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]}
"""
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}
"""
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.
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.
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
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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?
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
By the way, I've merged your comments into a single comment and cleaned up a little.
i will take care of it and thanks for the suggestions
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
-pto the dry-run code.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 therawFastqcIn 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.