diff --git a/src/busco/busco/config.vsh.yaml b/src/busco/busco/config.vsh.yaml index 33af0c54..43c1c7d3 100644 --- a/src/busco/busco/config.vsh.yaml +++ b/src/busco/busco/config.vsh.yaml @@ -153,12 +153,12 @@ functionality: arguments: - name: --contig_break type: integer - default: 10 + required: false description: | Number of contiguous Ns to signify a break between contigs in BBTools analysis. - name: --limit type: integer - default: 3 + required: false description: | Number of candidate regions (contig or transcript) from the BLAST output to consider per BUSCO. This option is only effective in pipelines using BLAST, i.e. the genome pipeline (see --augustus) or the prokaryota transcriptome pipeline. @@ -171,7 +171,7 @@ functionality: arguments: - name: --e_value type: double - default: 0.001 + required: false description: | E-value cutoff for BLAST searches. diff --git a/src/busco/busco/test.sh b/src/busco/busco/test.sh index b46ef50b..1d6ce29f 100644 --- a/src/busco/busco/test.sh +++ b/src/busco/busco/test.sh @@ -7,7 +7,6 @@ echo "> Running busco" --mode protein \ --lineage_dataset stramenopiles_odb10 \ --output_dir output -ls -la output/run_stramenopiles_odb10 echo ">> Checking output" [ ! -f "output/full_table.tsv" ] && echo "full_table.tsv does not exist" && exit 1