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Add default profile to set Snakemake CLI args #13

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Add default profile to set Snakemake CLI args #13

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4 changes: 4 additions & 0 deletions profiles/default/config.yaml
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@victorlin victorlin Apr 30, 2024

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I would think to not introduce the additional complexity of profiles here - we don't use use them for most pathogen repos.

If the goal is to remove the unnecessary --cores argument, we can already remove that - it's not required as of Nextstrain CLI 4.0.0.

Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
cores: all
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@genehack genehack Apr 30, 2024

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The PR overall looks good to me, but I wonder if this should be cores: 1 to better reflect how the current tutorial instructions tell people to run things?

rerun-incomplete: true
printshellcmds: true
reason: true