A nextflow pipeline to calculate depth of coverage from a metagenomic set of bins.
First, we need our initial set of bins to be pre-processed and merged into a single FASTA file (.fna, .fa). Also, a comma-separated input file declaring information about samples and their raw short-reads (.fastq or .fq -compressed- files).
#usage/help:
nextflow run nf-mag-depths/main.nf -c nf-mag-depths/mag_depths.config --help
The pipeline uses bwa-mem2 to index the reference assembly and to map it back to the raw reads for each metagenomic sample. After, it uses samtools to generate a sorted .bam file, which will be the input for jgi_summarize_bam_contig_depths (a tool from the MetaBAT2 MAG binner suite) to calculate the coverage or depths of all bins from the reference across all samples.
See the input.csv file as an example of how to declare the parameters regarding sample names and short-reads paths.
sample,read1,read2
S1,reads/S1.R1.fq.gz,reads/S1.R2.fq.gz
S2,reads/S2.R1.fq.gz,reads/S2.R2.fq.gz
S3,reads/S3.R1.fq.gz,reads/S3.R2.fq.gz
S7,reads/S7.R1.fq.gz,reads/S7.R2.fq.gz
S15,reads/S15.R1.fq.gz,reads/S15.R2.fq.gz
S17,reads/S17.R1.fq.gz,reads/S17.R2.fq.gz
The needed environment for running the pipeline is declared in the env.yml file (included).
micromamba create -f env.yml
micromamba activate mag_depths
micromamba deactivate
Last, a config file for nextflow is necessary for the execution, in which we declare global variables along with processes parameters. See the file: mag_depths.config.
Once we have set all execution parameters, files, paths and other configurations, we can run the pipeline as follows:
nextflow -bg run nf-mag-depths/main.nf -c nf-mag-depths/mag_depths.config --input input.csv -profile singularity {-resume}
| Software | Version |
|---|---|
| Nextflow | 23.04.2 |
| bwa-mem2 | 2.2.1 |
| samtools | 1.16.1 |
| MetaBAT2 | 2.15 |