Merge pull request #15 from skrakau/busco-script-suggestions

Suggestions for BUSCO script
nf-core · May 25, 2023 · 0dfad70 · 0dfad70
2 parents 2f0d31d + bb4cefd
commit 0dfad70
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diff --git a/bin/run_busco.sh b/bin/run_busco.sh
@@ -147,6 +147,9 @@ if [ -f BUSCO/logs/prodigal_out.log ]; then
     mv BUSCO/logs/prodigal_out.log "${bin}_prodigal.gff"
 fi
 
+# output value of most_spec_db
+echo ${most_spec_db} > info_most_spec_db.txt
+
 # if needed delete temporary BUSCO files
 if [ ${busco_clean} = "Y" ]; then
     find . -depth -type d -name "augustus_config" -execdir rm -rf "{}" \;

diff --git a/modules/local/busco.nf b/modules/local/busco.nf
@@ -39,6 +39,7 @@ process BUSCO {
     }
     """
     run_busco.sh "${p}" "${cp_augustus_config}" "${db}" "${bin}" ${task.cpus} "${lineage_dataset_provided}" "${busco_clean}"
+    most_spec_db=\$(<info_most_spec_db.txt)
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":