From 0557f4e0622915bf07801e6d268e08b56e53b6d0 Mon Sep 17 00:00:00 2001 From: praveenraj2018 <43108054+praveenraj2018@users.noreply.github.com> Date: Tue, 14 Dec 2021 21:15:12 +0100 Subject: [PATCH 1/2] Renamed star_index directory --- conf/pipeline/rnavar/munin.config | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/conf/pipeline/rnavar/munin.config b/conf/pipeline/rnavar/munin.config index 9a96357..c2c8335 100644 --- a/conf/pipeline/rnavar/munin.config +++ b/conf/pipeline/rnavar/munin.config @@ -23,8 +23,9 @@ params { known_indels_tbi = '/data1/references/annotations/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi' // STAR index - star_index = '/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/star150bp.idx/' - + star_index = '/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/STAR.2.7.9a_2x151bp/' + read_length = 151 + // Annotation settings annotation_cache = true cadd_cache = true From 00a3ed0fa60b055e005b8e75eb05c127d3b75d11 Mon Sep 17 00:00:00 2001 From: praveenraj2018 <43108054+praveenraj2018@users.noreply.github.com> Date: Tue, 14 Dec 2021 21:24:18 +0100 Subject: [PATCH 2/2] Formatting --- docs/pipeline/rnavar/munin.md | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/docs/pipeline/rnavar/munin.md b/docs/pipeline/rnavar/munin.md index 2938fb2..e4fd11f 100644 --- a/docs/pipeline/rnavar/munin.md +++ b/docs/pipeline/rnavar/munin.md @@ -16,21 +16,22 @@ Specific configurations for `MUNIN` has been made for rnavar. Genome references -`fasta` set to `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa` -`fasta_fai` set to `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.fai` -`gtf` set to `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.gtf` -`gene_bed` set to `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.bed` +* Path to `fasta`: `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa` +* Path to `fasta_fai`: `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.fai` +* Path to `gtf`: `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.gtf` +* Path to `gene_bed`: `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.bed` Known genome resources -`dbsnp set to` `/data1/references/annotations/GATK_bundle/dbsnp_146.hg38.vcf.gz` -`dbsnp_tbi set` to `/data1/references/annotations/GATK_bundle/dbsnp_146.hg38.vcf.gz.tbi` -`known_indels set` to `/data1/references/annotations/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz` -`known_indels_tbi` set to `/data1/references/annotations/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi` +* Path to `dbsnp`: `/data1/references/annotations/GATK_bundle/dbsnp_146.hg38.vcf.gz` +* Path to `dbsnp_tbi`: `/data1/references/annotations/GATK_bundle/dbsnp_146.hg38.vcf.gz.tbi` +* Path to `known_indels`: `/data1/references/annotations/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz` +* Path to `known_indels_tbi`: `/data1/references/annotations/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi` STAR index -`star_index` set to `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/star150bp.idx/` +* Path to `star_index`: `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/STAR.2.7.9a_2x151bp/` +* Params `read_length` set to `151` Variant annotation configurations