Logging to stdout and better errors

CHANGELOG.md

@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - [#180](https://github.com/nf-core/epitopeprediction/pull/180) - Add support for `VEP` annotated VCF files [#172](https://github.com/nf-core/epitopeprediction/issues/172)
+- [#186](https://github.com/nf-core/epitopeprediction/pull/186) - Log messages from `epaa.py` script to stdout and provide `sys.exit` error messages.
 
 ### `Changed`
 

bin/epaa.py

@@ -31,9 +31,15 @@
 # instantiate global logger object
 logger = logging.getLogger(__name__)
 # turn off passing of messages to root logger
-logger.propagate = False
+# logger.propagate = False
 logger.setLevel(logging.DEBUG)
 
+handler = logging.StreamHandler(sys.stdout)
+handler.setLevel(logging.DEBUG)
+formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
+handler.setFormatter(formatter)
+logger.addHandler(handler)
+
 ID_SYSTEM_USED = EIdentifierTypes.ENSEMBL
 transcriptProteinMap = {}
 transcriptSwissProtMap = {}
@@ -498,7 +504,7 @@ def read_vcf(filename, pass_only=True):
                     list_vars.append(var)
             else:
                 logger.error("No supported variant annotation string found. Aborting.")
-                sys.exit(1)
+                sys.exit("No supported variant annotation string found. Input VCFs require annotation with SNPEff or VEP prior to running the epitope prediction pipeline.")
     transToVar = {}
 
     # fix because of memory/timing issues due to combinatorial explosion
@@ -1294,9 +1300,14 @@ def __main__():
 
     if len(sys.argv) <= 1:
         parser.print_help()
-        sys.exit(1)
+        sys.exit("Provide at least one argument to epaa.py.")
+
+    filehandler = logging.FileHandler("{}_prediction.log".format(args.identifier))
+    filehandler.setLevel(logging.DEBUG)
+    filehandler.setFormatter(formatter)
+    logger.addHandler(filehandler)
 
-    logger.addHandler(logging.FileHandler("{}_prediction.log".format(args.identifier)))
+    logger.info("Running Epitope Prediction And Annotation version: " + str(VERSION))
     logger.info("Starting predictions at " + str(datetime.now().strftime("%Y-%m-%d %H:%M:%S")))
 
     metadata = []
@@ -1308,9 +1319,11 @@ def __main__():
 
     # read in variants or peptides
     if args.peptides:
+        logger.info("Running epaa for peptides...")
         peptides, metadata = read_peptide_input(args.peptides)
     else:
         if args.somatic_mutations.endswith(".GSvar") or args.somatic_mutations.endswith(".tsv"):
+            logger.info("Running epaa for variants...")
             variant_list, transcripts, metadata = read_GSvar(args.somatic_mutations)
         elif args.somatic_mutations.endswith(".vcf"):
             variant_list, transcripts, metadata = read_vcf(args.somatic_mutations)

modules/local/epytope_peptide_prediction.nf

@@ -12,8 +12,8 @@ process EPYTOPE_PEPTIDE_PREDICTION {
 
     output:
     tuple val(meta), path("*.json"), emit: json
-    tuple val(meta), path("*.tsv"), optional: true, emit: predicted
-    tuple val(meta), path("*.fasta"), optional: true, emit: fasta
+    tuple val(meta), path("*.tsv"), emit: predicted, optional: true
+    tuple val(meta), path("*.fasta"), emit: fasta, optional: true
     path "versions.yml", emit: versions
 
     script: