remove options to avoid confusion

microbiomedata · Jan 14, 2021 · e877ae4 · e877ae4
1 parent 5f54d5d
commit e877ae4
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Showing 3 changed files with 6 additions and 7 deletions.
diff --git a/mbin_nmdc.wdl b/mbin_nmdc.wdl
@@ -4,6 +4,7 @@ workflow nmdc_mags {
     File contig_file
     File sam_file
     File gff_file
+    String container = "microbiomedata/nmdc_mbin:0.1.0"
     File? map_file
     File? domain_file
     Int cpu=32
@@ -19,7 +20,8 @@ workflow nmdc_mags {
                  map=map_file, 
                  domain=domain_file, 
 		 cpu=cpu,
-                 database=database
+                 database=database,
+	         container=container
     }
 
     call make_output {
@@ -65,11 +67,13 @@ task mbin_nmdc {
 	File? domain
         String database
 	Int cpu
+        String container
 	String filename_outlog="stdout.log"
 	String filename_errlog="stderr.log"
 	String filename_stat="checkm_qa.out"
 	String dollar="$"
 	runtime {
+                docker: container
 		mem: "120 GiB"
 		cpu:  cpu
 		database: database

diff --git a/options.json b/options.json
diff --git a/submit.sh b/submit.sh
@@ -13,4 +13,4 @@
 
 cd /global/cfs/projectdirs/m3408/aim2/metagenome/MAGs
 
-java -Dconfig.file=shifter.conf -jar /global/common/software/m3408/cromwell-45.jar run -i input.json -o options.json -m /global/cfs/projectdirs/m3408/aim2/metagenome/MAGs/metadataOut/test.json mbin_nmdc.wdl 
+java -Dconfig.file=shifter.conf -jar /global/common/software/m3408/cromwell-45.jar run -i input.json  -m /global/cfs/projectdirs/m3408/aim2/metagenome/MAGs/metadataOut/test.json mbin_nmdc.wdl
Original file line number	Diff line number	Diff line change
Expand Up		@@ -13,4 +13,4 @@

		cd /global/cfs/projectdirs/m3408/aim2/metagenome/MAGs

		java -Dconfig.file=shifter.conf -jar /global/common/software/m3408/cromwell-45.jar run -i input.json -o options.json -m /global/cfs/projectdirs/m3408/aim2/metagenome/MAGs/metadataOut/test.json mbin_nmdc.wdl
		java -Dconfig.file=shifter.conf -jar /global/common/software/m3408/cromwell-45.jar run -i input.json -m /global/cfs/projectdirs/m3408/aim2/metagenome/MAGs/metadataOut/test.json mbin_nmdc.wdl