From 8d0c90aaf9061193e17732457f74c59fc9009ccd Mon Sep 17 00:00:00 2001 From: Kaitlyn Jiayi Li Date: Tue, 15 Oct 2024 08:02:31 -0700 Subject: [PATCH 1/4] removed unused git submodule, updated spades container --- .gitmodules | 3 --- jgi_assembly.wdl | 8 +++++--- jgi_meta_wdl | 1 - shortReads_assembly.wdl | 2 +- 4 files changed, 6 insertions(+), 8 deletions(-) delete mode 160000 jgi_meta_wdl diff --git a/.gitmodules b/.gitmodules index 6dcda7d..e69de29 100644 --- 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 index 54a3926..2c8379e 100644 --- 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" } @@ -30,7 +30,8 @@ workflow jgi_metaAssembly{ call int.make_interleaved_reads{ input: input_files = input_files, - container = bbtools_container + 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 deleted file mode 160000 index bc7c437..0000000 --- a/jgi_meta_wdl +++ /dev/null @@ -1 +0,0 @@ -Subproject commit bc7c4371ea0fa83355bada341ec353b9feb3eff2 diff --git a/shortReads_assembly.wdl b/shortReads_assembly.wdl index 5452326..9f7741a 100755 --- 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 } From 547f3a8557cf6a741b4612a825922af589ab2397 Mon Sep 17 00:00:00 2001 From: Kaitlyn Jiayi Li Date: Tue, 15 Oct 2024 10:01:03 -0700 Subject: [PATCH 2/4] bump version --- version.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/version.txt b/version.txt index cb84361..7969702 100644 --- a/version.txt +++ b/version.txt @@ -1,3 +1,3 @@ -v1.0.5 +v1.0.6 From 6c98933bcb215976e751624999f232f24ceac11c Mon Sep 17 00:00:00 2001 From: Kaitlyn Jiayi Li Date: Tue, 15 Oct 2024 11:09:15 -0700 Subject: [PATCH 3/4] add runtime mem for interleave --- make_interleaved_WDL/make_interleaved_reads.wdl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/make_interleaved_WDL/make_interleaved_reads.wdl b/make_interleaved_WDL/make_interleaved_reads.wdl index 20e95b8..6c1fd5b 100644 --- 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 { From c8283f10684a778d9d0b68d9d3ae06cad6e32143 Mon Sep 17 00:00:00 2001 From: Kaitlyn Li Date: Wed, 16 Oct 2024 08:53:51 -0600 Subject: [PATCH 4/4] remove extra comma --- jgi_assembly.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/jgi_assembly.wdl b/jgi_assembly.wdl index 2c8379e..3076f92 100644 --- a/jgi_assembly.wdl +++ b/jgi_assembly.wdl @@ -30,7 +30,7 @@ workflow jgi_metaAssembly{ call int.make_interleaved_reads{ input: input_files = input_files, - container = bbtools_container, + container = bbtools_container } }