Merge pull request #117 from fmalmeida/116-integron_finder_2gff-terminated-with-an-error

Fix issues #116

Author: fmalmeida

.zenodo.json

@@ -2,7 +2,7 @@
     "description": "<p>The pipeline</p>\n\n<p>bacannot, is a customisable, easy to use, pipeline that uses state-of-the-art software for comprehensively annotating prokaryotic genomes having only Docker and Nextflow as dependencies. It is able to annotate and detect virulence and resistance genes, plasmids, secondary metabolites, genomic islands, prophages, ICEs, KO, and more, while providing nice an beautiful interactive documents for results exploration.</p>", 
     "license": "other-open", 
     "title": "fmalmeida/bacannot: A generic but comprehensive bacterial annotation pipeline", 
-    "version": "v3.3", 
+    "version": "v3.3.2", 
     "upload_type": "software",
     "creators": [
         {

markdown/CHANGELOG.md

@@ -2,6 +2,10 @@
 
 The tracking for changes started in v2.1
 
+## v3.3.2 [09-February-2024]
+
+* [[#116](https://github.com/fmalmeida/bacannot/issues/116)] -- Small update to avoid having `integron_finder` gbks with start position as 0, since it breaks conversion to gff.
+
 ## v3.3.1 [29-October-2023]
 
 * [[#111](https://github.com/fmalmeida/bacannot/issues/111)] -- Updated `falmeida-py` package version to fix problem with missing key for Summary.

modules/MGEs/integron_finder_2gff.nf

@@ -12,13 +12,13 @@ process INTEGRON_FINDER_2GFF {
     script:
     def args = task.ext.args ?: ''
     """    
+    # fix 0-based sequences
+    sed -e 's/ 0\\.\\./ 1\\.\\./g' -e 's/complement(0\\.\\./complement(1\\.\\./g' $gbk > fixed.gbk
+    
     # convert to gff if available
-    touch ${prefix}_integrons.gff ;
-    for gbk in \$(ls *.gbk) ; do
-        conda run -n perl bp_genbank2gff3 \$gbk -o - | \
-            grep 'integron_id' | \
-            sed 's|ID=.*integron_id=|ID=|g' | \
-            sed 's/GenBank/Integron_Finder/g' >> ${prefix}_integrons.gff
-    done
+    conda run -n perl bp_genbank2gff3 fixed.gbk -o - | \\
+        grep 'integron_id' | \\
+        sed 's|ID=.*integron_id=|ID=|g' | \\
+        sed 's/GenBank/Integron_Finder/g' >> ${prefix}_integrons.gff
     """
 }

nextflow.config

@@ -108,7 +108,7 @@ manifest {
     homePage        = "https://github.com/fmalmeida/bacannot"
     mainScript      = "main.nf"
     nextflowVersion = "!>=22.10.1"
-    version         = '3.3'
+    version         = '3.3.2'
 }
 
 // Function to ensure that resource requirements don't go beyond