Merge pull request #352 from alexhbnr/busco_nomarkers

Bump up BUSCO version to 5.4.3 and escape lack of marker genes

CHANGELOG.md

@@ -15,9 +15,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#345](https://github.com/nf-core/mag/pull/345) - Bowtie2 mode changed to global alignment for ancient DNA mode (`--very-sensitive` mode) to prevent soft clipping at the end of reads when running in local mode.
 - [#349](https://github.com/nf-core/mag/pull/349) - Add a warning that pipeline will reset minimum contig size to 1500 specifically MetaBAT2 process, if a user supplies below this threshold.
+- [#352](https://github.com/nf-core/mag/pull/352) - Escape the case in the BUSCO module that BUSCO can just detect a root lineage but is not able to find any marker genes
 
 ### `Dependencies`
 
+| Tool  | Previous version | New version |
+| ----- | ---------------- | ----------- |
+| BUSCO | 5.1.0            | 5.4.3       |
+
 ## v2.2.1 - 2022/08/25
 
 ### `Added`

modules/local/busco.nf

@@ -1,10 +1,10 @@
 process BUSCO {
     tag "${bin}"
 
-    conda (params.enable_conda ? "bioconda::busco=5.1.0" : null)
+    conda (params.enable_conda ? "bioconda::busco=5.4.3" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/busco:5.1.0--py_1' :
-        'quay.io/biocontainers/busco:5.1.0--py_1' }"
+        'https://depot.galaxyproject.org/singularity/busco:5.4.3--pyhdfd78af_0':
+        'quay.io/biocontainers/busco:5.4.3--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(bin)
@@ -120,6 +120,10 @@ process BUSCO {
                     break
                 done
 
+            elif egrep -q \$'INFO:\t\\S+ selected' ${bin}_busco.log && egrep -q \$'INFO:\tNo marker genes were found. Root lineage \\S+ is kept' ${bin}_busco.log ; then
+                echo "Domain could be selected by BUSCO, but no more specific lineage."
+                cp BUSCO/short_summary.specific.\${db_name_spec}.BUSCO.txt short_summary.domain.\${db_name_spec}.${bin}.txt
+
             elif egrep -q \$'INFO:\t\\S+ selected' ${bin}_busco.log && egrep -q \$'INFO:\tNot enough markers were placed on the tree \\([0-9]*\\). Root lineage \\S+ is kept' ${bin}_busco.log ; then
                 echo "Domain could be selected by BUSCO, but no more specific lineage."
                 cp BUSCO/short_summary.specific.\${db_name_spec}.BUSCO.txt short_summary.domain.\${db_name_spec}.${bin}.txt