From 2440e393338a037c623ee7d844d1920d4c0edb99 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Taavi=20P=C3=A4ll?= Date: Fri, 22 Nov 2019 10:20:54 +0200 Subject: [PATCH] updated config.yaml --- config.yaml | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/config.yaml b/config.yaml index 77a2ecd..a8a3a12 100644 --- a/config.yaml +++ b/config.yaml @@ -28,25 +28,25 @@ split_fasta: n_files: 2 # Path to RepeatMasker Repbase file (path/to/RMRBSeqs.embl) -repbase_file: /gpfs/hpchome/taavi74/databases/Repbase/Libraries/RMRBSeqs.embl +repbase_file: # path to/Repbase/Libraries/RMRBSeqs.embl # Path to reference genome -ref_genome: /gpfs/software/VirusSeeker/databases/ref_genomes/human_g1k_v37.fasta -ref_bacteria: /gpfs/software/VirusSeeker/databases/bacteria_ref_sequence/Bacteria_ref_genome.fna +ref_genome: # path to reference genome +ref_bacteria: # path to bacteria ref genome # Path to virus database -virus_nt: /gpfs/software/VirusSeeker/databases/VirusDBNT_20160802/VirusDBNT_20160802_ID98.fa -virus_nr: /gpfs/software/VirusSeeker/databases/VirusDBNR_20160802/VirusDBNR_20160802_ID98.fa +virus_nt: # path to /VirusDBNT_20160802/VirusDBNT_20160802_ID98.fa +virus_nr: # path to /VirusDBNR_20160802/VirusDBNR_20160802_ID98.fa # Path to taxonomy database -vhunter: /gpfs/software/VirusSeeker/databases/taxdump_300817/vhunter.db -names: /gpfs/software/VirusSeeker/databases/taxdump_300817/names.dmp -nodes: /gpfs/software/VirusSeeker/databases/taxdump_300817/nodes.dmp -division: /gpfs/software/VirusSeeker/databases/taxdump_300817/division.dmp +vhunter: # path to /taxdump_300817/vhunter.db +names: # path to /taxdump_300817/names.dmp +nodes: # path to /taxdump_300817/nodes.dmp +division: # path to /taxdump_300817/division.dmp # Paths to nt and nr blast database -nt: /gpfs/software/VirusSeeker/databases/nt/nt -nr: /gpfs/software/VirusSeeker/databases/nr/nr +nt: # bath to blast nt db +nr: # bath to blast nr db # Rule parameters --------------------- # Filter repeatmasker and tantan output