Problem with Snakemake
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Entering edit mode
12 months ago
viv3kanand ▴ 10

I wanted to align samples one by one using a snakemake script and here however it is pasting all together. Here is the script. I couldn't figure out exactly what's going on with this.

SAMPLES, = glob_wildcards("fastq/{smp}.fastq")
rule minimap:
    input:
        expand("fastq/{smp}.fastq", smp=SAMPLES)
    output:
        expand("fastq_minon/{smp}.bam", smp=SAMPLES)
    params:
        ref = FASTA
    threads: 40
    shell:
        """
        minimap2 -a -x map-ont -t {threads} {params.ref} {input} | samtools view -bS -F 4 - | samtools sort -o {output}
        """

And the logs below

Building DAG of jobs...
Job counts:
        count   jobs
        1       minimap
        1

[Tue May  5 03:28:50 2020]
rule minimap:
    input: fastq/sample02.fastq, fastq/sample03.fastq, fastq/sample01.fastq
    output: fastq_minon/sample02.bam, fastq_minon/sample03.bam, fastq_minon/sample01.bam
    jobid: 0


        minimap2 -a -x map-ont -t 1 /staging/reference.fasta fastq/sample02.fastq fastq/sample03.fastq fastq/sample01.fastq | samtools view -bS -F 4 - | samtools sort -o fastq_minon/sample02.bam fastq_minon/sample03.bam fastq_minon/sample01.bam

Job counts:
        count   jobs
        1       minimap
        1
This was a dry-run (flag -n). The order of jobs does not reflect the order of execution.
snakemake alignment • 316 views
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