The local test dataset does not contain a file at the given location.

[mahesh-panchal]

Description of the bug

The instructions give some info on how to test locally.

cd ${TREEVAL_TEST_DATA}
curl https://tolit.cog.sanger.ac.uk/test-data/resources/treeval/TreeValTinyData.tar.gz | tar xzf -

sed -i "s|/home/runner/work/treeval/treeval|${TREEVAL_TEST_DATA}|" TreeValTinyData/gene_alignment_data/fungi/csv_data/LaetiporusSulphureus.gfLaeSulp1-data.csv
sed -i "s|/home/runner/work/treeval/treeval|${TREEVAL_TEST_DATA}|" assets/github_testing/TreeValTinyTest.yaml
nextflow run main.nf -profile test_github,singularity {OTHER ARGUMENTS}

However there's no file extracted called assets/github_testing/TreeValTinyTest.yaml so the second sed command fails.

Also I may be simpler for users if the sed instructions were:

sed -i "s|/home/runner/work/treeval/treeval|${PWD}|" TreeValTinyData/gene_alignment_data/fungi/csv_data/LaetiporusSulphureus.gfLaeSulp1-data.csv
sed -i "s|/home/runner/work/treeval/treeval|${PWD}|" assets/github_testing/TreeValTinyTest.yaml

Since we're in that directory already

Command used and terminal output

$ sed -i "s|/home/runner/work/treeval/treeval|${PWD}|" assets/github_testing/TreeValTinyTest.yaml
sed: can't read assets/github_testing/TreeValTinyTest.yaml: No such file or directory

Relevant files

No response

System information

No response

[mahesh-panchal]

Ah, I see. You're expecting that we've cloned the workflow in that location too.

[DLBPointon]

Hi Mahesh,

Your right.
The setup docs have been neglected for a little while now and should really be reviewed.
We are coming up to a release for #361, I'll add a review to the docs for that.

Thanks for the updated sed commands too.