Update assembly_workflow.py

WillNickols · Dec 7, 2023 · 3aae629 · 3aae629
1 parent 6fe995b
commit 3aae629
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/assembly_workflow.py b/assembly_workflow.py
@@ -850,10 +850,10 @@ def copy_bins(name):
 	os.makedirs(checkm_qa_scratch + name.split("/")[-1] + "/", exist_ok=True)
 	os.makedirs(qa_unmerged_dir + name.split("/")[-1] + "/", exist_ok=True)
 	if args.grid_jobs > 0:
-		command = "if ls " + metabat_out + "*.bin.[0-9]*.fa; then " + this_folder + "checkm2/bin/checkm2 predict -x fa --input " + checkm_bin_name + " --output-directory " + checkm_qa_scratch + name.split("/")[-1] + "/" + " --threads " + str(args.cores) + " " + args.checkm_predict_options + "; " + \
+		command = "if ls " + metabat_out + "*.bin.[0-9]*.fa; then checkm2 predict -x fa --input " + checkm_bin_name + " --output-directory " + checkm_qa_scratch + name.split("/")[-1] + "/" + " --threads " + str(args.cores) + " " + args.checkm_predict_options + "; " + \
 			"else echo -e \"Name\tCompleteness\tContamination\tCompleteness_Model_Used\tTranslation_Table_Used\tCoding_Density\tContig_N50\tAverage_Gene_Length\tGenome_Size\tGC_Content\tTotal_Coding_Sequences\tAdditional_Notes\" > " + qa_unmerged_dir + name.split("/")[-1] + "/quality_report.tsv; fi"
 	else:
-		command = "if ls " + metabat_out + "*.bin.[0-9]*.fa; then " + this_folder + "checkm2/bin/checkm2 predict -x fa --input " + checkm_bin_name + " --output-directory " + qa_unmerged_dir + name.split("/")[-1] + "/" + " --threads " + str(args.cores) + " " + args.checkm_predict_options + "; " + \
+		command = "if ls " + metabat_out + "*.bin.[0-9]*.fa; then checkm2 predict -x fa --input " + checkm_bin_name + " --output-directory " + qa_unmerged_dir + name.split("/")[-1] + "/" + " --threads " + str(args.cores) + " " + args.checkm_predict_options + "; " + \
 			"else echo -e \"Name\tCompleteness\tContamination\tCompleteness_Model_Used\tTranslation_Table_Used\tCoding_Density\tContig_N50\tAverage_Gene_Length\tGenome_Size\tGC_Content\tTotal_Coding_Sequences\tAdditional_Notes\" > " + qa_unmerged_dir + name.split("/")[-1] + "/quality_report.tsv; fi"
 	workflow.add_task_gridable(actions=command,
 	depends=list_targets(name=name, step="copy_bins", paired=paired),