new v4 files added and made default

Author: kopardev

config/config.yaml

@@ -87,16 +87,34 @@ adapters: "PIPELINE_HOME/resources/TruSeq_and_nextera_adapters.consolidated.fa"
 # ref_bowtie1_index: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.v3/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC"
 # genepred_w_geneid: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.v3/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.genes.genepred_w_geneid"
 
+# Here we are adding the different strain of HSV-1 virus to the reference. NC_001806.2 is absent from this assembly
+# this is different from v3 as the GTF for HSV-1 has been updated.
+#
+#   | RefSeq  Sequence | RefSeq assembly accession | Notes                                                        |
+#   | ---------------- | ------------------------- | ------------------------------------------------------------ |
+#   | KT899744         | KT899744                  | HSV-1 strain KOS with only 1 copy of repeat sequences
+#
+
+ref_fa: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.v4/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.fa"
+ref_gtf: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.v4/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.gtf"
+regions: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.v4/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.fa.regions"
+star_index_dir: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.v4/STAR_index_no_GTF_2.7.6a"
+ref_bwa_index: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.v4/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC"
+ref_hisat_index: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.v4/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC"
+ref_bowtie1_index: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.v4/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC"
+genepred_w_geneid: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.v4/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.genes.genepred_w_geneid"
+
+
 # replace ERCC with Biotynlated probes
 
-ref_fa: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot.fa"
-ref_gtf: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot.gtf"
-regions: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot.fa.regions"
-star_index_dir: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot/STAR_index_no_GTF_2.7.6a"
-ref_bwa_index: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot"
-ref_hisat_index: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot"
-ref_bowtie1_index: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot"
-genepred_w_geneid: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot.genes.genepred_w_geneid"
+# ref_fa: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot.fa"
+# ref_gtf: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot.gtf"
+# regions: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot.fa.regions"
+# star_index_dir: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot/STAR_index_no_GTF_2.7.6a"
+# ref_bwa_index: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot"
+# ref_hisat_index: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot"
+# ref_bowtie1_index: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot"
+# genepred_w_geneid: "/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_Biot.genes.genepred_w_geneid"