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Commit b97da7d9 authored by Valentina Galata's avatar Valentina Galata
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updated configs: updated mapping rule names in slurm configs; other minor changes

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config/GDB/config.yaml
+ 4
− 6
View file @ b97da7d9
......@@ -185,16 +185,14 @@ quast:
# https://github.com/soedinglab/MMseqs2
mmseqs2:
threads: 30
createdb: "--dbtype 2 --shuffle -v"
easycluster: "--kmer-per-seq-scale 0.5 --cov-mode 0 -c 0.5 --min-seq-id 0.9"
easylinclust: "--kmer-per-seq-scale 0.5 --cov-mode 0 -c 0.5 --min-seq-id 0.9"
# path: "/home/users/sbusi/apps/mmseqs/bin"
# createdb: "/home/users/sbusi/apps/mmseqs/bin/mmseqs createdb"
# rbh: "/home/users/sbusi/apps/mmseqs/bin/mmseqs rbh"
# convertalis: "/home/users/sbusi/apps/mmseqs/bin/mmseqs convertalis"
# Seq. alignment
# https://mummer4.github.io/
mummer:
archive: "https://github.com/mummer4/mummer/releases/download/v3.9.4alpha/mummer-3.9.4alpha.tar.gz"
##############################
# Taxonomy
......@@ -238,4 +236,4 @@ mash:
# threads: 14
# rebaler:
# threads: 28
\ No newline at end of file
# threads: 28
config/GDB/slurm.yaml
+ 6
− 109
View file @ b97da7d9
......@@ -69,7 +69,7 @@ assembly_hy_operams:
explicit: ""
# Mapping
bwa_index_assembly:
mapping_bwa_idx_assembly:
time: "00-02:00:00"
partition: "batch"
qos: "qos-batch"
......@@ -77,7 +77,7 @@ bwa_index_assembly:
n: 1
explicit: ""
bwa_mem_assembly_sr:
mapping_bwa_mem_assembly_sr:
time: "00-02:00:00"
partition: "batch"
qos: "qos-batch"
......@@ -85,7 +85,7 @@ bwa_mem_assembly_sr:
n: 1
explicit: ""
bwa_mem_assembly_lr:
mapping_bwa_mem_assembly_lr:
time: "00-06:00:00"
partition: "batch"
qos: "qos-batch"
......@@ -93,7 +93,7 @@ bwa_mem_assembly_lr:
n: 1
explicit: ""
bwa_mem_assembly_hy:
mapping_bwa_mem_assembly_hy:
time: "00-02:00:00"
partition: "batch"
qos: "qos-batch"
......@@ -102,7 +102,7 @@ bwa_mem_assembly_hy:
explicit: ""
# Assembly polishing
bwa_index_assembly_polishing:
mapping_bwa_idx_polishing:
time: "00-02:00:00"
partition: "batch"
qos: "qos-batch"
......@@ -110,7 +110,7 @@ bwa_index_assembly_polishing:
n: 1
explicit: ""
bwa_mem_assembly_polishing:
mapping_bwa_mem_polishing:
time: "00-06:00:00"
partition: "batch"
qos: "qos-batch"
......@@ -182,106 +182,3 @@ kraken2_lr:
nodes: 1
n: 1
explicit: ""
# "mmseq2_compare":
# {
# "n": 1,
# "ncpus": 12,
# "time": "00-04:00:00",
# "partition": "bigmem",
# "qos": "qos-bigmem",
# "mail-type": "end"
# },
# "run_nonpareil_on_short_reads":
# {
# "time": "00-04:00:00",
# "n": 1,
# "ncpus": 14,
# "partition": "bigmem",
# "qos": "qos-bigmem",
# "mail-type": "ALL"
# },
# "ANNOTATE":
# {
# "time": "00-00:01:00",
# "n": 1,
# "ncpus": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "mail-type": "ALL"
# },
# "COVERAGE_OF_REFERENCES":
# {
# "time": "00-00:01:00",
# "n": 1,
# "ncpus": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "mail-type": "ALL"
# },
# "ASSEMBLE_AND_COVERAGE":
# {
# "time": "00-00:01:00",
# "n": 1,
# "ncpus": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "mail-type": "ALL"
# },
# "run_rebaler_on_short_read_contigs":
# {
# "time": "00-04:00:00",
# "n": 1,
# "ncpus": 28,
# "partition": "batch",
# "qos": "qos-batch"
# },
# "maxbin2":
# {
# "time": "0-10:00:00",
# "n": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "ncpus": 24
# },
# "metabat2":
# {
# "time": "0-12:00:00",
# "n": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "ncpus": 24
# },
# "scaffold_list":
# {
# "time": "0-02:00:00",
# "n": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "ncpus": 2
# },
# "DAS_Tool":
# {
# "time": "0-6:00:00",
# "n": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "ncpus": 24
# },
# "gtdbtk":
# {
# "time": "1-00:00:00",
# "n": 1,
# "partition": "bigmem",
# "qos": "qos-bigmem",
# "ncpus": 8
# },
# "checkm":
# {
# "time": "1-00:00:00",
# "n": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "ncpus": 24
# }
# }
config/GIS20/config.yaml
+ 4
− 6
View file @ b97da7d9
......@@ -120,7 +120,7 @@ racon:
# Mapper
# http://bio-bwa.sourceforge.net/
bwa:
threads: 10
threads: 24
long_reads_index:
opts: "-aY -A 5 -B 11 -O 2,1 -E 4,3 -k 8 -W 16 -w 40 -r 1 -D 0 -y 20 -L 30,30 -T 2.5"
......@@ -185,16 +185,14 @@ quast:
# https://github.com/soedinglab/MMseqs2
mmseqs2:
threads: 30
createdb: "--dbtype 2 --shuffle -v"
easycluster: "--kmer-per-seq-scale 0.5 --cov-mode 0 -c 0.5 --min-seq-id 0.9"
easylinclust: "--kmer-per-seq-scale 0.5 --cov-mode 0 -c 0.5 --min-seq-id 0.9"
# path: "/home/users/sbusi/apps/mmseqs/bin"
# createdb: "/home/users/sbusi/apps/mmseqs/bin/mmseqs createdb"
# rbh: "/home/users/sbusi/apps/mmseqs/bin/mmseqs rbh"
# convertalis: "/home/users/sbusi/apps/mmseqs/bin/mmseqs convertalis"
# Seq. alignment
# https://mummer4.github.io/
mummer:
archive: "https://github.com/mummer4/mummer/releases/download/v3.9.4alpha/mummer-3.9.4alpha.tar.gz"
##############################
# Taxonomy
......
config/GIS20/slurm.yaml
+ 8
− 111
View file @ b97da7d9
......@@ -69,7 +69,7 @@ assembly_hy_operams:
explicit: ""
# Mapping
bwa_index_assembly:
mapping_bwa_idx_assembly:
time: "00-02:00:00"
partition: "batch"
qos: "qos-batch"
......@@ -77,23 +77,23 @@ bwa_index_assembly:
n: 1
explicit: ""
bwa_mem_assembly_sr:
time: "00-4:00:00"
mapping_bwa_mem_assembly_sr:
time: "00-8:00:00"
partition: "bigmem"
qos: "qos-bigmem"
nodes: 1
n: 1
explicit: ""
bwa_mem_assembly_lr:
time: "00-4:00:00"
mapping_bwa_mem_assembly_lr:
time: "00-8:00:00"
partition: "bigmem"
qos: "qos-bigmem"
nodes: 1
n: 1
explicit: ""
bwa_mem_assembly_hy:
mapping_bwa_mem_assembly_hy:
time: "00-4:00:00"
partition: "bigmem"
qos: "qos-bigmem"
......@@ -102,7 +102,7 @@ bwa_mem_assembly_hy:
explicit: ""
# Assembly polishing
bwa_index_assembly_polishing:
mapping_bwa_idx_polishing:
time: "00-02:00:00"
partition: "batch"
qos: "qos-batch"
......@@ -110,7 +110,7 @@ bwa_index_assembly_polishing:
n: 1
explicit: ""
bwa_mem_assembly_polishing:
mapping_bwa_mem_polishing:
time: "00-8:00:00"
partition: "bigmem"
qos: "qos-bigmem"
......@@ -182,106 +182,3 @@ kraken2_lr:
nodes: 1
n: 1
explicit: ""
# "mmseq2_compare":
# {
# "n": 1,
# "ncpus": 12,
# "time": "00-04:00:00",
# "partition": "bigmem",
# "qos": "qos-bigmem",
# "mail-type": "end"
# },
# "run_nonpareil_on_short_reads":
# {
# "time": "00-04:00:00",
# "n": 1,
# "ncpus": 14,
# "partition": "bigmem",
# "qos": "qos-bigmem",
# "mail-type": "ALL"
# },
# "ANNOTATE":
# {
# "time": "00-00:01:00",
# "n": 1,
# "ncpus": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "mail-type": "ALL"
# },
# "COVERAGE_OF_REFERENCES":
# {
# "time": "00-00:01:00",
# "n": 1,
# "ncpus": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "mail-type": "ALL"
# },
# "ASSEMBLE_AND_COVERAGE":
# {
# "time": "00-00:01:00",
# "n": 1,
# "ncpus": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "mail-type": "ALL"
# },
# "run_rebaler_on_short_read_contigs":
# {
# "time": "00-04:00:00",
# "n": 1,
# "ncpus": 28,
# "partition": "batch",
# "qos": "qos-batch"
# },
# "maxbin2":
# {
# "time": "0-10:00:00",
# "n": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "ncpus": 24
# },
# "metabat2":
# {
# "time": "0-12:00:00",
# "n": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "ncpus": 24
# },
# "scaffold_list":
# {
# "time": "0-02:00:00",
# "n": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "ncpus": 2
# },
# "DAS_Tool":
# {
# "time": "0-6:00:00",
# "n": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "ncpus": 24
# },
# "gtdbtk":
# {
# "time": "1-00:00:00",
# "n": 1,
# "partition": "bigmem",
# "qos": "qos-bigmem",
# "ncpus": 8
# },
# "checkm":
# {
# "time": "1-00:00:00",
# "n": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "ncpus": 24
# }
# }
config/Zymo/slurm.yaml
+ 6
− 109
View file @ b97da7d9
......@@ -69,7 +69,7 @@ assembly_hy_operams:
explicit: ""
# Mapping
bwa_index_assembly:
mapping_bwa_idx_assembly:
time: "00-10:00:00"
partition: "batch"
qos: "qos-batch"
......@@ -77,7 +77,7 @@ bwa_index_assembly:
n: 1
explicit: ""
bwa_mem_assembly_sr:
mapping_bwa_mem_assembly_sr:
time: "00-10:00:00"
partition: "batch"
qos: "qos-batch"
......@@ -85,7 +85,7 @@ bwa_mem_assembly_sr:
n: 1
explicit: ""
bwa_mem_assembly_lr:
mapping_bwa_mem_assembly_lr:
time: "00-10:00:00"
partition: "batch"
qos: "qos-batch"
......@@ -93,7 +93,7 @@ bwa_mem_assembly_lr:
n: 1
explicit: ""
bwa_mem_assembly_hy:
mapping_bwa_mem_assembly_hy:
time: "00-10:00:00"
partition: "batch"
qos: "qos-batch"
......@@ -102,7 +102,7 @@ bwa_mem_assembly_hy:
explicit: ""
# Assembly polishing
bwa_index_assembly_polishing:
mapping_bwa_idx_polishing:
time: "00-10:00:00"
partition: "batch"
qos: "qos-batch"
......@@ -110,7 +110,7 @@ bwa_index_assembly_polishing:
n: 1
explicit: ""
bwa_mem_assembly_polishing:
mapping_bwa_mem_polishing:
time: "00-10:00:00"
partition: "batch"
qos: "qos-batch"
......@@ -182,106 +182,3 @@ kraken2_lr:
nodes: 1
n: 1
explicit: ""
# "mmseq2_compare":
# {
# "n": 1,
# "ncpus": 12,
# "time": "00-04:00:00",
# "partition": "bigmem",
# "qos": "qos-bigmem",
# "mail-type": "end"
# },
# "run_nonpareil_on_short_reads":
# {
# "time": "00-04:00:00",
# "n": 1,
# "ncpus": 14,
# "partition": "bigmem",
# "qos": "qos-bigmem",
# "mail-type": "ALL"
# },
# "ANNOTATE":
# {
# "time": "00-00:01:00",
# "n": 1,
# "ncpus": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "mail-type": "ALL"
# },
# "COVERAGE_OF_REFERENCES":
# {
# "time": "00-00:01:00",
# "n": 1,
# "ncpus": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "mail-type": "ALL"
# },
# "ASSEMBLE_AND_COVERAGE":
# {
# "time": "00-00:01:00",
# "n": 1,
# "ncpus": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "mail-type": "ALL"
# },
# "run_rebaler_on_short_read_contigs":
# {
# "time": "00-04:00:00",
# "n": 1,
# "ncpus": 28,
# "partition": "batch",
# "qos": "qos-batch"
# },
# "maxbin2":
# {
# "time": "0-10:00:00",
# "n": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "ncpus": 24
# },
# "metabat2":
# {
# "time": "0-12:00:00",
# "n": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "ncpus": 24
# },
# "scaffold_list":
# {
# "time": "0-02:00:00",
# "n": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "ncpus": 2
# },
# "DAS_Tool":
# {
# "time": "0-6:00:00",
# "n": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "ncpus": 24
# },
# "gtdbtk":
# {
# "time": "1-00:00:00",
# "n": 1,
# "partition": "bigmem",
# "qos": "qos-bigmem",
# "ncpus": 8
# },
# "checkm":
# {
# "time": "1-00:00:00",
# "n": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "ncpus": 24
# }
# }
config/ganges/slurm.yaml
+ 8
− 111
View file @ b97da7d9
......@@ -69,7 +69,7 @@ assembly_hy_operams:
explicit: ""
# Mapping
bwa_index_assembly:
mapping_bwa_idx_assembly:
time: "00-02:00:00"
partition: "batch"
qos: "qos-batch"
......@@ -77,23 +77,23 @@ bwa_index_assembly:
n: 1
explicit: ""
bwa_mem_assembly_sr:
time: "00-4:00:00"
mapping_bwa_mem_assembly_sr:
time: "00-8:00:00"
partition: "bigmem"
qos: "qos-bigmem"
nodes: 1
n: 1
explicit: ""
bwa_mem_assembly_lr:
time: "00-4:00:00"
mapping_bwa_mem_assembly_lr:
time: "00-8:00:00"
partition: "bigmem"
qos: "qos-bigmem"
nodes: 1
n: 1
explicit: ""
bwa_mem_assembly_hy:
mapping_bwa_mem_assembly_hy:
time: "00-4:00:00"
partition: "bigmem"
qos: "qos-bigmem"
......@@ -102,7 +102,7 @@ bwa_mem_assembly_hy:
explicit: ""
# Assembly polishing
bwa_index_assembly_polishing:
mapping_bwa_idx_polishing:
time: "00-02:00:00"
partition: "batch"
qos: "qos-batch"
......@@ -110,7 +110,7 @@ bwa_index_assembly_polishing:
n: 1
explicit: ""
bwa_mem_assembly_polishing:
mapping_bwa_mem_polishing:
time: "00-8:00:00"
partition: "bigmem"
qos: "qos-bigmem"
......@@ -158,106 +158,3 @@ annotation_plasflow:
nodes: 1
n: 1
explicit: ""
# "mmseq2_compare":
# {
# "n": 1,
# "ncpus": 12,
# "time": "00-04:00:00",
# "partition": "bigmem",
# "qos": "qos-bigmem",
# "mail-type": "end"
# },
# "run_nonpareil_on_short_reads":
# {
# "time": "00-04:00:00",
# "n": 1,
# "ncpus": 14,
# "partition": "bigmem",
# "qos": "qos-bigmem",
# "mail-type": "ALL"
# },
# "ANNOTATE":
# {
# "time": "00-00:01:00",
# "n": 1,
# "ncpus": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "mail-type": "ALL"
# },
# "COVERAGE_OF_REFERENCES":
# {
# "time": "00-00:01:00",
# "n": 1,
# "ncpus": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "mail-type": "ALL"
# },
# "ASSEMBLE_AND_COVERAGE":
# {
# "time": "00-00:01:00",
# "n": 1,
# "ncpus": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "mail-type": "ALL"
# },
# "run_rebaler_on_short_read_contigs":
# {
# "time": "00-04:00:00",
# "n": 1,
# "ncpus": 28,
# "partition": "batch",
# "qos": "qos-batch"
# },
# "maxbin2":
# {
# "time": "0-10:00:00",
# "n": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "ncpus": 24
# },
# "metabat2":
# {
# "time": "0-12:00:00",
# "n": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "ncpus": 24
# },
# "scaffold_list":
# {
# "time": "0-02:00:00",
# "n": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "ncpus": 2
# },
# "DAS_Tool":
# {
# "time": "0-6:00:00",
# "n": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "ncpus": 24
# },
# "gtdbtk":
# {
# "time": "1-00:00:00",
# "n": 1,
# "partition": "bigmem",
# "qos": "qos-bigmem",
# "ncpus": 8
# },
# "checkm":
# {
# "time": "1-00:00:00",
# "n": 1,
# "partition": "batch",
# "qos": "qos-batch",
# "ncpus": 24
# }
# }
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