Tools or Method for batch analysis of Paired end WES data in a queue way.

Question

[NikhilP]

Hello Everyone,

Hope you are doing well.

So the thing is I have a Exome Analysis Script pipeline which I have written in shell. Currently it does analysis of paired end samples one by one. Means from Alignment to VCF Generation of One sample and then it goes for another sample.

Is there anyway where I can do such a thing that as soon as the alignment of one sample is completed and goes down for further analysis, another sample should enter for alignment and so on.

I read that Snakemake and Nextflow helps in Pipeline creation for Batch Jobs, But does those tools does this.

[ATpoint]

Can you give some details on your script, and how it implements switching from one to another sample. Is this via a loop or something?

[Jeremy Leipzig]

those tools definitely work in a breadth-first manner as you wanted