updated example json, fixes to run time memory for JAWS compatiblity,…

… fixes to finish_reads task
microbiomedata · Jan 10, 2023 · 3defae7 · 3defae7
1 parent 2c6f2c6
commit 3defae7
Show file tree

Hide file tree

Showing 3 changed files with 14 additions and 15 deletions.
diff --git a/ReadbasedAnalysis.wdl b/ReadbasedAnalysis.wdl
@@ -163,16 +163,16 @@ task finish_reads {
         ln ${kraken2_report_tsv} ${prefix}_kraken2_report.tsv
         ln ${kraken2_krona_html} ${prefix}_kraken2_krona.html
 
-        /scripts/generate_object_json.py \ 
+        /scripts/generate_object_json.py \
             --type "nmdc:ReadBasedAnalysisActivity" \
             --set read_based_taxonomy_analysis_activity_set \
             --part ${proj} \
             -p "name=ReadBased Analysis Activity for ${proj}" \
                 was_informed_by=${informed_by} \
                 started_at_time=${start} \
                 ended_at_time=$end \
-                execution_resource=${resource} \
-                git_url=${git_url} \ 
+                execution_resource="${resource}" \
+                git_url=${git_url} \
                 version="v1.0.2-beta" \
             --url ${url_root}${proj}/ReadbasedAnalysis/ \
             --inputs ${input_file} \

diff --git a/ReadbasedAnalysisTasks.wdl b/ReadbasedAnalysisTasks.wdl
@@ -28,7 +28,7 @@ task profilerGottcha2 {
         cpu: CPU
         node: 1
         nwpn: 1
-        mem: "45G"
+        memory: "45G"
         time: "04:00:00"
     }
     meta {
@@ -65,7 +65,7 @@ task profilerCentrifuge {
         cpu: CPU
         node: 1
         nwpn: 1
-        mem: "45G"
+        memory: "45G"
         time: "04:00:00"
     }
     meta {
@@ -104,7 +104,7 @@ task profilerKraken2 {
         cpu: CPU
         node: 1
         nwpn: 1
-        mem: "45G"
+        memory: "45G"
         time: "04:00:00"
     }
     meta {
@@ -128,7 +128,7 @@ task generateSummaryJson {
         docker: DOCKER
         node: 1
         nwpn: 1
-        mem: "45G"
+        memory: "45G"
         time: "04:00:00"
     }
     meta {
@@ -164,4 +164,4 @@ task stage {
      maxRetries: 1
      docker: container
    }
-}
+}
diff --git a/ReadbasedAnalysis_inputs.json b/ReadbasedAnalysis_inputs.json
@@ -9,12 +9,11 @@
     "kraken2": "/global/cfs/projectdirs/m3408/aim2/database/kraken2/",
     "centrifuge": "/global/cfs/projectdirs/m3408/aim2/database/centrifuge/p_compressed"
   },
-  "ReadbasedAnalysis.reads": [
-    "/path/to/SRR7877884.1.fastq.gz",
-    "/path/to/SRR7877884.2.fastq.gz"
-  ],
+  "ReadbasedAnalysis.input_file": "/path/to/test.fastq.gz",
   "ReadbasedAnalysis.paired": true,
-  "ReadbasedAnalysis.prefix": "SRR7877884",
-  "ReadbasedAnalysis.outdir": "/global/cfs/projectdirs/m3408/aim2/metagenome/ReadbasedAnalysis/SRR7877884",
-  "ReadbasedAnalysis.cpu": 8
+  "ReadbasedAnalysis.prefix": "TEST",
+  "ReadbasedAnalysis.cpu": 8,
+  "ReadbasedAnalysis.proj": "TEST",
+  "ReadbasedAnalysis.resource": "NERSC - CORI",
+  "ReadbasedAnalysis.informed_by": "None"
 }