An WorkflowError with wildcards

Question

I want to use snakemake to QC the fastq file, but it show that : WorkflowError:

Target rules may not contain wildcards. Please specify concrete files or a rule without wildcards.

The code I wrote is like this

SAMPLE = ["A","B","C"]

rule trimmomatic:
    input:
        "/data/samples/{sample}.fastq"
    output:
        "/data/samples/{sample}.clean.fastq"
    shell:
        "trimmomatic SE -threads 5 -phred33 -trimlog trim.log {input} {output} LEADING:20 TRAILING:20 MINLEN:16"

I'm a novice, if anyone know that, please tell me. Thanks so much!

Manavalan Gajapathy Manavalan Gajapathy · Accepted Answer · 2018-04-03T03:47:35

You could do one of the following, but chances are you want to do the latter one.

Explicitly specifiy output filenames via commandline:
```
snakemake  data/samples/A.clean.fastq
```
This would run rule to create file data/samples/A.clean.fastq

Specify target output files to be created in Snakefile itself using rule all. See here to learn more about adding targets via rule all

SAMPLE_NAMES = ["A","B", "C"]

rule all:
    input:
        expand("data/samples/{sample}.clean.fastq", sample=SAMPLE_NAMES)

rule trimmomatic:
    input:
        "data/samples/{sample}.fastq"
    output:
        "data/samples/{sample}.clean.fastq"
    shell:
        "trimmomatic SE -threads 5 -phred33 -trimlog trim.log {input} {output} LEADING:20 TRAILING:20 MINLEN:16"

An WorkflowError with wildcards

1 Answers