In silico validation of putative microbial species identified by kraken2 or krakenuniq screen.

nextflow run selkamand/micrite-sleuth \
  -profile docker \
  --sample sample_id \
  --r1 R1.fq --r2 R2.fq \
  --kraken output.kraken \
  --kreport output.kreport \
  --taxid 9606

Due to the number of parameters required by microbial-sleuth we recommend running using a parameters.yaml file. E.g. to run from the root directory of this repo:

nextflow run . -profile docker -params-file params.yaml

Extracts reads mapping to a specific taxid or its descendents and summarises their number and length. If over 200 reads are identified proceeds with the following analysis:

Aligns reads to target reference genome + a set of user-specified control genomes

Subsamples 200 short reads for downstream nucleotide blast analysis.

Attempts a de novo assembly, genome annotation, resistance gene identification and MLST analyses to confirm identity.

Also does a whole genome alignment against target reference genome (& panel of comparative samples).

From inside this directory.

Build local version for OSX

docker buildx build --platform linux/arm64 --load --tag selkamandcci/micrite-sleuth:0.0.1 .

Build final version to push to dockerhub

docker buildx build --push --platform linux/amd64,linux/arm64 --tag selkamandcci/microbe-sleuth:0.0.1 .

There are three main ways to test the nextflow pipeline and ensure it runs on your machine

You can use the test profile

nextflow run selkamand/micrite-sleuth -profile test

Alternatively, clone github repo, cd into it and run `nf-test (requires nf-test is installed)

nf-test test