gravatar for kat

1 hour ago by

Thank you for the quick reply! Yes, I have tried that, unsuccessfully. Is there something obvious I'm missing?

# List of parameters - move to config file
SAMPLES=['T1-XX-2017-1068_S51','L-14-54_S56']
REFS = ['H37Rv']
MAPPERS= ['bowtie2']
FILTERS = ['qfilt','qnoppe']


    # Define target files.
rule all:
      input:
         fastas=expand('results/{samp}/fasta/{samp}_{mapper}_{ref}_{filter}.fa',samp=SAMPLES, ref=REFS, mapper=MAPPERS, filter=FILTERS)

    # Filter variants.     
    rule filter_vars:
      input:
        ref_path='{ref}.fa',
        vcf='results/{samp}/vars/{samp}_{mapper}_{ref}_deep.g.vcf.gz',
      log: 
        'results/{samp}/logs/{samp}_{mapper}_{ref}_filt_vcf_stats.txt'
      output:
        filt_vcf='results/{samp}/vars/{samp}_{mapper}_{ref}_qfilt.vcf.gz',
        noppe_vcf='results/{samp}/vars/{samp}_{mapper}_{ref}_qnoppe.vcf.gz'
      shell:
        "scripts/filter_vars.sh {input.ref_path} {input.vcf} {output.filt_vcf} > {log}"

    # Convert single_sample VCF to fasta. 
    rule vcf_to_fasta:
      input: 
        ref_path='{ref}.fa',
        filt_vcf='results/{samp}/vars/{samp}_{mapper}_{ref}_{filter}.vcf.gz'
      output:
        fasta='results/{samp}/fasta/{samp}_{mapper}_{ref}_{filter}.fa'   
      shell:
        "scripts/vcf2fasta.sh {input.ref_path} {input.filt_vcf} {output.fasta}"

I get the same error that I'm missing an input file:

Building DAG of jobs...
MissingInputException in line 44 of /oak/stanford/scg/lab_jandr/walter/tb/test/Snakefile:
Missing input files for rule all:
results/T1-XX-2017-1068_S51/fasta/T1-XX-2017-1068_S51_bowtie2_H37Rv_qfilt.fa
results/T1-XX-2017-1068_S51/fasta/T1-XX-2017-1068_S51_bowtie2_H37Rv_qnoppe.fa
results/L-14-54_S56/fasta/L-14-54_S56_bowtie2_H37Rv_qfilt.fa
results/L-14-54_S56/fasta/L-14-54_S56_bowtie2_H37Rv_qnoppe.fa

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written
1 hour ago
by

kat10



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