Simplified version with wrapper for sciCORE

assembly/README.md

@@ -8,7 +8,7 @@ The genome assembly workflow includes the following tools/steps:
   - [minimap2](https://doi.org/10.1093/bioinformatics/bty191): Map the long reads back against the assembly. The resulting alignments can be used to check for inconsistencies between reads and assemblies.  
 
 
-# Run the pipeline
+# Run the pipeline on sciCORE
 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. 
@@ -29,6 +29,7 @@ ref:
   gbf: resources/H37Rv.gbf # Used for bakta annotation step
 
 bakta_db: resources/bakta_db # Used for bakta annotation step
+container: containers/assemblySMK.sif # Singularity container containing all reuquired software
 
 threads_per_job: 4 # Should match cpus-per-task in the snakemake command
  

assembly/run_assembly_pipeline.py

+
+import argparse
+import os
+import yaml
+
+def get_args():
+
+    parser = argparse.ArgumentParser(
+        description='')
+
+    parser.add_argument(
+        '-c', '--configfile',
+        dest='config',
+        required=True,
+        help='.'
+        )
+
+    parser.add_argument(
+        '-j', '--njobs',
+        dest="win_size",
+        required=True, type=int, 
+        help='Window size.'
+        )
+
+    parser.add_argument(
+        '-t',
+        dest='threads',
+        type=int, default=0,
+        help='Threads per job.'
+        )
+
+    args=parser.parse_args()
+    return args
+
+
+def main():    
+    
+    args = get_args()
+
+    with open(args.config, 'r') as file:
+        config = yaml.safe_load(file)
+
+    
+    # Infer pipeline location from path of run_assembly_pipeline.py
+    
+
+
+
+    cmd = [
+        "snakemake",
+        "--profile", "", 
+        "--snakefile", "/scicore/home/gagneux/GROUP/PacbioSnake/assembly/workflow/Snakefile",
+        "--directory", "/scicore/home/gagneux/GROUP/PacbioSnake/assembly",
+        "--configfile", "/scicore/home/gagneux/stritt0001/TB/projects/pacbio_microscale/results/demo/config.yml",
+        "--jobs", "4",
+        "--latency-wait", "60", 
+        "--cleanup-shadow",
+        "--shadow-prefix", 
+        "--verbose",
+        "--use-singularity", "--singularity-args", "--bind /scicore/home/gagneux/GROUP/tbresearch/genomes/IN_PROGRESS/PacBio_genomes/Gagneux --bind /scicore/home/gagneux/stritt0001 --bind /scratch",
+        "--cluster", "sbatch --job-name=pbassembly --cpus-per-task=4 --mem-per-cpu=4G --time=06:00:00 --qos=6hours --output=/scicore/home/gagneux/stritt0001/TB/projects/pacbio_microscale/results/demo/pbassembly.o%j --error=/scicore/home/gagneux/stritt0001/TB/projects/pacbio_microscale/results/demo/pbassembly.e%j"
+    ]
+
+    os.system(" ".join(cmd))
+    
+if __name__ == '__main__':
+    main()