From f6b5cb3e46f33b31b2c85e6f4cf8ad7681da296f Mon Sep 17 00:00:00 2001 From: alsmith Date: Thu, 25 Jan 2024 11:16:11 +0000 Subject: [PATCH] Update file paths in hub.smk --- seqnado/workflow/rules/hub.smk | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/seqnado/workflow/rules/hub.smk b/seqnado/workflow/rules/hub.smk index 8344728b..36c93660 100644 --- a/seqnado/workflow/rules/hub.smk +++ b/seqnado/workflow/rules/hub.smk @@ -63,9 +63,10 @@ def get_hub_input(wildcards): if config["call_peaks"]: input_files.extend( expand( - "seqnado_output/peaks/{method}/{sample}.bigBed", + "seqnado_output/peaks/{method}/{sample}_{treatment}.bigBed", method=config["peak_calling_method"], sample=SAMPLE_NAMES_IP, + treatment=IP + CONTROL, ) ) @@ -112,7 +113,7 @@ rule bed_to_bigbed: resources: mem_mb=500, log: - "seqnado_output/logs/bed_to_bigbed/{directory}_{sample}.log", + "seqnado_output/logs/bed_to_bigbed/{directory}/{sample}.log", shell: """ sort -k1,1 -k2,2n {input.bed} | grep '#' -v > {input.bed}.tmp &&