Snakemake command line arguments

Question

[blackadder]

Hello and Happy New Year to everyone!

I am a novice snakemake/programming user and I am still trying to figure some things out. So bare with me!

I am trying to make a pipeline with various steps that run different programs. In each step I would like to give the option to the user to choose which program to use.

In my mind I have it like this:

Snakemake --cores 10 --assembly metaspades --binning metabat --trimming trimmomatic

I would like the user to choose which software to run at each step. Is that possible or I am talking nonsense?And if yes, how can I do this?

Thanking you in advance!

[blackadder]

Hello,

Thank you guys for your input! Your suggestions helped a lot! I am sure that I will have more questions in the near future, but I managed to move forward with my pipeline.

Until next time!

Thanks

Answer 1

[gb]

It is a bit of a broad question but for inspiration:

Snakemake --cores 10 --config assembly="metaspades" binning="metabat" trimming="trimmomatic"

And sometinhg like:

rule assembly:
    input:
        fastq = "yourinput.fq",
    output:
        bam = "youroutput.bam"
    run:
        if config["assembly"] == "metaspades":
            shell("metaspades command")
       if config["assembly"] == "bowtie":
            shell("bowtie command")

Ofcourse there is much more to it to make a snakemake pipeline but just as inspiration.

[blackadder]

Thank you for the reply! I will give it a try!

[liorglic]

I also suggest that if there many parameters to be set by the user, use --configfile instead of --config. But it's basically the same. This page should have the documentation you need.

Answer 2

[Eric Lim]

As @gb and @liorglic mentioned, using --config or --configfile is a good option. I personally prefer to leave a footprint of what was done in the file names. For example,

rule trimmomatic:
    output: touch('{prefix}.trimmomatic.txt')

rule trim_galore:
    output: touch('{prefix}.trim_galore.txt')

rule star:
    input: '{prefix}.{trim}.txt'
    output: touch('{prefix}.{trim}.star.txt')

rule bowtie:
    input: '{prefix}.{trim}.txt'
    output: touch('{prefix}.{trim}.bowtie.txt')

Then I use the output file name to direct Snakemake on what rules to use.

To combine trimmomatic and star:

(base) [~/Downloads/scratch/biostar/tmp]$ snakemake my_sample.trimmomatic.star.txt --summary
Building DAG of jobs...
output_file date    rule    version log-file(s) status  plan
my_sample.trimmomatic.star.txt  -   -   -   -   missing update pending
my_sample.trimmomatic.txt   -   -   -   -   missing update pending

To combine trim_galore and bowtie:

(base) [~/Downloads/scratch/biostar/tmp]$ snakemake my_sample.trim_galore.bowtie.txt --summary
Building DAG of jobs...
output_file date    rule    version log-file(s) status  plan
my_sample.trim_galore.bowtie.txt    -   -   -   -   missing update pending
my_sample.trim_galore.txt   -   -   -   -   missing update pending