snakemake input wildcards

Please, can anybody explain what the **wildcards in the code below does. Also, I have come across both *wildcards and **wildcards, how are they different?

In this case, does **wildcards mean wildcards.sample?

def STAR_input(wildcards):
        if config["PE_or_SE"] == "SE":
            fq1="analysis/trimmed_data/{sample}_R1_trimmed.fq.gz".format(**wildcards)
            return fq1
        elif config["PE_or_SE"] == "PE":
            fq1 = "analysis/trimmed_data/{sample}_R1_val_1.fq.gz".format(**wildcards)
            fq2 = "analysis/trimmed_data/{sample}_R2_val_2.fq.gz".format(**wildcards)
            return [fq1,fq2]

python snakemake

• 1,158 views • link

updated 3.5 years ago by Ram

• written 4.8 years ago by ohu20a •

**wildcards notation is for kwargs e.g: https://realpython.com/python-kwargs-and-args/

• 0 views • link

written 4.8 years ago by Pierre Lindenbaum

def STAR_input(wildcards):
    # ** is named parameters
    # statements below all accomplish the same thing
    fq1="analysis/trimmed_data/{sample}_R1_trimmed.fq.gz".format(**wildcards)
    fq1="analysis/trimmed_data/{}_R1_trimmed.fq.gz".format(wildcards.sample)
    fq1=f"analysis/trimmed_data/{wildcards.sample}_R1_trimmed.fq.gz"

rule:
  input: STAR_input
  output: '{sample}.do.something.txt'

• 0 views • link

written 4.8 years ago by Eric Lim

0 answers

No answers yet.

More posts like this

Snakemake fails to find conda in PBS
written 2.3 years ago by yixinzeng •

I tried to run snakemake on the PBS cluster, but snakemake reported an error as follows, the home directory is hidden with $HOME ``` $ …
Wildcards in Snakemake
written 2.8 years ago by Begonia_pavonina •

I wish to input the names of my samples in a table with the corresponding files of reads forward and reverse to use them in …
Using wildcards to accept paired-end reads from Snakemake
written 6.2 years ago by moldach686 •

I've ran into a problem trying to update my snakemake workflow to accept input from multiple directories. Originally I had used `glob_wildcards()` _within_ my `Snakefile` …
Understanding RNA-Seq Pipeline: newbie
written 7.0 years ago by WUSCHEL

I am new to bioinformatics and RNA-seq. I am planning to use below workflow for my `Arabidopsis thaliana RNAseq` data analysis, but I am not …
MissingInputException in snakemake workflow
written 7.0 years ago by jmat •

Hello all, I'm testing this simple `snakemake` pipeline. import pandas as pd configfile: "config.yaml" units = pd.read_csv( config["units"], dtype=str, sep="\t").set_index(["sample", "unit"], drop=False) units.index = units.index.set_levels( …
Tutorial: Use a workflow management tool to manage your computational pipelines
written 9.8 years ago by Eric Lim

Our group recently had to take over the development and maintenance of a collaborator's computational workflow. I received an email from the PI this morning …