fastp snakemake

Question

[nishimalhotra2612]

Hi all

I tried to make a snakemake pipeline for fastp but somehow I feel I'm going wrong or code is incorrect I'm posting my code so can you suggest where am I going wrong because I'm new to snakemake and I'm confused

This is my code

import os 

SRA,FRR=glob_wildcards("rawReads/{sra}_{frr}.fastq.gz")

rule all:

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

rule rawFastqc:


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


     input:
         read1="rawReads/{sra}_1.fastq.gz",
         read2="rawReads/{sra}_2.fastq.gz"
     output:
         forwardpaired="trimmedreads/{sra}_1P.fastq.gz",
         reversepaired="trimmedreads/{sra}_2P.fastq.gz",
         report_html=trimmedreads{sra}_{frr}_fastq.html
     threads:
         4
     shell:
         """
         fastp -i {input[read1]} -I{input[read2]} -o{output[read1]} -O {output[read2]}
         """

[Jeremy Leipzig]

in your rule fastp, how is snakemake supposed to match up {frr} to anything? need quotes there. also the input and output variables aren't indexed with [] but use . like you did in the rawFastqc

[cpad0112]

In addition, rule all has input for rule fastqc only, not for fastp rule. In fastp rule, output html is not quoted like other outputs. Threads in fastp rule are declared, but not used.

[Ram]

I feel I'm going wrong or code is incorrect

Does the snakemake interpreter agree with your feelings that the code is incorrect? What does it say exactly when you try to run a rule?

[nishimalhotra2612]

When I dry run the code I get this kind of message, but according to me it should show me my jobs that are running fastqc and fastp and that's the reason I feel something is not right

[Ram]

1. Please show us everything including the command you're running.
2. Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the code formatting option shown below).

By the way, I've merged your comments into a single comment and cleaned up a little.

[nishimalhotra2612]

i will take care of it and thanks for the suggestions

[cpad0112]

can you post the command you are running? Since it is a dry-run there would not be any jobs (and ids) AFAIK. But if you want to check what programs are going to be executed with parameter, try adding -p to the dry-run code.

Answer 1

[dariober]

As explained in the comments, there are several issues with the code you posted. This is only a guess of what you are trying to do and hopefully it will move you forward:

SRA,FRR = glob_wildcards("rawReads/{sra}_{frr}.fastq.gz")

rule all:
    input:
        expand("rawQC/{sra}_{frr}_fastqc.{extension}", sra=SRA, frr=FRR, extension=["gz","html"]),
        expand("trimmedreads{sra}_fastq.html", sra=SRA),


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


rule fastp:
     input:
         read1="rawReads/{sra}_1.fastq.gz",
         read2="rawReads/{sra}_2.fastq.gz",
     output:
         read1="trimmedreads/{sra}_1P.fastq.gz",
         read2="trimmedreads/{sra}_2P.fastq.gz",
         report_html= "trimmedreads{sra}_fastq.html",
     threads: 4
     shell:
         """
         fastp --thread {threads} -i {input.read1} -I {input.read2} -o {output.read1} -O {output.read2} -h {output.report_html}
         """

[cpad0112]

Can you please change

 fastp --thread {threads} -i {input[read1]} -I {input[read2]} -o {output[read1]} -O {output[read2]} -h {output[report_html]}

to

fastp --thread {threads} -i {input.read1} -I {input.read2} -o {output.read1} -O {output.read2} -h {output.report_html}

?

Please also remove extra , in rule all input second line and at the end of fastp rule output report_html.

[dariober]

cpad0112 Thanks for the suggestions. I agree that {input.read1} is better than {input[read1]} but I didn't want to edit the original code too much. In fact, there are a few other things I would change. Regarding the comma in rule all, I prefer to have all items in input, output, params terminated by comma (I vaguely remember a snakemake formatting guideline recommending it also) - again my code is not consistent for the same reason above.

[cpad0112]

Thanks for code comments and I agree with you on them @ dariober

[nishimalhotra2612]

heyy really a big thank you for this i understood where i m going wrong, this code ran but there is an issue in rule for fastqc i again posted about it though

thanks again