I have project folder structure like Below : which has size of more than 50 GB .

When i am creating Dockerfile such that Snakefile workflow which utilizes data from these folders , should run inside Docker and snakemake command should be entrypoint .

├── adapters.fa

├── Dockerfile

├── genome

│ ├──

├── genomeIndex

│ ├──

├── RawReads

│ ├── sample_1.fastq.gz

│ └── sample_2.fastq.gz

├── RNAindex

│ ├──

└── Snakefile

How should i create Dockerfile and build Image , where i dont want to copy some folders like RawReads , genome , genomeIndex but can link to snakemake rules . Such that when i run docker container on command should run whole snakemake workflow and create results folders .

Sample Dockerfile and Snakefile are shown below :

Snakefile :

rule starAlignment:
input:
    trimmed1="Trimmed/{id}_forward.fastq",
    trimmed2="Trimmed/{id}_reverse.fastq"
output:
    "starOut/{id}Unmapped.out.mate1",
    "starOut/{id}Unmapped.out.mate2",
    "starOut/{id}Aligned.sortedByCoord.out.bam",
    "starOut/{id}Log.final.out"
params:
    prefix="starOut/{id}"
threads: 20
shell:
    """
    STAR --runThreadN {threads} --genomeLoad LoadAndKeep --genomeDir genomeIndex --readFilesIn {input.trimmed1} {input.trimmed2} --outFilterIntronMotifs RemoveNoncanonical --outFileNamePrefix {params.prefix} --limitBAMsortRAM 15000000000 --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate  --outReadsUnmapped Fastx
        """

Dockerfile :

FROM condaforge/mambaforge:22.9.0-3
RUN mamba install -c bioconda samtools bedtools fastqc multiqc trimmomatic bwa star picard rseqc subread snakemake 
WORKDIR /app

ENTRYPOINT [ "snakemake"]