Merge pull request #226 from skrakau/fix_busco_issue

Fix handling of BUSCO output with auto lineage selection
nf-core · Jul 28, 2021 · 2fecf1f · 2fecf1f
2 parents 481a002 + c5cd2f7
commit 2fecf1f
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -15,6 +15,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#218](https://github.com/nf-core/mag/pull/218) - Update to nf-core 2.0.1 `TEMPLATE` (DSL2)
 
+### `Fixed`
+
+- [#226](https://github.com/nf-core/mag/pull/226) - Fix handling of `BUSCO` output when run in auto lineage selection mode and selected specific lineage is the same as the generic one.
+
 ## v2.0.0 - 2021/06/01
 
 ### `Added`

diff --git a/modules/local/busco.nf b/modules/local/busco.nf
@@ -111,15 +111,18 @@ process BUSCO {
                 echo "Domain and specific lineage could be selected by BUSCO."
                 cp BUSCO/short_summary.specific.\${db_name_spec}.BUSCO.txt short_summary.specific_lineage.\${db_name_spec}.${bin}.txt
 
+                db_name_gen=""
                 summaries_gen=(BUSCO/short_summary.generic.*.BUSCO.txt)
-                if [ \${#summaries_gen[@]} -ne 1 ]; then
-                    echo "ERROR: none or multiple 'BUSCO/short_summary.generic.*.BUSCO.txt' files found. Expected one."
-                    exit 1
+                if [ \${#summaries_gen[@]} -lt 1 ]; then
+                    echo "No 'BUSCO/short_summary.generic.*.BUSCO.txt' file found. Assuming selected domain and specific lineages are the same."
+                    cp BUSCO/short_summary.specific.\${db_name_spec}.BUSCO.txt short_summary.domain.\${db_name_spec}.${bin}.txt
+                    db_name_gen=\${db_name_spec}
+                else
+                    [[ \$summaries_gen =~ BUSCO/short_summary.generic.(.*).BUSCO.txt ]];
+                    db_name_gen="\${BASH_REMATCH[1]}"
+                    echo "Used generic lineage dataset: \${db_name_gen}"
+                    cp BUSCO/short_summary.generic.\${db_name_gen}.BUSCO.txt short_summary.domain.\${db_name_gen}.${bin}.txt
                 fi
-                [[ \$summaries_gen =~ BUSCO/short_summary.generic.(.*).BUSCO.txt ]];
-                db_name_gen="\${BASH_REMATCH[1]}"
-                echo "Used generic lineage dataset: \${db_name_gen}"
-                cp BUSCO/short_summary.generic.\${db_name_gen}.BUSCO.txt short_summary.domain.\${db_name_gen}.${bin}.txt
 
                 for f in BUSCO/run_\${db_name_gen}/busco_sequences/single_copy_busco_sequences/*faa; do
                     cat BUSCO/run_\${db_name_gen}/busco_sequences/single_copy_busco_sequences/*faa | gzip >${bin}_buscos.\${db_name_gen}.faa.gz