I am running a docker file using snakemake command wrapped in a bash script, but it does not give the output (just giving a dry run). Not sure what I am missing. I am attaching the files for your reference. Any help would be much appreciated.

Bash script : (test.sh)

#!/bin/bash
snakemake --cores 5 -s test_snk.py

snakemake: (snk.py)

SAMPLES, = glob_wildcards("data/{sample}.fastq.gz")

rule all:
    """
    Collect the main outputs of the workflow.
    """
    input:
        expand("output/{sample}_fastqc.zip", sample = SAMPLES),



rule bbduk_adapter_trim:
    """
    run bbduk to trim adapters
    """
    input:
        fq = "data/{sample}.fastq.gz",
        ref="/refs/adapters.fa"
    output:
        "data/{sample}.fq"
    conda:
        "environment.yml"
    shell:
        """
        bbduk.sh in={input.fq} outu={output} ref={input.ref} ktrim=r k=23 mink=11 hdist=1 tpe tbo
        """


rule fastqc:
    """
    fastqc does a quick quality control checks
    """
    input: 
        "data/{sample}.fq"
    output: 
        "output/{sample}_fastqc.zip"
    shell: 
        "fastqc -o output/ {input}"

dockerfile:

FROM continuumio/miniconda:latest

WORKDIR /work

COPY env.yml ./
COPY snk.py ./
COPY test.sh ./
COPY data/L001.fastq.gz ./
COPY data/L002.fastq.gz ./



RUN chmod +x test.sh

RUN conda env create -f env.yml

RUN echo "source activate myenv"; /bin/bash
ENV PATH /opt/conda/envs/myenv/bin:$PATH

CMD ["sh","./test.sh"]