make docker image(s) for dependencies

[Phuong-Le]

can be

• 1 docker image for the entire pipeline

• or a docker image for each process of the pipeline

@Phuong-Le to ask Harry about his experience with multiple docker images in one pipeline

[Phuong-Le]

Harry's script for pre-pulling singularity images before running pipeline

https://github.com/sanger-bentley-group/gps-pipeline/blob/master/modules/singularity.nf

[Phuong-Le]

@Phuong-Le @Rashesh7 docker image for mpboot

[Phuong-Le]

For completeness, the following images are needed for the corresponding processes, with priority levels indicated

• [ ] gatk: (medium)
  • conpairPileup
• [ ] python + pandas + numpy: (high)
  • conpairFilter
  • verifyConcordance
  • conpairContamination
  • concatMatrices
• [ ] hairpin (not required as will switch to Mathijs script)
  • hairpin
• [ ] cgpVaf/Vafcorrect (high, already implemented by CASM IT) at https://github.com/cancerit/vafCorrect/blob/dev/Dockerfile and https://quay.io/repository/wtsicgp/vafcorrect), to be tested
  • cgpVaf
• [x] R + data.table + VGAM (high)
  • betaBinomFilterIndex
• [ ] tabix/samtools (medium, likely already implemented somewhere)
  • betaBinomFilter
• [x] python/pandas + mpboot + R/ape/treemut/ggplot/ggtree (very high)
  • getPhylogeny
• [x] SigProfilerMatrixGenerator (high, Dockerfile available at https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/blob/master/Dockerfile)
  • matrixGeneratorOnSamples
  • matrixGeneratorOnBranches
• [x] SigProfilerPlotting (high, Dockerfile available at https://github.com/AlexandrovLab/SigProfilerPlotting/blob/master/Dockerfile)
  • SigprofilerPlotSnpBySamples
  • SigprofilerPlotSnpByBranches

[Phuong-Le]

@alextidd above are the images that need to be built plus the modules associated with them. Will you be able to have a look?

Also could you push the code for the Dockerfile this morning?