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snakemake

hi i m making a pipeline for checking the quality of single end reads and below is my code

SRA = glob_wildcards("rawReads/{sra}.fastq.gz")

rule all:

input:
    expand("rawQC/{sra}_fastqc.{extension}", sra=SRA,extension=["zip","html"]),

rule rawFastqc:

input:
    rawread="rawReads/{sra}.fastq.gz",
output:
    zip="rawQC/{sra}_fastqc.zip",
    html="rawQC/{sra}_fastqc.html",
threads:
    1
params:
    path="rawQC/",
shell:
    """
    fastqc {input.rawread} --threads {threads} -o {params.path}
    """

this is the error message i m getting

MissingInputException in line 7 of /mnt/d/snakemake/f1.py:

Missing input files for rule rawFastqc: output: rawQC/['SRR1158613']_fastqc.zip, rawQC/['SRR1158613']_fastqc.html wildcards: sra=['SRR1158613'] affected files: rawReads/['SRR1158613'].fastq.gz

i have my files in rawReads folder but i confused on why it is still showing error

thanks

pipeline fastqc snakemake
• 1,441 views • link
written by nishimalhotra2612 • nishimalhotra2612

What does the SRA object look like? (You could put a print statement straight into your Snakefile to check it.) It's a bit weird that it's trying to access paths like this:

rawReads/['SRR1158613'].fastq.gz

That makes me wonder if it's a nested list or something instead of a flat one.

• 0 views • link
written by Jesse • Jesse

i changed my code and i think i solved the error

(SAMPLE,)=glob_wildcards("rawReads/{sample}.fastq.gz")

rule all:

input:
    expand("rawQC/{sample}_fastqc.{extension}", sample=SAMPLE,extension=["zip","html"]),

rule rawFastqc:

input:
    rawread="rawReads/{sample}.fastq.gz",
output:
    zip="rawQC/{sample}_fastqc.zip",
    html="rawQC/{sample}_fastqc.html",
threads:
    1
params:
    path="rawQC/",
shell:
    """
    fastqc {input.rawread} --threads {threads} -o {params.path}
    """

so now the pipeline will work

thanks for the suggestion

• 0 views • link
written by nishimalhotra2612 • nishimalhotra2612

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