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ONT_pilot_gitlab
Commits
fd8b873f
Commit
fd8b873f
authored
Jan 12, 2021
by
Valentina Galata
Browse files
config: updated aquifer
parent
69380046
Changes
6
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config/aquifer/config.fast5.yaml
View file @
fd8b873f
work_dir
:
"
/scratch/users/vgalata/
A
quifer"
work_dir
:
"
/scratch/users/vgalata/
a
quifer"
# input/output (can be relative to work_dir)
single_fast5_dir
:
"
/scratch/users/sbusi/aquifer/"
# leave empty, i.e. "", if input are multi-FAST5 files
...
...
config/aquifer/config.yaml
View file @
fd8b873f
...
...
@@ -3,16 +3,16 @@
# Steps to be done
# steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
steps
:
[
"
assembly"
]
steps_annotation
:
[
"
rgi"
,
"
plasflow"
,
"
minced"
,
"
barrnap"
,
"
kegg"
]
# prodigal is run in any case
steps_analysis
:
[
"
quast"
,
"
mash"
,
"
mashmap"
,
"
fastani"
,
"
mummer"
,
"
cdhit"
,
"
diamond"
,
"
cov
"
]
steps
:
[
"
preprocessing"
,
"
assembly"
]
steps_annotation
:
[
"
rgi"
,
"
plasflow"
,
"
minced"
,
"
barrnap"
]
# prodigal is run in any case
, no kegg
steps_analysis
:
[
"
quast"
,
"
mash"
,
"
mashmap"
,
"
fastani"
,
"
cdhit"
,
"
diamond"
]
# no mummer
, cov
steps_taxonomy
:
[
"
kraken2"
,
"
kaiju"
]
############################################################
# INPUT
# working directory: will contain the results (should be writeable)
work_dir
:
"
/scratch/users/
vgalata/A
quifer"
work_dir
:
"
/scratch/users/
sbusi/a
quifer"
# Paths WITHIN the working directory
# directory containing required DBs (should be writeable)
...
...
@@ -28,7 +28,7 @@ data:
r1
:
"
/mnt/isilon/projects/ecosystem_biology/ONT_pilot/external_data/aquifer/sr/ERR3654041/ERR3654041_1.fastq.gz"
r2
:
"
/mnt/isilon/projects/ecosystem_biology/ONT_pilot/external_data/aquifer/sr/ERR3654041/ERR3654041_2.fastq.gz"
ont
:
fastq
:
"
/scratch/users/vgalata/
A
quifer/basecalling/lr.fastq.gz"
fastq
:
"
/scratch/users/vgalata/
a
quifer/basecalling/lr.fastq.gz"
# Meta-transcriptomics
metat
:
sr
:
...
...
@@ -59,8 +59,8 @@ fastqc:
# List of assemblers for different read types: assembler names MUST be UNIQUE
assemblers
:
sr
:
[
"
megahit"
,
"
metaspades"
]
lr
:
[
"
flye"
,
"
canu
"
]
hy
:
[
"
metaspadeshybrid"
,
"
operamsmegahit"
,
"
operamsmetaspades"
]
lr
:
[
"
flye"
,
"
raven
"
]
hy
:
[
"
metaspadeshybrid"
]
# excluded:
"operamsmegahit", "operamsmetaspades"
# https://github.com/fenderglass/Flye
flye
:
...
...
@@ -71,6 +71,10 @@ canu:
threads
:
24
genome_size
:
"
1g"
# https://github.com/lbcb-sci/raven
raven
:
threads
:
10
# https://github.com/ablab/spades
metaspades
:
threads
:
10
...
...
@@ -81,7 +85,7 @@ megahit:
# https://github.com/CSB5/OPERA-MS
operams
:
threads
:
1
0
threads
:
1
2
##############################
# Assembly polishing
...
...
config/aquifer/sbatch.fast5.sh
View file @
fd8b873f
...
...
@@ -12,8 +12,8 @@
# conda env name or path
SMK_ENV
=
"/scratch/users/vgalata/miniconda3/ONT_pilot"
# CHANGE as needed
# config files
SMK_CONFIG
=
"config/
A
quifer/config.fast5.yaml"
SMK_SLURM
=
"config/
A
quifer/slurm.fast5.yaml"
SMK_CONFIG
=
"config/
a
quifer/config.fast5.yaml"
SMK_SLURM
=
"config/
a
quifer/slurm.fast5.yaml"
# slurm cluster call
SMK_CLUSTER
=
"sbatch --partition {cluster.partition} {cluster.qos} {cluster.explicit} --nodes {cluster.nodes}
\
--ntasks {cluster.ntasks} --cpus-per-task {threads} --time {cluster.time} --job-name={cluster.job-name}"
...
...
config/aquifer/sbatch.sh
View file @
fd8b873f
...
...
@@ -10,15 +10,16 @@
#SBATCH -q long
# conda env name or path
SMK_ENV
=
"/scratch/users/vgalata/miniconda3/ONT_pilot"
# CHANGE as needed
SMK_ENV
=
$1
SMK_CONDA
=
"/scratch/users/vgalata/miniconda3/ONT_pilot"
# CHANGE as needed
# config files
SMK_CONFIG
=
"config/
A
quifer/config.yaml"
SMK_SLURM
=
"config/
A
quifer/slurm.yaml"
SMK_CONFIG
=
"config/
a
quifer/config.yaml"
SMK_SLURM
=
"config/
a
quifer/slurm.yaml"
# slurm cluster call
SMK_CLUSTER
=
"sbatch --partition {cluster.partition} {cluster.qos} {cluster.explicit} --nodes {cluster.nodes}
\
--ntasks {cluster.ntasks} --cpus-per-task {threads} --time {cluster.time} --job-name={cluster.job-name}"
conda activate
${
SMK_ENV
}
&&
\
snakemake
-s
workflow/Snakefile
-rp
--jobs
5
--local-cores
1
\
--configfile
${
SMK_CONFIG
}
--use-conda
--conda-prefix
${
CONDA
_PREFIX
}
/pipeline
\
snakemake
-s
workflow/Snakefile
-rp
--jobs
1
--local-cores
1
--rerun-incomplete
\
--configfile
${
SMK_CONFIG
}
--use-conda
--conda-prefix
${
SMK_
CONDA
}
\
--cluster-config
${
SMK_SLURM
}
--cluster
"
${
SMK_CLUSTER
}
"
config/aquifer/slurm.fast5.yaml
View file @
fd8b873f
...
...
@@ -5,7 +5,7 @@ __default__:
nodes
:
1
ntasks
:
1
explicit
:
"
"
job-name
:
"
ONT_
A
quifer_FAST5.{rule}"
job-name
:
"
ONT_
a
quifer_FAST5.{rule}"
create_multifast5s
:
time
:
"
00-04:00:00"
...
...
config/aquifer/slurm.yaml
View file @
fd8b873f
...
...
@@ -5,32 +5,32 @@ __default__:
nodes
:
1
ntasks
:
1
explicit
:
"
"
job-name
:
"
ONT_
A
quifer.{rule}"
job-name
:
"
ONT_
a
quifer.{rule}"
# Preprocessing
fastp_sr
:
time
:
"
00-0
1:0
0:00"
time
:
"
00-0
0:3
0:00"
partition
:
"
batch"
rm_rrna_bbmap
:
time
:
"
00-
4:0
0:00"
time
:
"
00-
01:3
0:00"
partition
:
"
batch"
rm_host_bbmap_sr_metat
:
time
:
"
00-
4
:00:00"
time
:
"
00-
02
:00:00"
partition
:
"
bigmem"
rm_host_bbmap_sr_metag
:
time
:
"
00-
4
:00:00"
time
:
"
00-
02
:00:00"
partition
:
"
bigmem"
rm_host_bbmap_lr_metag
:
time
:
"
00-
4
:00:00"
time
:
"
00-
03
:00:00"
partition
:
"
bigmem"
# Assembly
assembly_lr_flye
:
time
:
"
00-
8
:00:00"
time
:
"
00-
14
:00:00"
partition
:
"
bigmem"
assembly_lr_canu
:
...
...
@@ -38,85 +38,150 @@ assembly_lr_canu:
partition
:
"
bigmem"
qos
:
"
--qos
long"
assembly_lr_raven
:
time
:
"
00-08:00:00"
partition
:
"
bigmem"
assembly_sr_megahit
:
time
:
"
0
1-4
:00:00"
time
:
"
0
0-08
:00:00"
partition
:
"
bigmem"
assembly_sr_metaspades
:
time
:
"
01-
8
:00:00"
time
:
"
01-
00
:00:00"
partition
:
"
bigmem"
assembly_hy_metaspades
:
time
:
"
01-
12
:00:00"
time
:
"
01-
00
:00:00"
partition
:
"
bigmem"
assembly_hy_operams
:
time
:
"
0
0-16
:00:00"
time
:
"
0
8-00
:00:00"
partition
:
"
bigmem"
qos
:
"
--qos
long"
# Assembly polishing
polishing_racon_lr
:
time
:
"
00-6:00:00"
time
:
"
00-
0
6:00:00"
partition
:
"
bigmem"
polishing_racon_sr
:
time
:
"
00-6:00:00"
time
:
"
00-
0
6:00:00"
partition
:
"
bigmem"
polishing_medaka_lr
:
time
:
"
01-
00
:00:00"
time
:
"
01-
12
:00:00"
partition
:
"
bigmem"
# Mapping
mapping_bwa_idx_asm
:
time
:
"
00-0
2
:00:00"
time
:
"
00-0
1
:00:00"
partition
:
"
batch"
mapping_bwa_mem_asm_sr
:
time
:
"
00-0
2
:00:00"
partition
:
"
b
atch
"
time
:
"
00-0
6
:00:00"
partition
:
"
b
igmem
"
mapping_bwa_mem_asm_lr
:
time
:
"
00-12:00:00"
partition
:
"
b
atch
"
partition
:
"
b
igmem
"
mapping_bwa_mem_asm_hy
:
time
:
"
00-0
2
:00:00"
time
:
"
00-0
4
:00:00"
partition
:
"
batch"
# Annotation
annotation_prodigal
:
time
:
"
00-
2
:00:00"
time
:
"
00-
03
:00:00"
partition
:
"
batch"
annotation_hmm_kegg
:
time
:
"
00-8:00:00"
annotation_rgi
:
time
:
"
00-02:00:00"
partition
:
"
batch"
annotation_minced
:
time
:
"
00-00:40:00"
partition
:
"
batch"
annotation_plasflow
:
time
:
"
00-01:00:00"
partition
:
"
bigmem"
annotation_barrnap
:
time
:
"
00-00:40:00"
partition
:
"
batch"
annotation_hmm_kegg
:
time
:
"
00-12:00:00"
partition
:
"
bigmem"
# Analysis
analysis_mashmap_one2one
:
analysis_quast
:
time
:
"
00-00:20:00"
partition
:
"
batch"
analysis_mash_sketch_sr
:
time
:
"
00-01:00:00"
partition
:
"
batch"
analysis_mash_sketch_lr
:
time
:
"
00-01:00:00"
partition
:
"
batch"
analysis_mash_reads
:
time
:
"
00-00:30:00"
partition
:
"
batch"
analysis_mash_sketch_asm
:
time
:
"
00-00:20:00"
partition
:
"
batch"
analysis_mash_asm
:
time
:
"
00-00:20:00"
partition
:
"
batch"
analysis_mashmap_one2one
:
time
:
"
00-02:00:00"
partition
:
"
batch"
analysis_fastani_one2one
:
time
:
"
00-02:00:00"
partition
:
"
batch"
analysis_mummer_dnadiff
:
time
:
"
00-04:00:00"
partition
:
"
bigmem"
analysis_cdhit
:
time
:
"
00-02:00:00"
partition
:
"
batch"
analysis_diamond
:
time
:
"
00-02:00:00"
partition
:
"
batch"
analysis_diamond_db
:
time
:
"
00-6:00:00"
time
:
"
00-12:00:00"
partition
:
"
batch"
analysis_genomecov_pergene
:
time
:
"
01-00:00:00"
partition
:
"
batch"
analysis_genomecov_segmentation
:
time
:
"
00-12:00:00"
partition
:
"
bigmem"
# Taxonomy
tax_kraken2_contigs
:
time
:
"
00-00:30:00"
partition
:
"
bigmem"
tax_kraken2_sr
:
time
:
"
00-0
0:3
0:00"
time
:
"
00-0
1:0
0:00"
partition
:
"
bigmem"
tax_kraken2_lr
:
time
:
"
00-0
0:3
0:00"
time
:
"
00-0
1:0
0:00"
partition
:
"
bigmem"
tax_kaiju
:
...
...
@@ -124,5 +189,5 @@ tax_kaiju:
partition
:
"
bigmem"
tax_kaiju_summary
:
time
:
"
00-00:
1
0:00"
time
:
"
00-00:
3
0:00"
partition
:
"
batch"
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