Merge pull request #357 from nf-core/dev

release 2.3.2

bin/megafusion.py

@@ -97,10 +97,21 @@ def build_fusioninspector_dataframe(file, map):
 
 
 def read_build_fusionreport(fusionreport_file):
-    with open(fusionreport_file) as fusionreport:
-        from_html = [line.split('rows": [')[1] for line in fusionreport if 'name="fusion_list' in line]
+    with open(fusionreport_file) as f:
+        from_html = [line.split('rows": [')[1] for line in f if 'name="fusion_list' in line]
         expression = from_html[0].split('], "tool')[0]
-        return pd.DataFrame.from_dict(ast.literal_eval(expression)).set_index("fusion")
+    fusion_report = pd.DataFrame.from_dict(ast.literal_eval(expression)).set_index("fusion")
+    if not "arriba" in fusion_report.columns:
+        fusion_report["arriba"] = ""
+    if not "fusioncatcher" in fusion_report.columns:
+        fusion_report["fusioncatcher"] = ""
+    if not "pizzly" in fusion_report.columns:
+        fusion_report["pizzly"] = ""
+    if not "squid" in fusion_report.columns:
+        fusion_report["squid"] = ""
+    if not "starfusion" in fusion_report.columns:
+        fusion_report["starfusion"] = ""
+    return fusion_report
 
 
 def column_manipulation(df):

modules/local/megafusion/main.nf

@@ -4,8 +4,8 @@ process MEGAFUSION {
 
     conda "conda-forge::python=3.8.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/python:3.9--1' :
-        'quay.io/biocontainers/python:3.9--1' }"
+        'https://depot.galaxyproject.org/singularity/pandas:1.5.2' :
+        'quay.io/biocontainers/pandas:1.5.2' }"
 
     input:
     tuple val(meta), path(tsv), path(report)

nextflow.config

@@ -256,7 +256,7 @@ manifest {
     description     = """Nextflow rnafusion analysis pipeline, part of the nf-core community."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version = '2.3.0'
+    version = '2.3.2'
     doi             = ''
 }