cschu / vortex_knight

vortex_knight

Installing locally and running from local installation

1. Clone the repo from GitHub.

git clone https://github.com/cschu/vortex_knight.git

2. Create a conda environment with NextFlow, e.g. by using the provided environment.yml.

cd vortex_knight
conda env create -f environment.yml
conda activate vortex_knight

3. Make a copy of the config/run.config file and adjust it to your environment.

4. Run the pipeline

nextflow run /path/to/vortex_knight/main.nf --input_dir /path/to/input_files --output_dir /path/to/output_dir -c /path/to/run.config

Note: Nextflow itself requires at least 5GB of memory.

Running from GitHub

This requires a local nextflow installation. If you don't have one, see Steps 1/2 above.

1. Make a local copy of the run configuration file and adjust to your environment.

2. Run the pipeline

nextflow run cschu/vortex_knight --input_dir /path/to/input_files --output_dir /path/to/output_dir -c /path/to/run.config

Note: Nextflow itself requires at least 5GB of memory.

Input parameters

• --input_dir should be a folder with bam files or with gzipped fastq files. For fastq files, individual samples should be separated into individual folders.
• --output_dir is vknight_out in the local directory by default.
• --skip_<analysis>, --run_<analysis> skips, resp. explicitly requires execution of the specified analysis (motus, pathseq, count_reads, mtags, mapseq, kraken2)
• --publishMode allows to switch between various modes of how results files are placed in the output_dir (cf. NextFlow documentation)

Notes

• mapseq can only run in combination with mtags and when the parameter mapseq_bin is explicitly set.
• kraken2 can only run when the parameter kraken_database is set.
• pathseq can only run when the parameter pathseq_database is set.
• a pre-downloaded motus database can be set with the parameter motus_database.
• results are only collated if the parameter collate_script is set. (TODO -> change to baseDir?)

5. Outputs

The output folder contains:

• one subdirectory otu_tables containing the summarised mapseq otu tables
• a subdirectory per sample (named <sample>) with
  • the kraken2 report <sample>.kraken2_report.txt
  • the library size <sample>.libsize.txt
  • the mOTUs report <sample>.motus.txt
  • pathseq output
    • <sample>.pathseq.bam
    • <sample>.pathseq.bam.sgi
    • <sample>.pathseq.score_metrics
    • <sample>.pathseq.scores

Note that by default, all files in the output folder are symlinks into the work dir! Before you delete the work dir, ensure you have dereferenced copies. Alternatively, change the --publishMode parameter to copy or link (if the target file system supports hard links).