GETUTR

GETUTR Nextflow method workflow

This is the initial version of the GETUTR method workflow.

Input

The input is a samplesheet.csv file:

sample,bam
sample1,/full/path/sample1.bam
sample2,/full/path/sample2.bam
...

For each sample line, the results are stored in results/$sample.PAVA.cps.2.0.0.bed and results/$sample.PAVA.smoothed.2.0.0.bed. For the Mayr samples, the memory requirements are high, around 128GB for the larger samples (bam file of 8GB).

Output

GETUTR outputs identification and relative usage quantification bed files.

Parameters

Parameters used to run GETUTR are specified in conf/modules.config file. Parameters relevant to the workflow are:

• run_identification - set to true to obtain identification challenge output.
• run_relative_usage_quantification - set to true to obtain relative usage quantification challenge output.
• identification_out_suffix - suffix of the output file(s) for the current run ending with .bed when running identification, the prefix will be the different sample names obtained from the sample column in the sample sheet
• relative_usage_quantification_out_suffix - suffix of the output file(s) for the current run ending with .bed when running relative usage quantification, the prefix will be the different sample names obtained from the sample column in the sample sheet

Running

Running the nextflow once you define the samplesheet.csv is a one line command:

nextflow main.nf --input samplesheet.csv --gtf /full/path/genome.gtf -profile docker to run with docker or nextflow main.nf --input samplesheet.csv --gtf /full/path/genome.gtf -profile singularity to run with singularity Voila