL C
 ENV PATH=/opt:/opt/scripts:/opt/scripts/common:/opt/juicer/misc:$PATH

hic.wdl

@@ -14,9 +14,9 @@ struct BamAndLigationCount {
 
 workflow hic {
     meta {
-        version: "1.3.1"
-        caper_docker: "encodedcc/hic-pipeline:1.3.1"
-        caper_singularity: "docker://encodedcc/hic-pipeline:1.3.1"
+        version: "1.4.0"
+        caper_docker: "encodedcc/hic-pipeline:1.4.0"
+        caper_singularity: "docker://encodedcc/hic-pipeline:1.4.0"
         croo_out_def: "https://raw.githubusercontent.com/ENCODE-DCC/hic-pipeline/dev/croo_out_def.json"
     }
 
@@ -37,6 +37,7 @@ workflow hic {
         Boolean no_call_loops = false
         Boolean no_call_tads = false
         Boolean no_eigenvectors = false
+        Boolean no_slice = false
         Int align_num_cpus = 32
         Int? create_hic_num_cpus
         Int? add_norm_num_cpus
@@ -258,6 +259,25 @@ workflow hic {
             }
         }
     }
+
+    if (!no_slice) {
+        File hic_file = select_first([add_norm.output_hic[1], input_hic])
+
+        call slice as slice_25kb { input:
+            hic_file = hic_file,
+            resolution = 25000,
+        }
+
+        call slice as slice_50kb { input:
+            hic_file = hic_file,
+            resolution = 50000,
+        }
+
+        call slice as slice_100kb { input:
+            hic_file = hic_file,
+            resolution = 100000,
+        }
+    }
 }
 
 task get_ligation_site_regex {
@@ -778,7 +798,7 @@ task hiccups {
         cpu : "1"
         bootDiskSizeGb: "20"
         disks: "local-disk 100 HDD"
-        docker: "encodedcc/hic-pipeline:1.3.1_hiccups"
+        docker: "encodedcc/hic-pipeline:1.4.0_hiccups"
         gpuType: "nvidia-tesla-p100"
         gpuCount: 1
         memory: "8 GB"
@@ -828,6 +848,42 @@ task create_eigenvector {
     }
 }
 
+task slice {
+    input {
+        File hic_file
+        Int resolution = 25000
+        Int minimum_num_clusters = 2
+        Int maximum_num_clusters = 13
+        Int num_kmeans_runs = 4
+    }
+
+    command {
+        set -euo pipefail
+        java \
+            -Xmx20G \
+            -jar /opt/MixerTools.jar \
+            slice \
+            --encode-mode \
+            -r ~{resolution} \
+            ~{hic_file} \
+            ~{minimum_num_clusters},~{maximum_num_clusters},~{num_kmeans_runs} \
+            slice_results \
+            cell_type
+        gzip -n slice_results/*.bed
+        mv slice_results/slice_subcompartment_clusters.bed.gz slice_subcompartment_clusters_~{resolution}.bed.gz
+    }
+
+    output {
+        File subcompartments = "slice_subcompartment_clusters_~{resolution}.bed.gz"
+    }
+
+    runtime {
+        cpu : "1"
+        disks: "local-disk 100 SSD"
+        memory : "24 GB"
+    }
+}
+
 task exit_early {
     input {
         String message

hic_pipeline/__init__.py

@@ -1,5 +1,5 @@
 __title__ = "hic-pipeline"
-__version__ = "1.3.1"
+__version__ = "1.4.0"
 __description__ = "ENCODE Hi-C uniform processing pipeline."
 __url__ = "https://github.com/ENCODE-DCC/hic-pipeline"
 __uri__ = __url__

make_restriction_site_locations.wdl

@@ -2,9 +2,9 @@ version 1.0
 
 workflow make_restriction_site_locations {
     meta {
-        version: "1.3.1"
-        caper_docker: "encodedcc/hic-pipeline:1.3.1"
-        caper_singularity: "docker://encodedcc/hic-pipeline:1.3.1"
+        version: "1.4.0"
+        caper_docker: "encodedcc/hic-pipeline:1.4.0"
+        caper_singularity: "docker://encodedcc/hic-pipeline:1.4.0"
     }
 
     parameter_meta {

tests/functional/json/test_hic.json

@@ -11,6 +11,7 @@
   ],
   "hic.no_call_loops": true,
   "hic.no_call_tads": true,
+  "hic.no_slice": true,
   "hic.reference_index": "tests/data/ce10_selected.tar.gz",
   "hic.restriction_enzymes": [
     "MboI"

tests/functional/json/test_hic_nonspecific.json

@@ -11,6 +11,7 @@
   ],
   "hic.no_call_loops": true,
   "hic.no_call_tads": true,
+  "hic.no_slice": true,
   "hic.reference_index": "tests/data/ce10_selected.tar.gz",
   "hic.restriction_enzymes": [
     "none"

tests/functional/json/test_hic_with_read_group.json

@@ -12,6 +12,7 @@
   ],
   "hic.no_call_loops": true,
   "hic.no_call_tads": true,
+  "hic.no_slice": true,
   "hic.reference_index": "tests/data/ce10_selected.tar.gz",
   "hic.restriction_enzymes": [
     "MboI"

tests/functional/json/test_multiple_libraries.json

@@ -21,6 +21,7 @@
   ],
   "hic.no_call_loops": true,
   "hic.no_call_tads": true,
+  "hic.no_slice": true,
   "hic.reference_index": "tests/data/ce10_selected.tar.gz",
   "hic.restriction_enzymes": [
     "MboI"

tests/functional/json/test_no_pairs.json

@@ -12,6 +12,7 @@
   "hic.no_call_loops": true,
   "hic.no_call_tads": true,
   "hic.no_pairs": true,
+  "hic.no_slice": true,
   "hic.reference_index": "tests/data/ce10_selected.tar.gz",
   "hic.restriction_enzymes": [
     "MboI"

tests/functional/json/test_ultima.json

@@ -11,6 +11,7 @@
   "hic.no_call_loops": true,
   "hic.no_call_tads": true,
   "hic.no_eigenvectors": true,
+  "hic.no_slice": true,
   "hic.reference_index": "tests/data/hg38_chr19_chrM_GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.tar.gz",
   "hic.restriction_enzymes": [
     "none"