snakemake wildcard for fastq files

Question

[arshil]

Hi everyone, can anyone help me out setting up the wild card for list of paired end fastq files.(SRR7058331_1.fastq.gz, SRR7058331_2.fastq.gz I am trying to access the files from config.yaml file which looks like

sourcedir: /t6/h7/data/expression
refdir: /AA/Reference_genomes
datadirs:
  fastq: $sourcedir/demo_data
  bam: $sourcedir/bam
  quant: $sourcedir/quant

The code which I am is.
import yaml
configfile: "config.yaml
SAMPLES,=glob_wildcards(config['sourcedir'] + config['datadirs']['fastq']  + "/" +  "{sample}_R1.fastq.gz"))
READS=["1","2"]

its not working. I am pretty new to this.

[Jeremy Leipzig]

you need to follow up on your older questions first. you keep posting variations of the same problem without resolving earlier issues.

[arshil]

import yaml 
configfile: "config.yaml 
SAMPLES,=glob_wildcards(config['sourcedir'] + config['datadirs']['fastq'] + "/" + "{sample}_R1.fastq.gz")
READS=["1","2"]

[GenoMax]

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Always edit the original post if you are adding useful information.

Thank you!

Answer 1

[bari.ballew]

It looks like you may have duplicated part of your path. Right now, your path to your data reads: /t6/h7/data/expression/t6/h7/data/expression/demo_data/{sample}_R1.fastq.gz

I'm assuming you need to access the paired fastq files in tandem for alignment or something similar. Try something like this:

import glob
import os

configfile: "config.yaml"
fastqDir = config['datadirs']['fastq'] + '/'

SAMPLES = glob.glob(fastqDir + '*_R1.fastq.gz')  # read in file list
SAMPLES = [os.path.basename(x) for x in SAMPLES]  # remove path from filenames
SAMPLES = [x.replace('_R1.fastq.gz','') for x in SAMPLES]  # isolate sample ID from filename

def get_r1(wildcards):
    return glob.glob(fastqDir + wildcards.sample + '_R1.fastq.gz')

def get_r2(wildcards):
    return glob.glob(fastqDir + wildcards.sample + '_R2.fastq.gz')

rule do_something:
    input: 
        r1 = get_r1,
        r2 = get_r2
...