cwl kallisto sleuth

runs/kallisto_sleuth/README.md

+
+# cwltool README
+
+## First cd into the (runs) folder, with the .yml file
+
+cd /Users/dominikbrilhaus/03_DataPLANT_gitlab/samplearc_rnaseq/runs/kallisto_sleuth
+
+## Let it flow
+
+```bash
+### store arc root (two levels up from here) as variable
+arc_root=$(echo ${PWD%/*/*})
+
+### replace arc root line in yml (specific to the machine from where this is run)
+### not sure, if this works on linux... 
+sed -i '' "s|^arc_root:.*|arc_root: $arc_root|g" kallisto_sleuth.yml
+
+### run with cwltool
+cwltool ../../workflows/kallisto_sleuth.cwl kallisto_sleuth.yml
+
+```

runs/kallisto_sleuth/kallisto_sleuth.yml

+cores: 1
+r_script:
+  class: File
+  path: ../../workflows/kallisto_sleuth.R
+in_sleuth: runs/kallisto_collect/kallisto_sleuthObject.RData
+out_folder: runs/kallisto_sleuth
+arc_root: /Users/dominikbrilhaus/03_DataPLANT_gitlab/samplearc_rnaseq
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workflows/kallisto_sleuth.R

+#!/usr/bin/env Rscript
+
+################################################
+### Diff. gene expression with sleuth ##########
+################################################
+
+################################################
+#### Test area (Within R)
+################################################
+
+# arc_root <- "~/03_DataPLANT_gitlab/samplearc_rnaseq/"
+# in_sleuth <- "runs/kallisto_collect/kallisto_sleuthObject.RData"
+# out_folder <- "runs/kallisto_sleuth"
+
+
+################################################
+#### Load required library
+################################################
+
+library(sleuth)
+
+################################################
+#### Read arguments from CLI
+################################################
+
+args <- commandArgs(trailingOnly = T)
+
+arc_root <- args[1]
+in_sleuth <- args[2]
+out_folder <- args[3]
+
+################################################
+#### If it does not exist, create out dir
+################################################
+
+dir.create(paste(arc_root, out_folder, sep = "/"), recursive = T, showWarnings = F)
+
+################################################
+#### Load sleuth object
+################################################
+
+load(file = paste(arc_root, in_sleuth, sep = "/"))
+
+################################################
+#### Run sleuth fit
+################################################
+
+so <- sleuth_fit(so)
+so <- sleuth_fit(so, ~condition, "full")
+so <- sleuth_fit(so, ~1, "reduced")
+so <- sleuth_lrt(so, "reduced", "full")
+
+sleuth_table <- sleuth_results(so, "reduced:full", "lrt", show_all = FALSE)
+
+################################################
+#### write to file
+################################################
+
+write.csv(sleuth_table, paste(arc_root, out_folder, "sleuth_dge.csv", sep = "/"), row.names = F)

workflows/kallisto_sleuth.cwl

+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.2
+class: CommandLineTool
+
+inputs:
+- id: r_script
+  type: File
+  inputBinding:
+    position: 0
+- id: arc_root
+  type: string
+  inputBinding:
+    position: 1
+- id: in_sleuth
+  type: string
+  inputBinding:
+    position: 2
+- id: out_folder
+  type: string
+  inputBinding:
+    position: 3
+
+outputs:
+- id: outdir
+  type:
+    type: array
+    items: Directory
+  outputBinding:
+    glob: $(runtime.outdir)/$(inputs.out_folder)
+
+baseCommand:
+- Rscript
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