From 6c6372864e7b504a6ae1510050b292282934c6d3 Mon Sep 17 00:00:00 2001 From: Vishal Koparde Date: Mon, 5 Dec 2022 17:49:35 -0500 Subject: [PATCH] adding mmul to config --- config/config.yaml | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/config/config.yaml b/config/config.yaml index 64a61f8..7ee6012 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -29,6 +29,7 @@ samplemanifest: "WORKDIR/samples.tsv" # genome: "hg38" # genome: "hg19" genome: "mm10" +# genome: "mmul" # setting below this line should be changed carefully... defaults are set after considerable optimizations. @@ -75,6 +76,16 @@ mm10: promoterbed: "PIPELINE_HOME/resources/frip/mm10.promoters.bed.gz" enhancerbed: "PIPELINE_HOME/resources/frip/mm10.enhancers.bed.gz" +mmul: + indexdir: "/data/CCBR_Pipeliner/db/PipeDB/Indices/mmul_10/indexes" + blacklistFa: "PIPELINE_HOME/resources/blacklistFa/mmul.blacklist.fa.gz" + tssBed: "PIPELINE_HOME/resources/tssBed/mmul_tssbeds.tar.gz" + homermotif: "PIPELINE_HOME/resources/motif/HOCOMOCOv11_full_HUMAN_MOUSE_mono_homer_format_0.001.motif" + mememotif: "PIPELINE_HOME/resources/motif/HOCOMOCOv11_core_HUMAN_MOUSE_mono_meme_format.tar.gz" + effectiveGenomeSize: 2000000000 + fripextra: + promoterbed: "PIPELINE_HOME/resources/frip/mmul.promoters.bed.gz" + # MACS2 arguments/parameters for peak calling # annotatePeaks: True ensures annotation of called peaks using ChIPSeeker # set annotatePeaks: False if genome cannot be annotated with ChIPSeeker @@ -83,7 +94,7 @@ macs2: extsize: 200 shiftsize: 100 annotatePeaks: True - +l # Genrich peak calling parameters # CCBR parameters genrich: