Merge pull request #24 from microbiomedata/23-update-to-spades-version-4

removed unused git submodule, updated spades container
microbiomedata · Oct 20, 2024 · 8d7df73 · 8d7df73
2 parents 58c8ad7 + c8283f1
commit 8d7df73
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Showing 6 changed files with 8 additions and 8 deletions.
diff --git a/.gitmodules b/.gitmodules
@@ -1,3 +0,0 @@
-[submodule "jgi_meta_wdl"]
-	path = jgi_meta_wdl
-	url = https://code.jgi.doe.gov/BFoster/jgi_meta_wdl.git

diff --git a/jgi_assembly.wdl b/jgi_assembly.wdl
@@ -1,7 +1,6 @@
 version 1.0
 import "shortReads_assembly.wdl" as srma
 import "make_interleaved_WDL/make_interleaved_reads.wdl" as int
-# import "jgi_meta_wdl/metagenome_improved/metaflye.wdl" as lrma
 import "https://code.jgi.doe.gov/BFoster/jgi_meta_wdl/-/raw/bc7c4371ea0fa83355bada341ec353b9feb3eff2/metagenome_improved/metaflye.wdl" as lrma
 
 workflow jgi_metaAssembly{
@@ -22,6 +21,7 @@ workflow jgi_metaAssembly{
         String minimap2_parameters = "-a -x map-hifi -t 32"
         String samtools_container = "staphb/samtools:1.18"
         String bbtools_container = "microbiomedata/bbtools:38.96"
+        String spades_container="staphb/spades:4.0.0"
     }
 
 
@@ -31,6 +31,7 @@ workflow jgi_metaAssembly{
 			input:
 			input_files = input_files,
             container = bbtools_container
+
        		}
     	}
         call srma.jgi_metaASM{
@@ -39,7 +40,8 @@ workflow jgi_metaAssembly{
             threads = threads,
             input_file = if length(input_files) > 1 then make_interleaved_reads.interleaved_fastq else input_files[0],
             proj = proj,
-            bbtools_container = bbtools_container
+            bbtools_container = bbtools_container,
+            spades_container = spades_container
 
         }
 

diff --git a/jgi_meta_wdl b/jgi_meta_wdl
diff --git a/make_interleaved_WDL/make_interleaved_reads.wdl b/make_interleaved_WDL/make_interleaved_reads.wdl
@@ -45,6 +45,8 @@ task interleave_reads{
 	
 	runtime {
 		docker: container
+		memory: "1 GiB"
+        cpu:  1
 	}
 
 	output {

diff --git a/shortReads_assembly.wdl b/shortReads_assembly.wdl
@@ -10,7 +10,7 @@ workflow jgi_metaASM {
         String rename_contig_prefix="scaffold"
         # Float uniquekmer=1000
         String bbtools_container="microbiomedata/bbtools:38.96"
-        String spades_container="microbiomedata/spades:3.15.0"
+        String spades_container="staphb/spades:4.0.0"
         String worflowmeta_container="microbiomedata/workflowmeta:1.1.1"
         Boolean paired = true
         }

diff --git a/version.txt b/version.txt
@@ -1,3 +1,3 @@
-v1.0.5
+v1.0.6