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Ensembl is having a bad day so adding some retries to thngs that touch their API
Getting Server 500 errors, this should probably be better handled in the python code, but for a quick fix this should be ok
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workflows/metadata/ensembl.nf

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@@ -17,6 +17,8 @@ process assemblies {
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process fetch_compara {
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when { params.databases.ensembl.vertebrates.run }
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errorStrategy 'retry'
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maxRetries 10
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output:
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path('*.nt.fasta.gz')
@@ -58,6 +60,8 @@ process proteins {
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process coordinate_systems {
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when { params.databases.ensembl.vertebrates.run }
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errorStrategy 'retry'
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maxRetries 10
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input:
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path(connections)
@@ -73,6 +77,8 @@ process coordinate_systems {
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process karyotypes {
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when { params.databases.ensembl.vertebrates.run }
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errorStrategy 'retry'
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maxRetries 10
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output:
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path('karyotypes.csv')

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