make anvi-self-test --suite workflow-contigs work

anvio/tests/run_workflow_tests_for_contigs.sh

@@ -7,12 +7,25 @@ SETUP_WITH_OUTPUT_DIR $1 $2
 
 INFO "Setting up the pan analysis directory"
 mkdir $output_dir/workflow_test
-cp $files/mock_data_for_pangenomics/*.fa $output_dir/workflow_test/
+cp $files/mock_data_for_pangenomics/*.db $output_dir/workflow_test/
 cp $files/workflows/contigs/* $output_dir/workflow_test/
 cd $output_dir/workflow_test
 
-INFO "compressing sample 1"
-gzip 01.fa
+# all we need a FASTA file here to get things to work, so we
+# will start by migrating the anvi'o contigs-db files
+anvi-migrate *.db --migrate-quickly --quiet
+
+# then generate some files as expected by the test:
+anvi-export-contigs -c E_faecalis_6240.db -o E_faecalis_6240.fa
+anvi-export-contigs -c E_faecalis_6255.db -o E_faecalis_6255.fa
+anvi-export-contigs -c E_faecalis_6512.db -o E_faecalis_6512.fa
+
+# compressing one of the FASTA files to match the `fasta.txt` coming
+# from `$files/workflows/contigs/fasta.txt`
+gzip E_faecalis_6240.fa
+
+# and get rid of the contigs-db files, and resume normal operations
+rm -rf E_fa*.db
 
 INFO "Creating a default config for contigs workflow"
 anvi-run-workflow -w contigs --get-default-config default-config.json

anvio/tests/sandbox/workflows/contigs/fasta.txt

@@ -1,4 +1,4 @@
 name	path
-s01	01.fa.gz
-s02	02.fa
-s03	03.fa
+E_faecalis_6240	E_faecalis_6240.fa.gz
+E_faecalis_6255	E_faecalis_6255.fa
+E_faecalis_6512	E_faecalis_6512.fa