Snakemake Wildcard Issue: Trouble Passing Config Field to Rule Input

Question

[blackadder]

Hello there!

I need your help with something...

I am trying to execute a rule in snakemake by passing a field from the config file to my rule input and, so far, i fail miserably.

My config file has the following:

input: "/hpc/data/raw/R0038/*.fq"

test: "R0038"

My Snakefile:

configfile: "config.yaml"

include: "rules/short_reads.smk"

path_short_reads=config["input"]
sample_id = config["test"]

short_reads=set()

for read in glob.glob(path_short_reads):
    short_reads.add(re.split("_R[0-9].fq", os.path.basename(read))[0])

rule all:
    input:
            expand("results/metaphlan/{sreads}/{sreads}.bowtie2.bz", sreads=short_reads),
            expand("results/metaphlan/{sreads}/{sreads}_profile.txt", sreads=short_reads),
            expand("results/metaphlan/{sreads}/{sreads}_profile_species.txt", sreads=short_reads)

My rule file:

rule metaphlan_short_paired_reads:
    """
    Profiling the composition of microbial communities from raw paired reads
    """
    input:
            read_1="/hpc/data/raw/{config[test]}/{sreads}_R1.fq",
            read_2="/hpc/data/raw/{config[test]}/{sreads}_R2.fq"
    output:
            bowtie2="results/metaphlan/{sreads}/{sreads}.bowtie2.bz",
            profile="results/metaphlan/{sreads}/{sreads}_profile.txt",
            final="results/metaphlan/{sreads}/{sreads}_profile_species.txt"
    params:
            type="fastq",
            db="/metaphlan/"
    shell:
            """
            metaphlan {input.read_1},{input.read_2} --bowtie2db {params.db} --bowtie2out {output.bowtie2} --unclassified_estimation --nproc 8 --input_type {params.ty>
            grep s__ {output.profile} | grep -v t__ | cut -f1,3 | sed "s/.*|//g" > {output.final}
            """

What i have tried so far without success in my input:

expand("/hpc/data/raw/{config[test]}/{sreads}_R{read}.fq", sreads=config[test], read=["1", "2"])

also

read_1="/hpc/data/raw/{config[test]}/{wildcards.sreads}_R1.fq",

read_2="/hpc/data/raw/{config[test]}/{wildcards.sreads}_R2.fq"

I also tried to pass it as python variable with sample_id

read_1="/hpc/data/raw/{sample_id}/{wildcards.sreads}_R1.fq",

read_2="/hpc/data/raw/{sample_id}/{wildcards.sreads}_R2.fq"

So far none of my attempts have worked! Any ideas on how to pass the sample filed in my config on my rule?

Thank you!

[DBScan]

What happens if you specify read_1and read_2outside of a rule, for instance like this: READ_1="/hpc/data/raw/" + config[test] + "/{sreads}_R1.fq"

and then use in rule metaphlan_short_paired_reads this:

input:
    read_1 = READ_1,
    read_2 = READ_2
`

[blackadder]

Hello,

It gives me the following error:

name 'READ_1' is not defined

But when i print (READ_1) i get :

/hpc/data/raw/R0038/{sreads}_R1.fq