Merge pull request #647 from broadinstitute/fix-viral-ngs-3x-illumina-import

fix: update illumina import for viral-ngs 3.x namespace restructure

Author: dpark01

pipes/WDL/tasks/tasks_demux.wdl

@@ -343,7 +343,7 @@ task illumina_demux {
     # the presence of a barcode_3 column with values in at least some of the rows.
     # We can lean on a Python call out to the SampleSheet class in illumina for this.
     collapse_duplicated_barcodes="false"
-    sample_sheet_barcode_collapse_potential=$(python -c 'import os; import illumina as il; ss=il.SampleSheet(os.path.realpath("~{samplesheet}"),allow_non_unique=True, collapse_duplicates=False); ssc=il.SampleSheet(os.path.realpath("~{samplesheet}"),allow_non_unique=True, collapse_duplicates=True); print("sheet_collapse_possible_true") if len(ss.get_rows())!=len(ssc.get_rows()) else print("sheet_collapse_possible_false")')
+    sample_sheet_barcode_collapse_potential=$(python -c 'import os; import viral_ngs.illumina as il; ss=il.SampleSheet(os.path.realpath("~{samplesheet}"),allow_non_unique=True, collapse_duplicates=False); ssc=il.SampleSheet(os.path.realpath("~{samplesheet}"),allow_non_unique=True, collapse_duplicates=True); print("sheet_collapse_possible_true") if len(ss.get_rows())!=len(ssc.get_rows()) else print("sheet_collapse_possible_false")')
     if [[ "$sample_sheet_barcode_collapse_potential" == "sheet_collapse_possible_true" ]]; then
       collapse_duplicated_barcodes="true"
       collapsed_barcodes_output_samplesheet_arg="--collapse_duplicated_barcodes=barcodes_if_collapsed.tsv"
@@ -356,7 +356,7 @@ task illumina_demux {
 
     # dump sample names from input sample sheet 'sample' col to sample_names.txt
     sample_names_expected_from_samplesheet_list_txt="sample_names.txt"
-    python -c 'import os; import illumina as il; ss=il.SampleSheet(os.path.realpath("~{samplesheet}"),allow_non_unique=True, collapse_duplicates=False); sample_name_list=[r["sample"]+"\n" for r in ss.get_rows()]; f=open("'${sample_names_expected_from_samplesheet_list_txt}'", "w"); f.writelines(sample_name_list); f.close()'
+    python -c 'import os; import viral_ngs.illumina as il; ss=il.SampleSheet(os.path.realpath("~{samplesheet}"),allow_non_unique=True, collapse_duplicates=False); sample_name_list=[r["sample"]+"\n" for r in ss.get_rows()]; f=open("'${sample_names_expected_from_samplesheet_list_txt}'", "w"); f.writelines(sample_name_list); f.close()'
     
     cols_to_revcomp="~{sep=' ' select_first([barcode_columns_to_rev_comp,[default_revcomp_barcode_column]])}"