From 186b772b62678020a4464c5ef94999473cd87fa7 Mon Sep 17 00:00:00 2001 From: "katarzyna.otylia.sikora@gmail.com" Date: Mon, 22 Apr 2024 09:14:02 +0200 Subject: [PATCH] seacr mode --- snakePipes/shared/rules/ChIP_peak_calling.snakefile | 2 +- snakePipes/shared/rules/ChIP_peak_calling_spikein.snakefile | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/snakePipes/shared/rules/ChIP_peak_calling.snakefile b/snakePipes/shared/rules/ChIP_peak_calling.snakefile index 247af518..33cd1640 100755 --- a/snakePipes/shared/rules/ChIP_peak_calling.snakefile +++ b/snakePipes/shared/rules/ChIP_peak_calling.snakefile @@ -279,7 +279,7 @@ rule SEACR_peaks_lenient: script=os.path.join(maindir, "shared","tools/SEACR-1.3/SEACR_1.3.sh") conda: CONDA_SEACR_ENV shell: """ - bash {params.script} {input.chip} {input.control} {params.fdr} "norm" "lenient" {params.prefix} 2>{log} + bash {params.script} {input.chip} {input.control} {params.fdr} "norm" "relaxed" {params.prefix} 2>{log} """ rule SEACR_peak_stringent_qc: diff --git a/snakePipes/shared/rules/ChIP_peak_calling_spikein.snakefile b/snakePipes/shared/rules/ChIP_peak_calling_spikein.snakefile index d05f4c8f..a8e48e6c 100755 --- a/snakePipes/shared/rules/ChIP_peak_calling_spikein.snakefile +++ b/snakePipes/shared/rules/ChIP_peak_calling_spikein.snakefile @@ -255,7 +255,7 @@ rule SEACR_peaks_stringent: else [] output: "SEACR/{chip_sample}_host.stringent.bed" - log: "SEACR/logs/{chip_sample}.log" + log: "SEACR/logs/{chip_sample}_stringent.log" params: fdr = lambda wildcards,input: fdr if not input.control else "", prefix = os.path.join(outdir,"SEACR/{chip_sample}_host"), @@ -272,14 +272,14 @@ rule SEACR_peaks_lenient: else [] output: "SEACR/{chip_sample}_host.lenient.bed" - log: "SEACR/logs/{chip_sample}.log" + log: "SEACR/logs/{chip_sample}_lenient.log" params: fdr = lambda wildcards,input: fdr if not input.control else "", prefix = os.path.join(outdir,"SEACR/{chip_sample}_host"), script=os.path.join(maindir, "shared","tools/SEACR-1.3/SEACR_1.3.sh") conda: CONDA_SEACR_ENV shell: """ - bash {params.script} {input.chip} {input.control} {params.fdr} "non" "lenient" {params.prefix} 2>{log} + bash {params.script} {input.chip} {input.control} {params.fdr} "non" "relaxed" {params.prefix} 2>{log} """