Questions tagged [workflow-management]

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BWA-MEM2 alignment-Snakemake

I have started using snakemake 6.5.2 to align fastq files with reference file. I have pasted the error below in this question. How to allocate memory in the snakefile and read the header from samfile, ...
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1answer
63 views

Nextflow: How to initialize channel from CSV file but only after CSV file created?

Process A runs a python script which generates a CSV file in some absolute file path say "/mnt/x/blah.csv". Process B needs to consume the CSV file line by line, after process A has finished....
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0answers
59 views

How to execute several processes sequentially, without channels?

Using DSL2. I have processes A, B, C which I want to run in sequence - B waits for A to finish, C waits for B to finish. They are not communicating via channels so I can't do A.out.collect(). I have ...
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1answer
34 views

How to trigger next process on completion of previous process?

Simple question but I am stumped. (I am still learning Nextflow) I have a process which takes as input a channel of files and processes each file separately. There is a second process which needs to ...
2
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1answer
59 views

How does cromwell and AWS batch decide which compute environment (on-demand or spot) to use?

For processing genomics workflows I make use of widdle and cromwell with an AWS back-end. I have followed all examples on the AWS cromwell tutorial. In my AWS batch console I can see there are 2 job ...
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1answer
204 views

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
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1answer
227 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
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2answers
430 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 ...
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1answer
2k 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 ...
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1answer
161 views

Dealing with absence of coverage

In my snakemake workflow, I use deeptools bamCoverage (in a make_bigwig rule), then ...
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4answers
884 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 ...
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3answers
462 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 ...