A Nextflow workflow for ctseq
to enable parallel deployment of jobs across many nodes.
See full details of ctseq here: https://github.com/ryanhmiller/ctseq
ctseq-nf
runs each step of ctseq analyze
as Nextflow process, allowing for parallel
deployment of jobs across any number of nodes.
ctseq-nf
will also manage resoruce allocation and request greater resources
when jobs with a large number of reads fail.
nextflow run ctseq-nf --fastq [full path to raw fastqs] --run [sequening run ID]
--panel
- The methalyation panel
- "${baseDir}/methPanel_v3_8_27_20"
--ctseqSing
- The Singularity container with
ctseq
- "${baseDir}/ctseq-v0.0.3.sif"
- The Singularity container with
--info
- The fragment info file required for plotting
- "${baseDir}/methPanel_v3_infoFile.txt"
Users can override these defaults at the command line on launching the workflow.
- Fastqs are combined by lane
- UMIs are added
- Alignments with Bismark
- Call molecules
- Combine all samples to call methylation for entire run
- Plot
At present, the freely available Singularity contaier does not have all resources
needed to run Nextflow. Therefore, each step of ctseq-nf
invokes the container and
watches for the output to appear in the working directory. A furture implemtation may
involve an updated container with all necessary dependences for Nextflow.