diff --git a/config/GDB/config.yaml b/config/GDB/config.yaml
index 48ffc94c9dca4767660bb2e59e4c27d1650072a0..5bddb151775bb4008a4d14230eb3878240c47722 100644
--- a/config/GDB/config.yaml
+++ b/config/GDB/config.yaml
@@ -3,7 +3,7 @@
# Steps to be done
# steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
-steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
+steps: ["preprocessing"]
steps_annotation: ["diamond", "rgi", "plasflow", "minced", "barrnap"] # prodigal is run in any case
steps_analysis: ["quast", "cdhit", "mash_dist"]
steps_taxonomy: ["kraken2", "kaiju"]
@@ -16,7 +16,7 @@ work_dir: "/scratch/users/vgalata/ont_pilot"
# Paths WITHIN the working directory
# directory containing required DBs (should be writeable)
-db_dir: "dbs"
+db_dir: "/mnt/lscratch/users/vgalata/ONT_pilot_DBs"
# results directory (will be created in work_dir)
results_dir: "results"
@@ -161,7 +161,7 @@ samtools:
# https://github.com/bbuchfink/diamond
diamond:
threads: 20
- db: "/work/projects/ecosystem_biology/local_tools/databases/nr_uniprot_trembl.dmnd" # TODO: data download
+ db: "nr_uniprot_trembl.dmnd" # file name in "dbs" folder
# CRISPR
# https://github.com/dnasko/CASC
@@ -202,25 +202,19 @@ cdhit:
# https://github.com/BioInfoTools/BBMap/
bbmap:
threads: 10
- # References to be used (w/ md5sums)
- rrna_refs: [
- # c0cd2aa2e84e3e3977859c34feb63cd5 /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/rfam-5.8s-database-id98.fasta
- # 703e4c270ab0a578deb4800c33b36367 /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/rfam-5s-database-id98.fasta
- # 8b4e6c6f17f6f35444a60fdc915e052c /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-arc-16s-id95.fasta
- # ca4edcdddb98d7868f93e2308e297704 /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-arc-23s-id98.fasta
- # db6e72022cf650c4b33bd888b92a0391 /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-bac-16s-id90.fasta
- # f347d2f8f8ffbfa28c785e3a9fe3db79 /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-bac-23s-id98.fasta
- # 878a413765d09c3ec75409fb1d1573f1 /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-euk-18s-id95.fasta
- # cbb973e63f52981bd591de0404df5839 /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-euk-28s-id98.fast
- "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/rfam-5.8s-database-id98.fasta",
- "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/rfam-5s-database-id98.fasta",
- "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-arc-16s-id95.fasta",
- "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-arc-23s-id98.fasta",
- "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-bac-16s-id90.fasta",
- "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-bac-23s-id98.fasta",
- "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-euk-18s-id95.fasta",
- "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-euk-28s-id98.fasta"
+ rrna_refs: [ # file names in "dbs" folder
+ "sortmerna/rfam-5.8s-database-id98.fasta",
+ "sortmerna/rfam-5s-database-id98.fasta",
+ "sortmerna/silva-arc-16s-id95.fasta",
+ "sortmerna/silva-arc-23s-id98.fasta",
+ "sortmerna/silva-bac-16s-id90.fasta",
+ "sortmerna/silva-bac-23s-id98.fasta",
+ "sortmerna/silva-euk-18s-id95.fasta",
+ "sortmerna/silva-euk-28s-id98.fasta"
]
+ host_refs: # keep empty if no host specific reads should be removed
+ # key: url of GZ archive
+ GCF_000001405.38_GRCh38.p12: "ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.38_GRCh38.p12/GCF_000001405.38_GRCh38.p12_genomic.fna.gz"
# Assembly quality
# https://github.com/ablab/quast
@@ -246,8 +240,8 @@ quast:
# https://github.com/DerrickWood/kraken2
kraken2:
threads: 10
- db:
- maxikraken: "/scratch/users/bkunath/Kraken2/maxikraken2_1903_140GB/"
+ db: # dir. name in "dbs" folder
+ maxikraken: "maxikraken2_1903_140GB"
class:
sr: "--gzip-compressed --paired"
lr: ""
@@ -258,13 +252,14 @@ kraken2:
# https://github.com/bioinformatics-centre/kaiju
kaiju:
threads: 10
- db: # key = basename of *.fmi
- kaiju_db_nr_euk: "/mnt/isilon/projects/ecosystem_biology/databases/kaiju/kaiju_db_nr_euk_2020-05-25"
+ db: # dir. name in "dbs" folder
+ # key = basename of *.fmi
+ kaiju_db_nr_euk: "kaiju_db_nr_euk_2020-05-25"
ranks: ["phylum", "class", "order", "family", "genus", "species"]
-# # XXX
-# GTDBTK:
-# DATA: "/home/users/sbusi/apps/db/gtdbtk/release89"
+# XXX
+GTDBTK: # dir. name in "dbs" folder
+ DATA: "gtdbtk_release89"
##############################
# MISC
diff --git a/config/GDB/slurm.yaml b/config/GDB/slurm.yaml
index 168089e77b1948297f6e806e7e1d7fada49d7fda..b0c31d96b280d3aa319c060f9b234d34bb1e09fb 100644
--- a/config/GDB/slurm.yaml
+++ b/config/GDB/slurm.yaml
@@ -35,6 +35,30 @@ rm_rrna_bbmap:
n: 1
explicit: ""
+rm_host_bbmap_sr_metat:
+ time: "00-4:00:00"
+ partition: "bigmem"
+ qos: "qos-bigmem"
+ nodes: 1
+ n: 1
+ explicit: ""
+
+rm_host_bbmap_sr_metag:
+ time: "00-4:00:00"
+ partition: "bigmem"
+ qos: "qos-bigmem"
+ nodes: 1
+ n: 1
+ explicit: ""
+
+rm_host_bbmap_lr_metag:
+ time: "00-4:00:00"
+ partition: "bigmem"
+ qos: "qos-bigmem"
+ nodes: 1
+ n: 1
+ explicit: ""
+
# Assembly
assembly_lr_flye:
time: "00-8:00:00"