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nextstrain / ncov

Nextstrain build for novel coronavirus SARS-CoV-2
https://nextstrain.org/ncov
MIT License
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Default run doesn't work #692

Open rneher opened 3 years ago

rneher commented 3 years ago

We used to be able to run an example workflow by simply doing

snakemake -j1

Now not even clean works anymore without specifying a profile with inputs:

(nextstrain) richard:~/Projects/SARS-CoV-2/ncov$ snakemake -n
ERROR: Your workflow does not define any input files to start with.
Update your configuration file (e.g., 'builds.yaml') to define at least one input dataset as follows and try running the workflow again:

  inputs:
    name: local-data
    metadata: data/example_metadata.tsv
    sequences: data/example_sequences.fasta.gz

SystemExit in line 95 of SARS-CoV-2/ncov/Snakefile:
1
  File "SARS-CoV-2/ncov/Snakefile", line 95, in <module>

Not such a big deal, but somewhat suboptimal.

huddlej commented 3 years ago

What inputs would a user expect when running snakemake with no arguments? I see this as akin to running augur filter with no inputs and expecting it to produce something.

Inability to run the clean rule (and other rules that don't depend on inputs) is definitely a bug.