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Updating WDL's to run on Tahoma #32

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Updating WDL's to run on Tahoma #32

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e2effb9
Change String to File
vlilanl Feb 4, 2025
44d8f9d
added in memory allocation for task stage
vlilanl Feb 4, 2025
de64be4
changed String to File
vlilanl Feb 5, 2025
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4 changes: 2 additions & 2 deletions input.json
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{
"jgi_metaAssembly.input_files":["/global/cfs/cdirs/m3408/www/test_data/SRR13128014.pacbio.subsample.ccs.fastq.gz"],
"jgi_metaAssembly.proj":"nmdc:503125_160870",
"jgi_metaAssembly.input_files":["https://portal.nersc.gov/project/m3408//test_data/SRR13128014.pacbio.subsample.ccs.fastq.gz"],
"jgi_metaAssembly.proj":"nmdc:XXXXXXXXX",
"jgi_metaAssembly.memory": "105G",
"jgi_metaAssembly.threads": "16",
"jgi_metaAssembly.shortRead": false
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3 changes: 1 addition & 2 deletions jgi_assembly.wdl
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Expand Up @@ -12,7 +12,7 @@ workflow jgi_metaAssembly {
String? memory
String? threads
# longReads parameters
Array[String] input_files
Array[File] input_files
String flye_container = "staphb/flye:2.9.2"
String flye_parameters = "--meta -o flye -t 32 --pacbio-hifi"
String smrtlink_container = "bryce911/smrtlink:12.0.0.177059"
Expand All @@ -24,7 +24,6 @@ workflow jgi_metaAssembly {
String spades_container="staphb/spades:4.0.0"
}


if (shortRead) {
if (length(input_files) > 1) {
call int.make_interleaved_reads {
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7 changes: 4 additions & 3 deletions shortReads_assembly.wdl
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Expand Up @@ -4,7 +4,7 @@ workflow jgi_metaASM {
# String? outdir
String? memory
String? threads
String? input_file
File? input_file
String proj
String prefix=sub(proj, ":", "_")
String rename_contig_prefix="scaffold"
Expand Down Expand Up @@ -119,7 +119,7 @@ workflow jgi_metaASM {
task stage {
input {
String container
String? input_file
File? input_file
String memory = "4G"
String target = "staged.fastq.gz"
String output1 = "input.left.fastq.gz"
Expand Down Expand Up @@ -150,6 +150,7 @@ task stage {
}
runtime {
cpu: 2
memory: "4 GiB"
maxRetries: 1
docker: container
}
Expand Down Expand Up @@ -341,7 +342,7 @@ task create_agp {
runtime {
docker: container
memory: "120 GiB"
cpu: 16
cpu: 16
}
command<<<
set -euo pipefail
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