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"
• --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.