Merge pull request #66 from CCBR/fix_reformatbed

fix: add rerun incomplete and fix bed
CCBR · Jan 9, 2024 · b59a71c · b59a71c
2 parents d1c527b + 1d7fd22
commit b59a71c
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/src/run.py b/src/run.py
@@ -596,6 +596,7 @@ def dryrun(outdir, config='config.json', snakefile=os.path.join('workflow', 'Sna
     try:
         dryrun_output = subprocess.check_output([
             'snakemake', '-npr',
+            '--rerun-incomplete',
             '-s', str(snakefile),
             '--use-singularity',
             '--cores', str(1),

diff --git a/workflow/scripts/reformat_bed.py b/workflow/scripts/reformat_bed.py
@@ -34,10 +34,9 @@
                 if (len(curr_cols) < 3):
                     sys.exit("Targets BED file must contain at least three columns: chr, start, end")
 
-
                 if (len(curr_cols) < 4):
-                    curr_cols[3]="."
-
+                    curr_cols.append(".")
+                                    
                 min_output=curr_cols[0] + "\t" + curr_cols[1]  + "\t" + curr_cols[2]
 
                 extra_fields=""