Command-line execution of Snakemake is handled by ATLAS, however, a user can still opt to use Snakemake outside of the ATLAS command line interface.

When executing a command from atlas, the first line of output will include the snakemake command. For example, if we are getting started and need to download the databases, we execute:

atlas download --jobs 1 --out-dir metaomics/references

Here is the abbreviated output from the above command:

[2017-06-30 11:48 INFO] Executing: snakemake -s /people/brow015/anaconda3/lib/python3.5/site-packages/atlas/Snakefile -d /pic/projects/mint/metaomics -p -j 1 --nolock --rerun-incomplete --config db_dir='/pic/projects/mint/metaomics/references' workflow=download --
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
    count   jobs
    1       all
    6       transfer_files

rule transfer_files:
    output: /pic/projects/mint/metaomics/references/silva_rfam_all_rRNAs.fa
    jobid: 1
    wildcards: filename=silva_rfam_all_rRNAs.fa

curl '' -s > /pic/projects/mint/metaomics/references/silva_rfam_all_rRNAs.fa

6 of 7 steps (86%) done

localrule all:
    input: /pic/projects/mint/metaomics/references/adapters.fa, /pic/projects/mint/metaomics/references/phiX174_virus.fa, /pic/projects/mint/metaomics/references/silva_rfam_all_rRNAs.fa, /pic/projects/mint/metaomics/references/refseq.tree, /pic/projects/mint/metaomics/references/refseq.dmnd, /pic/projects/mint/metaomics/references/refseq.db
    jobid: 0

Finished job 0.
7 of 7 steps (100%) done
All databases have downloaded and validated successfully.
When generating your configuration file, use '--database-dir /pic/projects/mint/metaomics/references'

We can see that the workflow being utilized is:


So any later or more complex use cases can simply call snakemake and specify --snakefile for their local instance.


Extra arguments on the command line are passed directly into the snakemake call, so even within atlas run we can do things like:

atlas run --jobs 24 -w test-dir --summary

This results in the call of:

snakemake --snakefile /path/to/atlas/Snakefile \
--directory WD \
--printshellcmds --jobs 12 --rerun-incomplete \
--configfile 'WD/config.yaml' \
--nolock --use-conda all

The output gives details per output file, which rule created the file, the creation date, and other information that is relevant to the file’s creation.

Snakemake’s --detailed-summary adds columns for input file as well as the shell command that was used.