From cbaf8f652b3a2db6e35f69bdf92f8796f5b84b60 Mon Sep 17 00:00:00 2001 From: miasteinberg Date: Mon, 6 Feb 2017 14:33:41 -0500 Subject: [PATCH] Update hpv16_config.yaml cleaned up paths --- hpv16_config.yaml | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/hpv16_config.yaml b/hpv16_config.yaml index 8cbd0dd..4e946e5 100644 --- a/hpv16_config.yaml +++ b/hpv16_config.yaml @@ -2,10 +2,10 @@ # 1) This is where the remapped bam files can be found. -glob_path: /CGF/Sequencing/IonTorrent/PGM_Primary_Data/projects/mks/RD153_CVT/Auto*/*.bam +glob_path: /path/to/*.bam # 2) This is name of the deliverable directory. -deliver_proj: HPV16_CVT_RD153_20160421 +deliver_proj: HPV_type_cohort_projectID_date # 3) Update the parser function in the Snakefile to match the bam filenames. @@ -19,26 +19,26 @@ deliver_proj: HPV16_CVT_RD153_20160421 # ------------------------------------------------------------- # Reference files -hg_fasta: /CGF/Sequencing/IonTorrent/PGM_Primary_Data/referenceLibrary/tmap-f3/HPV16Ref_hg19/HPV16Ref_hg19.fasta -len_bed: /CGF/Sequencing/Analysis/Research/RD_reference/HPV/HPV16/hpv16.bed -amp_bed: /CGF/Sequencing/Analysis/Research/RD_reference/HPV/HPV16/HPV16_amplicon_no_primer_01172015.bed +hg_fasta: /path/to/HPV16Ref_hg19.fasta +len_bed: /path/to/hpv16.bed +amp_bed: /path/to/HPV16_amplicon_no_primer_01172015.bed # Tools and packages # Warning - you MUST use GATK version 3.3! -gatk: /CGF/Sequencing/Analysis/ion_dev/GATK/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar +gatk: /path/to/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar -vc_bin: /CGF/Sequencing/Analysis/Research/RD_reference/HPV/tvc-5.0.3/bin -vc_pipe: /CGF/Sequencing/Analysis/Research/RD_reference/HPV/tvc-5.0.3/bin/variant_caller_pipeline.py +vc_bin: /path/to/tvc-5.0.3/bin +vc_pipe: /path/to/tvc-5.0.3/bin/variant_caller_pipeline.py # choose a TVC read depth of 4 or 6 -#vc_param: /CGF/Sequencing/Analysis/Research/RD_reference/HPV/germline_low_stringency_no_het.json -vc_param: /CGF/Sequencing/Analysis/Research/RD_reference/HPV/germline_low_stringency_no_het_low_depth.json +#vc_param: /path/to/germline_low_stringency_no_het.json +vc_param: /path/to/germline_low_stringency_no_het_low_depth.json -cov_dev: /CGF/Sequencing/Analysis/Research/RD_reference/HPV/cgrCoverageDev +cov_dev: /path/to/cgrCoverageDev -snpeff: /CGF/Sequencing/Analysis/ion_dev/snpEff/snpEff +snpeff: /path/to/snpEff # the bed file has a custom list of features (usually regulation) -snpeff_bed: /CGF/Sequencing/Analysis/ion_dev/snpEff/snpEff/data/hpv16/source/regulation.bed +snpeff_bed: /path/to/snpEff/data/hpv16/source/regulation.bed hpv_type: hpv16 # You need glu installed in your PATH