Update hpv16_config.yaml

cleaned up paths

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