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pythonsyntax-errorsnakemake

Unspecified syntax error in Snakemake rule

I have a very strange syntax error that I have been staring at for hours with no solution. I cannot figure out why/where the syntax error is coming from. This is my rule:

rule star_alignment:
    conda:
        "envs/star.yaml"
    input:
        R1 = "samples/{sampid}/original_R1.fastq",
        R2 = "samples/{sampid}/original_R2.fastq",
        genome = config['indexes']['star']
    output:
        aligned_bam = "results/{sampid}_GDC38.Aligned.out.bam",
        sorted_bam = "results/{sampid}_GDC38.Aligned.sortedByCoord.out.bam"
    params:
        out_prefix="results/{sampid}_GDC38."
    threads: workflow.cores
    shell:
        '''
        STAR\
            --runThreadN {threads}\
            --genomeDir {input.genome}\
            --readFilesIn {input.R1} {input.R2}
            --outSAMattributes NH HI NM MD AS XS\
            --outSAMtype BAM Unsorted SortedByCoordinate\
            --outFileNamePrefix {params.out_prefix}
        '''

This is the error:

SyntaxError in line 21 of /pbtech_mounts/homes064/bhs4002/DLBCL_HERV_atlas_GDC/workflow/rules/star_alignment.smk:
invalid syntax (star_alignment.smk, line 21)
  File "/pbtech_mounts/homes064/bhs4002/DLBCL_HERV_atlas_GDC/workflow/Snakefile", line 63, in <module>

Line 21 corresponds to the line that says STAR\. I'm not sure what line 63 is, because the .smk file for this rule is only 29 lines?

Solution

  • Turns out that the problem was with indentation! Some lines had spaces and others had tabs. I replaced all the tabs with spaces and this fixed the problem.