From 1d7fd22fa8ab38758de5c4c378fc4a79c7a58035 Mon Sep 17 00:00:00 2001 From: Darryl Nousome Date: Fri, 5 Jan 2024 13:28:45 -0500 Subject: [PATCH] fix: add rerun incomplete and fix bed --- src/run.py | 1 + workflow/scripts/reformat_bed.py | 5 ++--- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/run.py b/src/run.py index 518a613..5c23814 100644 --- 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 index 55da677..5e44499 100644 --- 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=""