parse_influenza_blast_results.py: fix missing var, remove unused thre…

…ads cli opt
peterk87 · Jul 10, 2023 · f7acaba · f7acaba
1 parent 78c5c4b
commit f7acaba
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Showing 2 changed files with 13 additions and 12 deletions.
diff --git a/bin/parse_influenza_blast_results.py b/bin/parse_influenza_blast_results.py
@@ -296,6 +296,7 @@ def find_h_or_n_type(df_merge, seg, is_iav):
     if is_iav:
         type_counts = df_segment["Genotype"].value_counts(sort=True)
         type_counts = type_counts.filter(~pl.col("Genotype").is_null())
+        reg_h_or_n_type = "[Hh]" if h_or_n == "H" else "[Nn]"
         df_type_counts = type_counts.with_columns(pl.lit(type_counts["Genotype"].str.extract(reg_h_or_n_type + r"(\d+)").alias(type_name)))
         df_type_counts = df_type_counts.filter(~pl.col(type_name).is_null())
         logging.debug(f"{df_type_counts}")
@@ -355,12 +356,19 @@ def find_h_or_n_type(df_merge, seg, is_iav):
     "--pident-threshold", default=0.85, help="BLAST percent identity threshold"
 )
 @click.option('--min-aln-length', default=50, help="Min BLAST alignment length threshold")
-@click.option("--threads", default=4, help="Number of BLAST result parsing threads.")
 @click.option("--get-top-ref", default=False, help="Get top ref accession id from ncbi database.")
 @click.option("--sample-name", default="", help="Sample Name.")
 @click.argument("blast_results", nargs=-1)
-def report(flu_metadata, blast_results, excel_report, top, pident_threshold,
-           min_aln_length, threads, get_top_ref, sample_name):
+def report(
+        flu_metadata,
+        blast_results,
+        excel_report,
+        top,
+        pident_threshold,
+        min_aln_length,
+        get_top_ref,
+        sample_name
+):
     from rich.traceback import install
     install(show_locals=True, width=120, word_wrap=True)
     logging.basicConfig(

diff --git a/modules/local/subtyping_report.nf b/modules/local/subtyping_report.nf
@@ -1,9 +1,3 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process SUBTYPING_REPORT {
   memory { 
     // Dynamically determine how much memory is required for this task based on 
@@ -33,17 +27,16 @@ process SUBTYPING_REPORT {
   path(blastn_results)
 
   output:
-  path('iav-subtyping-report.xlsx'), emit: report
+  path('nf-flu-subtyping-report.xlsx'), emit: report
   path('parse_influenza_blast_results.log'), emit: log
   path "versions.yml", emit: versions
 
   script:
   """
   parse_influenza_blast_results.py \\
-   --threads ${task.cpus} \\
    --flu-metadata $genomeset \\
    --top ${params.max_top_blastn} \\
-   --excel-report iav-subtyping-report.xlsx \\
+   --excel-report nf-flu-subtyping-report.xlsx \\
    --pident-threshold $params.pident_threshold \\
    $blastn_results
   ln -s .command.log parse_influenza_blast_results.log