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Pipeline for running PLAMB WIP

Pipeline for running Plamb: https://github.com/RasmussenLab/vamb/tree/vamb_n2v_asy

Running the pipeline

# clone this repository
git clone https://github.com/Las02/ptracker_workflow -b clean_up_the_code
cd ptracker_workflow

# Clone the Plamb directory and the Plamb helper script directory
mkdir bin
cd bin
git clone https://github.com/RasmussenLab/vamb -b vamb_n2v_asy
git clone https://github.com/Paupiera/ptracker

The pipeline can be configurated in: config/config.yaml Here the resources for each rule can be configurated as follows

mpSpades:
  walltime: "15-00:00:00"
  threads: 60
  mem_gb: 950

if no resourcess are configurated for a rule the defaults will be used which are also defined in: config/config.yaml

The input files for the pipeline can be configurated in config/accesions.txt As an example this could look like:

SAMPLE ID READ1 READ2
Airways 4 reads/errorfree/Airways/reads/4/fw.fq.gz reads/errorfree/Airways/reads/4/rv.fq.gz
Airways 5 reads/errorfree/Airways/reads/5/fw.fq.gz reads/errorfree/Airways/reads/5/rv.fq.gz

with an installation of snakemake run the following to dry-run the pipeline

	snakemake -np --snakefile snakefile.smk

and running the pipeline with 4 threads

	snakemake -p -c4 --snakefile snakefile.smk --use-conda

## Important Files
- snakefile.smk: The snakemake pipeline
- utils.py: utils used by the pipeline
- config: directory with the configuration files
  - accesions.txt: Sample information
  - config.yaml: configuration for the pipeline eg. resourcess
- envs: directory with the conda environment descriptions

## Misc files
Makefile - various small scripts for running the pipeline
clustersubmit.sh - script for submitting the snakefile to SLURM
parse_snakemake_output.py - small script for viewing snakefile logs