snakemake wildcard in shell

Question

[samuel]

I'm a newbie at snakemake. I'm trying to implement the GATK FastqToSam in a rule.

I have the following and it works if I hard code the samplename into the shell part but I was wanting to get the samplename from the config file. I tried using the params option like so:

configfile: "config.yaml"

fc = config["flowcell"]
index = config["index"]
samplename = config["sn"]
lane=["L01","L02","L03","L04"]


rule all:
    input:
        expand(["result/gatk4/{fc}_{lane}_{index}_fastqtosam.bam"], fc = fc, lane = lane, index = index)



rule fastqToSam:
    input:
        trimmed1 = "result/trimming/{fc}_{lane}_{index}_1_500k_trimmed.fq.gz",
        trimmed2 = "result/trimming/{fc}_{lane}_{index}_2_500k_trimmed.fq.gz"
    output:
        output="result/gatk4/{fc}_{lane}_{index}_fastqtosam.bam"
    log:
        "result/logs/fastqtosam/{fc}_{lane}_{index}.out"
    benchmark:
       "result/benchmarks/{fc}_{lane}_{index}.out"
    container:
        config["containers"]["gatk4"]
    params:
        RG="{fc}_{lane}",
        sn="{samplename}"
    threads: 8
    shell:
        """
        gatk --java-options "-Xmx8G" FastqToSam
        FASTQ={input.trimmed1}
        FASTQ2={input.trimmed2}
        OUTPUT={output.output}
        QUALITY_FORMAT=Standard
        READ_GROUP_NAME={params.RG}
        SAMPLE_NAME={params.sn}
        LIBRARY_NAME=PCRFree
        PLATFORM=MGI
        SEQUENCING_CENTER=CG 2>{log}
        """

But I get the error:

    WildcardError in line ** of snakefile:
    Wildcards in params cannot be determined from output files. Note that you have to use a function to deactivate automatic wildcard expansion in params strings, e.g., `lambda wildcards: '{test}'`. Also see https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules:
    'samplename'

Is there a way of getting the samplename from the config file and using it in the shell part of the snakemake rule?

Answer 1

[hugo.avila]

This happens because you used the Snakemake notation for wildcards "{samplename}". Since you've already loaded the configuration file as a dictionary and stored the sample name value in the "samplename" variable, you can simply pass it as is:

    params:
        RG="{fc}_{lane}",
        sn=samplename  # <------ HERE
    threads: 8
    shell:
        """
        gatk --java-options '-Xmx8G' FastqToSam #  <--- I also fix some quotation here the might bring you some problems. 
        FASTQ={input.trimmed1}
        FASTQ2={input.trimmed2}
        OUTPUT={output.output}
        QUALITY_FORMAT=Standard
        READ_GROUP_NAME={params.RG}
        SAMPLE_NAME={params.sn}
        LIBRARY_NAME=PCRFree
        PLATFORM=MGI
        SEQUENCING_CENTER=CG 2>{log}
        """

If I'm correct, this should work.

However, reading input parameters from the configuration file can be somewhat inflexible. I recommend following the Snakemake documentation and reading input information from an input table instead.

[samuel]

thanks hugo.avila I don't think I can accept your answer as it's a comment? Much appreciated!

[GenoMax]

Moved to answer. You can accept.

[hugo.avila]

Your welcome ;)

No worries, sometimes the mods add comments as an accepted answer if they see that the problem was soved. I thought that maybe i have gotten you question wrong so i submitted my answer as a comment, my bad.