.genome file not found for SnpEff

Question

[moldach686]

I'm running into the following error trying to run SnpEff from a container.

java.lang.RuntimeException: Property: 'variant_calling/varscan2/bwa-mem2/sambamba/picard/MTG324.vcf.genome' not found

The container comes with it's own config file so I'm trying to override the location using the -dataDir parameter like so:

rule snpeff_download:
    output:
        directory('resources/snpeff/WBcel235.86')
    log:
        'logs/snpeff/download/WBcel235.86.log'
    params:
        reference='WBcel235.86'
    resources:
        mem=1000,
        time=30
    container:
        'docker://resolwebio/snpeff:2.0.0'
    shell: """
    java -jar /opt/snpeff/snpeff/snpEff.jar download {params.reference} -dataDir /scratch/moldach/COOVAR/resources/snpeff
    """

The first rule runs successfully; however, I get the error from the second rule:

if (config['ANNOT_TOOL']=='snpeff'):
        rule snpeff:
            input:
                    calls=lambda wildcards: getVCFs(wildcards.sample),
                    ref = os.path.join(dirs_dict['REF_DIR'],config['REF_GENOME']),
                    db='resources/snpeff/WBcel235.86'
            output:
                    calls=os.path.join(dirs_dict['ANNOT_DIR'],config['ANNOT_TOOL'],config['CALLING_TOOL'],config['ALIGN_TOOL'],config['SORT_TOOL'],config['MARKDUP_TOOL'],'{sample}.annotated.vcf'),
                    stats=os.path.join(dirs_dict['ANNOT_DIR'],config['ANNOT_TOOL'],config['CALLING_TOOL'],config['ALIGN_TOOL'],config['SORT_TOOL'],config['MARKDUP_TOOL'],'{sample}.html'),
                    csvstats=os.path.join(dirs_dict['ANNOT_DIR'],config['ANNOT_TOOL'],config['CALLING_TOOL'],config['ALIGN_TOOL'],config['SORT_TOOL'],config['MARKDUP_TOOL'],'{sample}.csv')
            log:
                    os.path.join(dirs_dict['LOG_DIR'],config['ANNOT_TOOL'],config['CALLING_TOOL'],config['ALIGN_TOOL'],config['SORT_TOOL'],config['MARKDUP_TOOL'],'{sample}.log')
            params:
                    sample='{sample}',
            resources:
                    mem=3000,
                    time=60
            container:
                    'docker://resolwebio/snpeff:2.0.0'
            shell: """
            java -Xmx4g -jar /opt/snpeff/snpeff/snpEff.jar -dataDir /scratch/moldach/COOVAR/resources/snpeff {input.calls} > {output.calls}
            """

Answer 1

[moldach686]

There were multiple issues going on:

1. -dataDir needs to be included in both of the rules in-order to over-ride the settings in the configuration file provided with the Docker container.
2. By default it's looking _inside_ the containers PATH so I needed to add os.getcwd() to the params: section and append that before the output: directory.

Working Solution

rule snpeff_download:
    output:
        directory('resources/snpeff/WBcel235.86')
    log:
        'logs/snpeff/download/WBcel235.86.log'
    params:
        reference='WBcel235.86',
        dir='resources/snpeff',
        pwd=os.getcwd()
    resources:
        mem=1000,
        time=30
    container:
        'docker://resolwebio/snpeff:2.0.0'
    shell: """
    java -jar /opt/snpeff/snpeff/snpEff.jar download -dataDir {params.pwd}/{params.dir} {params.reference}
    """


if (config['ANNOT_TOOL']=='snpeff'):
        rule snpeff:
            input:
                    calls=lambda wildcards: getVCFs(wildcards.sample),
                    db='resources/snpeff/WBcel235.86'
            output:
                    calls=os.path.join(dirs_dict['ANNOT_DIR'],config['ANNOT_TOOL'],config['CALLING_TOOL'],config['ALIGN_TOOL'],config['SORT_TOOL'],config['MARKDUP_TOOL'],'{sample}.annotated.vcf'),
                    stats=os.path.join(dirs_dict['ANNOT_DIR'],config['ANNOT_TOOL'],config['CALLING_TOOL'],config['ALIGN_TOOL'],config['SORT_TOOL'],config['MARKDUP_TOOL'],'{sample}.html'),
                    csvstats=os.path.join(dirs_dict['ANNOT_DIR'],config['ANNOT_TOOL'],config['CALLING_TOOL'],config['ALIGN_TOOL'],config['SORT_TOOL'],config['MARKDUP_TOOL'],'{sample}.csv')
            log:
                    os.path.join(dirs_dict['LOG_DIR'],config['ANNOT_TOOL'],config['CALLING_TOOL'],config['ALIGN_TOOL'],config['SORT_TOOL'],config['MARKDUP_TOOL'],'{sample}.log')
            params:
                    extra='-Xmx4g',
                    dir='resources/snpeff',
                    pwd=os.getcwd()
            resources:
                    mem=3000,
                    time=60
            container:
                    'docker://resolwebio/snpeff:2.0.0'
            shell: """
            java -jar /opt/snpeff/snpeff/snpEff.jar \
                -dataDir {params.pwd}/{params.dir} \
                -stats {output.stats} \
                -csvStats {output.csvstats} \
                WBcel235.86 \
                {input.calls} > {output.calls}
            """