From 66ed13b56e6f5a8e1a81748c666738aa85cf8cb6 Mon Sep 17 00:00:00 2001
From: Adrian Zimmer <z.adrian1995@gmail.com>
Date: Sat, 13 Aug 2022 16:02:45 +0200
Subject: [PATCH] Dockerize kallisto_collect

---
 runs/kallisto_collect/README.md               | 10 +-----
 runs/kallisto_collect/kallisto_collect.yml    | 12 +++----
 runs/kallisto_collect/run.cwl                 | 30 ++++++++++++++++
 runs/kallisto_sleuth/run.cwl                  |  4 +--
 workflows/kallisto_collect/kallisto_collect.R | 27 +++++++-------
 workflows/kallisto_collect/workflow.cwl       | 36 ++++++++++---------
 6 files changed, 71 insertions(+), 48 deletions(-)
 create mode 100644 runs/kallisto_collect/run.cwl

diff --git a/runs/kallisto_collect/README.md b/runs/kallisto_collect/README.md
index 574080e..b43b9ca 100644
--- a/runs/kallisto_collect/README.md
+++ b/runs/kallisto_collect/README.md
@@ -8,14 +8,6 @@ cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_collec
 ## 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_collect.yml
-
 ### run with cwltool
-cwltool ../../workflows/kallisto_collect.cwl kallisto_collect.yml
-
+cwltool --enable-dev run.cwl kallisto_collect.yml
 ```
diff --git a/runs/kallisto_collect/kallisto_collect.yml b/runs/kallisto_collect/kallisto_collect.yml
index 1b30051..fa4ee11 100644
--- a/runs/kallisto_collect/kallisto_collect.yml
+++ b/runs/kallisto_collect/kallisto_collect.yml
@@ -1,10 +1,10 @@
 cores: 1
-r_script:
+in_kallisto_results: 
+  class: Directory
+  path: ../kallisto_sleuth/out
+in_metadata_file: 
   class: File
-  path: ../../workflows/kallisto_collect.R
-in_kallisto_results: "runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results"
-in_metadata_file: "runs/merged_isa_metadata/merged_isa.tsv"
+  path: ../merged_isa_metadata/merged_isa.tsv
 in_metadata_sample: "Sample.Name.2"
 in_metadata_factor: "Factor..Photosynthesis.mode."
-out_folder: runs/kallisto_collect
-arc_root: /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq
\ No newline at end of file
+out_folder: out
\ No newline at end of file
diff --git a/runs/kallisto_collect/run.cwl b/runs/kallisto_collect/run.cwl
new file mode 100644
index 0000000..3bd1e37
--- /dev/null
+++ b/runs/kallisto_collect/run.cwl
@@ -0,0 +1,30 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2.0-dev1
+class: Workflow
+inputs:
+  in_kallisto_results:
+    type: Directory
+  in_metadata_file:
+    type: File
+  in_metadata_sample:
+    type: string
+  in_metadata_factor:
+    type: string
+  out_folder:
+    type: string
+outputs:
+  out_dir:
+    type:
+      type: array
+      items: Directory
+    outputSource: kallisto_collect/outdir
+steps:
+  kallisto_collect:
+    run: ../../workflows/kallisto_collect/workflow.cwl
+    in:
+      in_kallisto_results: in_kallisto_results
+      in_metadata_file: in_metadata_file
+      in_metadata_sample: in_metadata_sample
+      in_metadata_factor: in_metadata_factor
+      out_folder: out_folder
+    out: [outdir]
diff --git a/runs/kallisto_sleuth/run.cwl b/runs/kallisto_sleuth/run.cwl
index 9565052..8035414 100644
--- a/runs/kallisto_sleuth/run.cwl
+++ b/runs/kallisto_sleuth/run.cwl
@@ -11,9 +11,9 @@ outputs:
     type:
       type: array
       items: Directory
-    outputSource: kallisto_quant/outdir
+    outputSource: kallisto_sleuth/outdir
 steps:
-  kallisto_quant:
+  kallisto_sleuth:
     run: ../../workflows/kallisto_sleuth/workflow.cwl
     in:
       in_sleuth: in_sleuth
diff --git a/workflows/kallisto_collect/kallisto_collect.R b/workflows/kallisto_collect/kallisto_collect.R
index 205be63..15e176c 100644
--- a/workflows/kallisto_collect/kallisto_collect.R
+++ b/workflows/kallisto_collect/kallisto_collect.R
@@ -1,4 +1,4 @@
-ö#!/usr/bin/env Rscript
+#!/usr/bin/env Rscript
 
 ################################################
 #### CWL-independent tests
@@ -25,31 +25,30 @@ library(jsonlite)
 
 args <- commandArgs(trailingOnly = T)
 
-arc_root <- args[1]
-in_kallisto_results <- args[2]
-in_metadata_file <- args[3]
-in_metadata_sample <- args[4]
-in_metadata_factor <- args[5]
-out_folder <- args[6]
+in_kallisto_results <- args[1]
+in_metadata_file <- args[2]
+in_metadata_sample <- args[3]
+in_metadata_factor <- args[4]
+out_folder <- args[5]
 
 
 ################################################
 #### If it does not exist, create out dir
 ################################################
 
-dir.create(paste(arc_root, out_folder, sep = "/"), recursive = T, showWarnings = F)
+dir.create(out_folder, recursive = T, showWarnings = F)
 
 ################################################
 #### Read ISA sample metadata
 ################################################
 
-samples <- read.table(file = paste(arc_root, in_metadata_file, sep = "/"), sep = "\t")
+samples <- read.table(file = in_metadata_file, sep = "\t")
 
 ################################################
 #### Read Kallisto results
 ################################################
 
-base_dir <- paste(arc_root, in_kallisto_results, sep = "/")
+base_dir <- in_kallisto_results
 
 # A list of paths to the kallisto results indexed by the sample IDs is collated with
 kal_dirs <- dir(base_dir, full.names = T) ## Sleuth requires full paths
@@ -67,7 +66,7 @@ s2c <- merge(s2c, path_df, by = "out_name")
 
 so <- sleuth_prep(s2c, full_model = ~condition, num_cores = 1)
 
-save(so, file = paste(arc_root, out_folder, "kallisto_sleuthObject.RData", sep = "/"))
+save(so, file = paste(out_folder, "kallisto_sleuthObject.RData", sep = "/"))
 
 
 ################################################
@@ -78,13 +77,13 @@ save(so, file = paste(arc_root, out_folder, "kallisto_sleuthObject.RData", sep =
 expression_data <- kallisto_table(so)
 
 ## write to file
-write.csv(expression_data, paste(arc_root, out_folder, "/kallisto_df.csv", sep = "/"), row.names = F)
+write.csv(expression_data, paste(out_folder, "/kallisto_df.csv", sep = "/"), row.names = F)
 
 ## as tpm matrix (gene x sample)
 tpm_table <- pivot_wider(expression_data, id_cols = target_id, names_from = sample, values_from = tpm)
 
 ## write to file
-write.csv(tpm_table, paste(arc_root, out_folder, "/kallisto_tpmMatrix.csv", sep = "/"), row.names = F)
+write.csv(tpm_table, paste(out_folder, "/kallisto_tpmMatrix.csv", sep = "/"), row.names = F)
 
 ################################################
 #### Summarize mapping stats
@@ -99,4 +98,4 @@ for (i in dir(kal_dirs, pattern = ".json", full.names = T))
   mapping_stats <- rbind(mapping_stats, z)
 }
 
-write.csv(mapping_stats, paste(arc_root, out_folder, "/kallisto_mappingStats.csv", sep = "/"), row.names = F)
+write.csv(mapping_stats, paste(out_folder, "/kallisto_mappingStats.csv", sep = "/"), row.names = F)
diff --git a/workflows/kallisto_collect/workflow.cwl b/workflows/kallisto_collect/workflow.cwl
index 8e3064c..73f215d 100644
--- a/workflows/kallisto_collect/workflow.cwl
+++ b/workflows/kallisto_collect/workflow.cwl
@@ -1,37 +1,39 @@
 #!/usr/bin/env cwl-runner
 
-cwlVersion: v1.2
+cwlVersion: v1.2.0-dev1
 class: CommandLineTool
-
+hints:
+  DockerRequirement:
+    dockerPull: zimmera95/rnaseq:latest
+requirements:
+  - class: InitialWorkDirRequirement
+    listing:
+      - class: File
+        location: kallisto_collect.R
+arguments:
+  - position: 0
+    valueFrom: kallisto_collect.R
 inputs:
-- id: r_script
-  type: File
-  inputBinding:
-    position: 0
-- id: arc_root
-  type: string
-  inputBinding:
-    position: 1
 - id: in_kallisto_results
-  type: string
+  type: Directory
   inputBinding:
-    position: 2
+    position: 1
 - id: in_metadata_file
-  type: string
+  type: File
   inputBinding:
-    position: 3
+    position: 2
 - id: in_metadata_sample
   type: string
   inputBinding:
-    position: 4
+    position: 3
 - id: in_metadata_factor
   type: string
   inputBinding:
-    position: 5
+    position: 4
 - id: out_folder
   type: string
   inputBinding:
-    position: 6
+    position: 5
 
 outputs:
 - id: outdir
-- 
GitLab