Containerize all nextflow processes

[kelly-sovacool]

Changes

Create and use containers for all nextflow processes

https://hub.docker.com/r/nciccbr/seurat_5/

test

./bin/sinclair run -profile test -resume --mode local 

Issues

• resolves Build Docker Container #6
• resolves Update to production Seurat5 #67
• resolves use containers instead of modules #69
• resolves unhelpful rmarkdown traceback #99
• resolves celldex expects access to a lock file in the user's home dir #199

PR Checklist

(Strikethrough any points that are not applicable.)

• This comment contains a description of changes with justifications, with any relevant issues linked.
• [ ] Write unit tests for any new features, bug fixes, or other code changes. testing framework not yet implemented
• [ ] Update docs if there are any API changes.
• [ ] If a new nextflow process is implemented, define the process container and stub.
• Update CHANGELOG.md with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/

[kelly-sovacool]

working on fixing the container here CCBR/Dockers2#306

[kelly-sovacool]

Current problem in seurat_merge:

ERROR ~ Error executing process > 'GEX_EXQC:SEURAT_MERGE (group1-group2-group3)'

Caused by:
  Process `GEX_EXQC:SEURAT_MERGE (group1-group2-group3)` terminated with an error exit status (1)


Command executed:

  Rscript -e 'rmarkdown::render("seurat_merge.Rmd",
      params=list(species="hg38",
          npcs="50",
          vars_to_regress="NULL",
          rdsFiles="sample5_seurat_preprocess.rds",
          gid="group1-group2-group3",
          samplesheet="input_manifest.csv",
          scRNA_functions="scRNA_functions.R",
          testing="N"),
      output_file = "group1-group2-group3_seurat_merged.html")'

Command exit status:
  1

Command output:
  1/10                  
  2/10 [setup]          
  3/10                  
  4/10 [processing]     
  5/10                  
  6/10 [merge_objs]     

Command error:
  WARNING: Not virtualizing pid namespace by configuration
  
  
  processing file: seurat_merge.Rmd
  1/10                  
  2/10 [setup]          
  3/10                  
  4/10 [processing]     
  5/10                  
  6/10 [merge_objs]     
  Error in `UseMethod()`:
  ! no applicable method for 'Project' applied to an object of class "NULL"
  Backtrace:
      x
   1. +-base::merge(reference.list[[1]], reference.list[2:length(reference.list)])
   2. +-base::merge(reference.list[[1]], reference.list[2:length(reference.list)])
   3. \-SeuratObject:::merge.Seurat(reference.list[[1]], reference.list[2:length(reference.list)])
   4.   \-base::vapply(X = objects, FUN = Project, FUN.VALUE = character(length = 1L))
   5.     \-SeuratObject (local) FUN(X[[i]], ...)
  
  Quitting from seurat_merge.Rmd:83-96 [merge_objs]
  Execution halted

Work dir:
  /vf/users/CCBR_Pipeliner/Pipelines/SINCLAIR/sinclair-dev-sovacool/work/de/1997647418b825920fecc29cac546f

Container:
  /data/CCBR_Pipeliner/SIFs/nciccbr-seurat_5-v1-dev.img

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '.nextflow.log' file for details

[wong-nw]

Container in CCBR/Dockers2#306 is building with update to Rv4.4.3. Testing SINCLAIR compatibility after pulling the container