document report param

pinellolab · May 30, 2019 · 3bcd50d · 3bcd50d
1 parent 7930343
commit 3bcd50d
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diff --git a/CRISPResso2/CRISPRessoCORE.py b/CRISPResso2/CRISPRessoCORE.py
@@ -3422,7 +3422,7 @@ def count_alternate_alleles(sub_base_vectors,ref_name,ref_sequence,ref_total_aln
 
         if not args.suppress_report:
             if (args.place_report_in_output_folder):
-                report_name = os.path.join(OUTPUT_DIRECTORY,"CRISPResso2_report.html")
+                report_name = _jp("CRISPResso2_report.html")
             else:
                 report_name = OUTPUT_DIRECTORY+'.html'
             CRISPRessoReport.make_report(crispresso2_info,report_name,OUTPUT_DIRECTORY,_ROOT)

diff --git a/README.md b/README.md
@@ -247,6 +247,8 @@ This should produce a folder called 'CRISPResso_on_base_editor'. Open the file c
 
 --suppress_plots: Suppress output plots (default: False)
 
+--place_report_in_output_folder: If true, report will be written inside the CRISPResso output folder. By default, the report will be written one directory up from the report output. (default: False)
+
 ## CRISPResso2 output
 The output of CRISPResso2 consists of a set of informative graphs that allow for the quantification and visualization of the position and type of outcomes within an amplicon sequence.