Updated CLI parameters and help messages

anglerfish/explore/cli.py

@@ -11,65 +11,68 @@
     "--threads",
     default=4,
     type=int,
-    help="Number of threads specified by minimap2",
+    help="Number of threads specified to minimap2",
 )
 @click.option(
-    "-n", "--no_overwrite", is_flag=True, help="Do not overwrite existing alignments"
+    "-e",
+    "--use-existing",
+    is_flag=True,
+    help="Use existing alignments if found in the specified output directory.",
 )
 @click.option(
     "-g",
     "--good_hit_threshold",
     default=0.9,
     type=float,
-    help="Fraction of bases before and after index insert required to match perfectly for a hit to be considered a good hit. Default=0.9",
+    help="Fraction of adaptor bases immediately before and immediately after index insert required to match perfectly for a hit to be considered a good hit (default=0.9).",
 )
 @click.option(
     "-i",
     "--insert_thres_low",
     default=4,
     type=int,
-    help="Lower threshold for insert length, with value included",
+    help="Lower threshold for index(+UMI) insert length, with value included (deafult=4).",
 )
 @click.option(
     "-j",
     "--insert_thres_high",
     default=30,
     type=int,
-    help="Upper threshold for insert length, with value included",
+    help="Upper threshold for index(+UMI) insert length, with value included (default=30).",
 )
 @click.option(
     "-B",
     "--minimap_b",
     default=4,
     type=int,
-    help="Minimap2 -B parameter, mismatch penalty",
+    help="Minimap2 -B parameter, mismatch penalty (default=4).",
 )
 @click.option(
     "-m",
     "--min_hits_per_adaptor",
     default=50,
     type=int,
-    help="Minimum number of good hits for an adaptor to be included in the analysis",
+    help="Minimum number of good hits for an adaptor to be included in the analysis (default=50).",
 )
 @click.option(
     "-u",
     "--umi_threshold",
     default=11,
     type=float,
-    help="Minimum number of bases in insert to perform entropy calculation",
+    help="Minimum number of bases in insert to perform entropy calculation (default=11).",
 )
 @click.option(
     "-k",
     "--kmer_length",
     default=2,
     type=int,
-    help="Length of k-mers to use for entropy calculation",
+    help="Length of k-mers to use for entropy calculation (default=2).",
 )
 def main(
     fastq,
     outdir,
     threads,
-    no_overwrite,
+    use_existing,
     good_hit_threshold,
     insert_thres_low,
     insert_thres_high,
@@ -82,7 +85,7 @@ def main(
         fastq,
         outdir,
         threads,
-        no_overwrite,
+        use_existing,
         good_hit_threshold,
         insert_thres_low,
         insert_thres_high,

anglerfish/explore/explore.py

@@ -16,7 +16,7 @@ def run_explore(
     fastq,
     outdir,
     threads,
-    no_overwrite,
+    use_existing,
     good_hit_threshold,
     insert_thres_low,
     insert_thres_high,
@@ -31,9 +31,9 @@ def run_explore(
         os.mkdir(outdir)
     except FileExistsError:
         log.info(f"Output directory {outdir} already exists")
-        if not no_overwrite:
+        if not use_existing:
             log.error(
-                f"Output directory {outdir} already exists, please use --no_overwrite to continue"
+                f"Output directory {outdir} already exists, please use --use_existing to continue"
             )
             exit(1)
         else:
@@ -52,7 +52,7 @@ def run_explore(
         # Align
         aln_path = os.path.join(outdir, f"{adaptor_name}.paf")
         alignments.append((adaptor, aln_path))
-        if os.path.exists(aln_path) and no_overwrite:
+        if os.path.exists(aln_path) and use_existing:
             log.info(f"Skipping {adaptor_name} as alignment already exists")
             continue
         adaptor_path = os.path.join(outdir, f"{adaptor_name}.fasta")