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authorAndreaGuarracino2020-07-23 22:28:37 +0200
committerAndreaGuarracino2020-07-27 12:15:05 +0200
commit088d0a7fa47d4dff5a38f42fe4d12b9841bb033e (patch)
tree3691ea7c09803bb974714b4418c799f743dab03b /workflows/pangenome-generate
parent8e052cb7355eed7ce4d7075b23c9b0439285f84e (diff)
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new workflow for odgi building from spoa gfa
Diffstat (limited to 'workflows/pangenome-generate')
-rw-r--r--workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl29
1 files changed, 29 insertions, 0 deletions
diff --git a/workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl b/workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl
new file mode 100644
index 0000000..2459ce7
--- /dev/null
+++ b/workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl
@@ -0,0 +1,29 @@
+cwlVersion: v1.1
+class: CommandLineTool
+inputs:
+ inputGFA: File
+outputs:
+ odgiGraph:
+ type: File
+ outputBinding:
+ glob: $(inputs.inputGFA.nameroot).unchop.sorted.odgi
+requirements:
+ InlineJavascriptRequirement: {}
+ ShellCommandRequirement: {}
+hints:
+ DockerRequirement:
+ dockerPull: "quay.io/biocontainers/odgi:v0.3--py37h8b12597_0"
+ ResourceRequirement:
+ coresMin: 4
+ ramMin: $(7 * 1024)
+ outdirMin: $(Math.ceil((inputs.inputGFA.size/(1024*1024*1024)+1) * 2))
+ InitialWorkDirRequirement:
+ listing:
+ - entry: $(inputs.inputGFA)
+ writable: true
+arguments: [odgi, build, -g, $(inputs.inputGFA), -o, -,
+ {shellQuote: false, valueFrom: "|"},
+ odgi, unchop, -i, -, -o, -,
+ {shellQuote: false, valueFrom: "|"},
+ odgi, sort, -i, -, -p, s, -o, $(inputs.inputGFA.nameroot).unchop.sorted.odgi
+ ]