Add commands for removing intermediates

jcmcnch · Nov 19, 2022 · 5524312 · 5524312
1 parent 8bf8b00
commit 5524312
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/qiime2-2022.2-DADA2-SILVA138.1-PR2_4.14.0/runscripts/02-format-data-for-plotting.sh b/qiime2-2022.2-DADA2-SILVA138.1-PR2_4.14.0/runscripts/02-format-data-for-plotting.sh
@@ -34,8 +34,8 @@ conda activate opedia-env
 #then edit manually to add in appropriate sample IDs
 
 #remove empty rows with pandas, passing empty-file as sys.argv[1]
-./scripts/remove-bad-columns-and-empty-rows.py lt5000seq-samples.txt 04-Formatted/${filestem}_normalized_sequence_counts_reordered.tsv 04-Formatted/${filestem}_counts.QCd.tsv
+./scripts/remove-bad-columns-and-empty-rows.py lt5000seq-samples.txt 04-Formatted/${filestem}_normalized_sequence_counts_reordered.tsv 04-Formatted/${filestem}_merged_16S_18S_counts.QCd.tsv
 
-./scripts/remove-bad-columns-and-empty-rows.py lt5000seq-samples.txt 04-Formatted/${filestem}_proportions_reordered.tsv 04-Formatted/${filestem}_proportions.QCd.tsv
+./scripts/remove-bad-columns-and-empty-rows.py lt5000seq-samples.txt 04-Formatted/${filestem}_proportions_reordered.tsv 04-Formatted/${filestem}_merged_16S_18S_proportions.QCd.tsv
 
 rm -f 04-Formatted/*reordered.tsv