diff --git a/.gitignore b/.gitignore
index 479190f97f1a8c16a3319dceee47caf8be1a0178..155279f82b41df9f3e30436c29c74f70191ce43f 100755
--- a/.gitignore
+++ b/.gitignore
@@ -7,3 +7,5 @@ assembly/resources/bakta_db
facienda.md
variantcalling/container/pggb_latest.sif
variantcalling/.snakemake
+assembly/logs
+assembly/.fontconfig
diff --git a/assembly/README.md b/assembly/README.md
index 8c339e5721c86fa4741a2b0c236bea8d961d7190..177b319bc29cad12ba7db7fdd5089842a3f0986d 100755
--- a/assembly/README.md
+++ b/assembly/README.md
@@ -13,14 +13,18 @@ The user needs to provide two things to run the workflow on her samples:
- a config file with some global options for the analysis
- a tab separate table, without header, that contains the sample names and the corresponding paths to the HiFi consensus reads.
+
+## Clone the directory
+
+
## Create conda environment containing snakemake and singularity
```
-conda env create -f environment.yml
+conda env create -f config/environment.yml
```
-## config.yml
+## Run the pipeline
In the file config/config.yaml some global parameters can be set:
```yaml
diff --git a/assembly/config/cluster_config.yaml b/assembly/cluster/config.yaml
similarity index 86%
rename from assembly/config/cluster_config.yaml
rename to assembly/cluster/config.yaml
index a8eb21698259a77bfd2a075f95285bb9c955f5ad..9deb95e863bcd5a6811ba91847f13cd99097dabe 100644
--- a/assembly/config/cluster_config.yaml
+++ b/assembly/cluster/config.yaml
@@ -9,16 +9,16 @@ cluster:
--output=logs/{rule}/{rule}-{wildcards}-%j.stdout
--error=logs/{rule}/{rule}-{wildcards}-%j.stderr
default-resources:
- - partition=scicore
- - qos=1day
- - time=12:00:00
- - mem_mb=20000
+ - "partition=scicore"
+ - "qos='1day'"
+ - "time='12:00:00'"
+ - "mem_mb=20000"
restart-times: 3
max-jobs-per-second: 10
max-status-checks-per-second: 1
local-cores: 1
latency-wait: 60
-jobs: 500
+jobs: 10
keep-going: True
rerun-incomplete: True
printshellcmds: True
diff --git a/assembly/config/config.yaml b/assembly/config/config.yaml
index eb11d3bea3047d9be05641541f294eb53ad152b0..ee2e9b6623ce042b85cf734465653384738b886a 100755
--- a/assembly/config/config.yaml
+++ b/assembly/config/config.yaml
@@ -2,15 +2,17 @@
#
##############################
-samples: config/samples.tsv
-outdir: ./results
+samples: "config/samples.tsv"
+outdir: "./results"
ref:
- genome_size: 4.4m
- gbf: resources/H37Rv.gbf
+ genome_size: "4.4m"
+ gbf: "resources/H37Rv.gbf"
-bakta_db: /scicore/home/gagneux/GROUP/PacbioSnake_resources/databases/bakta_db
-container: /scicore/home/gagneux/GROUP/PacbioSnake_resources/containers/assemblySC.sif
+bakta_db: "/scicore/home/gagneux/GROUP/PacbioSnake_resources/databases/bakta_db"
+container: "/scicore/home/gagneux/GROUP/PacbioSnake_resources/containers/assemblySC.sif"
+
+annotate: "No"
threads_per_job: 4
diff --git a/assembly/config/environment.yml b/assembly/config/environment.yml
index f5e4dfb68a298668efd08fbd932411e9cf7f2d77..1946e195954f0eb9e6493dfdc05d9f64059563eb 100644
--- a/assembly/config/environment.yml
+++ b/assembly/config/environment.yml
@@ -7,3 +7,4 @@ channels:
dependencies:
- snakemake=7.32.4
- singularity=3.8.6
+ - biopython
diff --git a/assembly/run_assembly_pipeline.py b/assembly/run_assembly_pipeline.py
index 388c61689988a8ac2eeeb7f139005c6a9f74435e..490b900ad352bcf6504fdb32d25e6665f0cc24c9 100755
--- a/assembly/run_assembly_pipeline.py
+++ b/assembly/run_assembly_pipeline.py
@@ -2,7 +2,6 @@
import argparse
import os
-import yaml
import sys
def get_args():
@@ -12,15 +11,17 @@ def get_args():
# Parameter groups
parser_io = parser.add_argument_group('INPUT/OUTPUT')
- parser_cluster = parser.add_argument_group('CLUSTER CONFIGURATION')
+ parser_cluster = parser.add_argument_group('CLUSTER CONFIGURATION (not implemented yet)')
# INPUT/OUTPUT
- parser_io.add_argument('-s', '--samples', required=True, help='Path to tab-separeted table, no header, with sample name and path to fastq with HiFi reads.')
+ parser_io.add_argument('-s', '--samples', required=True, help='Absolute path to tab-separated table, no header, with sample name and path to fastq with HiFi reads.')
- parser_io.add_argument('-o', '--outdir', required=True, help='Output directory for the results.')
+ parser_io.add_argument('-o', '--outdir', required=True, help='Absolute path to output directory.')
+ parser_io.add_argument('-n', '--dry_run', action='store_true', help='Do snakemake dry run.')
- # CLUSTER CONFIG
+
+ # CLUSTER CONFIG (not implemented, would have to temper with the cluster config file)
parser_cluster.add_argument('-j', '--njobs', default='4', help='Number of jobs to run in parallel. [4]')
parser_cluster.add_argument('-t', '--threads', default='10', help='Threads per job. [10]' )
@@ -36,8 +37,7 @@ def main():
# Infer pipeline location from path of run_assembly_pipeline.py
pl_path = os.path.dirname(os.path.abspath(sys.argv[0]))
- print(pl_path)
-
+
# Directories for which singularity needs to be given access
bind_dirs = [
"/scicore/home/gagneux/GROUP/tbresearch/genomes/IN_PROGRESS/PacBio_genomes/Gagneux",
@@ -47,24 +47,43 @@ def main():
pl_path
]
+ # Infer folders with samples, to add them to bind_dirs
+ sample_dirs = set()
+ with open(args.samples) as f:
+ for line in f:
+ fields = line.strip().split()
+ fastq_path = fields[1]
+ fastq_dir = os.path.dirname(os.path.realpath(fastq_path))
+ sample_dirs.add(fastq_dir)
+
+ bind_dirs = bind_dirs + list(sample_dirs)
+
singularity_args = "--bind " + " --bind ".join(bind_dirs)
- cmd = [
- "snakemake",
- "--snakefile", pl_path + "/workflow/Snakefile",
- "--directory", pl_path,
- "--configfile", pl_path + "/config/config.yaml",
- "--profile", pl_path + "/config/cluster_config.yaml",
- # Overwrite samples and outdir parameters
- "--config", "samples=" + args.samples,
- "--config", "outdir=" + args.outdir,
- "--jobs", args.njobs,
- "--cleanup-shadow",
- "--use-singularity",
- "--singularity-args" + " \"" + singularity_args + "\""
- ]
-
- #print(" ".join(cmd))
+ if args.dry_run:
+
+ cmd = [
+ "snakemake -n",
+ "--snakefile", pl_path + "/workflow/Snakefile",
+ "--directory", pl_path,
+ "--configfile", pl_path + "/config/config.yaml",
+ "--config", "samples=\"" + args.samples + "\"" + " outdir=\"" + args.outdir + "\""
+ ]
+
+ else:
+ cmd = [
+ "snakemake",
+ "--snakefile", pl_path + "/workflow/Snakefile",
+ "--directory", pl_path,
+ "--configfile", pl_path + "/config/config.yaml",
+ "--profile", pl_path + "/cluster",
+ "--use-singularity",
+ "--singularity-args" + " \"" + singularity_args + "\"",
+ # Overwrite samples and outdir parameters in configfile
+ "--config", "samples=\"" + args.samples + "\"" + " outdir=\"" + args.outdir + "\""
+ ]
+
+ print("\n" + " ".join(cmd) + "\n")
os.system(" ".join(cmd))
if __name__ == '__main__':