CODEWITHSUNDEEP
python-3.xsnakemake
Arun
Arun

Reputation: 669

Syntax error in snakemake snakefile

I tried to run snakemake to test a small job. The code is the following:

rule kallisto_quant:
    input:
        idx='/fullpath/snakemake-example/Kallisto_test/Arabidopsis_thaliana.fa.index'
        fwd='/fullpath/snakemake-example/Kallisto_test/Condition1_R1_008.trimmed.fastq.gz'
        rvs='/fullpath/snakemake-example/Kallisto_test/Condition1_R2_008.trimmed.fastq.gz'
    output:
        '/Condition1'
    threads: 10
    shell:
        'kallisto quant -i {input.idx} -o {output} -b 100 {input.fwd} {input.rvs}'

When I run this, I get syntax error:

SyntaxError in line 4 of /fullpath/snakemake-example/Snakefile:
invalid syntax

By referring to snakemake manual, I am unable to see any syntax error. What would be the problem here ?

Thanks in advance.

Upvotes: 1

Views: 2782

Answers (1)

Manavalan Gajapathy
Manavalan Gajapathy

Reputation: 4089

Commas missing in input. Also, I believe snakemake requires output to be files and not directory, which is what you used in your example.

rule kallisto_quant:
    input:
        idx='/fullpath/snakemake-example/Kallisto_test/Arabidopsis_thaliana.fa.index',
        fwd='/fullpath/snakemake-example/Kallisto_test/Condition1_R1_008.trimmed.fastq.gz',
        rvs='/fullpath/snakemake-example/Kallisto_test/Condition1_R2_008.trimmed.fastq.gz'
    output:
        '/Condition1'
    threads: 10
    shell:
        'kallisto quant -i {input.idx} -o {output} -b 100 {input.fwd} {input.rvs}'

Upvotes: 1

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