Write basic tests - Githubissues

EnzymeFunctionInitiative / EST

Programs for creating Sequence Similarity Networks and wrappers for pipeline submission on a torque cluster

GNU General Public License v3.0

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Write basic tests #20

Closed 1ndy closed 4 months ago

1ndy commented 4 months ago

Write basic tests that test the creation of parameter files under different import modes. These should not be designed to test edge cases but rather confirm that no changes have caused regressions.

[ ] Add option to specify which config to use

nilsoberg commented 4 months ago

--blast-query smalldata/blast_query.fa can be added to create_est_nextflow_params.py line in est_sequence_blast.sh to support BLAST input option.

A sequence for testing can be extracted from the small dataset:

perl -e '$h=0; while (<>) { last if (m/^>/ and ++$h > 1); next if m/^>/; $seq .= $_; } print $seq;' < smalldata/test.fasta > smalldata/blast_query.fa