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removed unused git submodule, updated spades container #24

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merged 4 commits into from
Oct 20, 2024
Merged

removed unused git submodule, updated spades container #24

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8d0c90a
removed unused git submodule, updated spades container
kaijli Oct 15, 2024
547f3a8
bump version
kaijli Oct 15, 2024
6c98933
add runtime mem for interleave
kaijli Oct 15, 2024
c8283f1
remove extra comma
kaijli Oct 16, 2024
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3 changes: 0 additions & 3 deletions .gitmodules
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Original file line number Diff line number Diff line change
@@ -1,3 +0,0 @@
[submodule "jgi_meta_wdl"]
path = jgi_meta_wdl
url = https://code.jgi.doe.gov/BFoster/jgi_meta_wdl.git
6 changes: 4 additions & 2 deletions jgi_assembly.wdl
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Original file line number Diff line number Diff line change
@@ -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{
Expand All @@ -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"
}


Expand All @@ -31,6 +31,7 @@ workflow jgi_metaAssembly{
input:
input_files = input_files,
container = bbtools_container

}
}
call srma.jgi_metaASM{
Expand All @@ -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

}

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1 change: 0 additions & 1 deletion jgi_meta_wdl
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Submodule jgi_meta_wdl deleted from bc7c43
2 changes: 2 additions & 0 deletions make_interleaved_WDL/make_interleaved_reads.wdl
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Expand Up @@ -45,6 +45,8 @@ task interleave_reads{

runtime {
docker: container
memory: "1 GiB"
cpu: 1
}

output {
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2 changes: 1 addition & 1 deletion shortReads_assembly.wdl
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Expand Up @@ -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
}
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2 changes: 1 addition & 1 deletion version.txt
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@@ -1,3 +1,3 @@
v1.0.5
v1.0.6