Questions tagged [workflow-management]

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Snakemake on cluster produces empty output files

Problem: When I run my Snakefile on our cluster, all the processes complete successfully. I can see from the logs that my shell scripts are being run correctly and are claiming to complete ...
3
votes
1answer
90 views

Access workdir defined on command line from within Snakefile

Snakemake provides access to a workflow object within a Snakefile. This allows one to, for example, have dynamic programmatic access to the directory containing the ...
3
votes
2answers
203 views

Autodetect max number of cores and pass as an argument in Nextflow

I am creating a pipeline in Nextflow. One step is creating a pangenome with Roary. Roary takes threads as an argument and if no number of threads is supplied as an argument it defaults to one. Is ...
12
votes
1answer
927 views

What is the difference between a Bioinformatics pipeline and workflow?

I want to understand the difference between pipeline systems and workflow engines. After reading A Review of Scalable Bioinformatics Pipelines I had a good overview of current bioinformatics ...
5
votes
1answer
121 views

Dealing with absence of coverage

In my snakemake workflow, I use deeptools bamCoverage (in a make_bigwig rule), then ...
8
votes
4answers
755 views

Ultimate reproducibility in R?

I'm looking for a convenient and reliable way to make an R analysis reproducible, either at different times or across collaborators. Listing the package versions or a ...
8
votes
3answers
406 views

What are the ways to keep track of branches in the analysis?

I'm going through an RNA-seq pipeline in R/Bioconductor and want to try multiple parameters at subsequent steps, for example, running clustering with different ...