add sleuth metadata

workflows/sleuth/sleuth.R

@@ -76,7 +76,7 @@ save(so, file = file.path(outFolder, "kallisto_sleuthObject.RData"))
 expression_data <- kallisto_table(so)
 
 ## write to file
-write.csv(expression_data, paste(outFolder, "/kallisto_df.csv", sep = "/"), row.names = F)
+write.csv(expression_data, file.path(outFolder, "kallisto_df.csv"), row.names = F)
 
 ## as tpm matrix (gene x sample)
 tpm_table <- reshape(expression_data, idvar = "target_id", timevar = "sample", direction = "wide", v.names = "tpm")

workflows/sleuth/workflow.cwl

@@ -6,6 +6,19 @@ class: CommandLineTool
 hints:
   DockerRequirement: 
     dockerPull: quay.io/biocontainers/mulled-v2-fdd016122f200fdc6dc30f6ea2fd0000e8067dff:f9531f6ac1f44332eff70b5912d7d5f3ebe8df38-0
+  SoftwareRequirement:  
+    packages:
+      - package: R
+        specs:
+          - https://identifiers.org/rrid/RRID:SCR_001905
+          - https://identifiers.org/biotools/r
+          - https://anaconda.org/bioconda/r
+        version: [ "4.2.3" ]
+      - package: sleuth
+        version: [ "0.30.1" ]
+        specs: 
+          - https://identifiers.org/rrid/RRID:SCR_016883
+          - https://identifiers.org/biotools/sleuth
 
 requirements:
   - class: InitialWorkDirRequirement
@@ -13,8 +26,8 @@ requirements:
       - entryname: sleuth.R
         entry:
           $include: sleuth.R
-  - class: NetworkAccess
-    networkAccess: true
+  # - class: NetworkAccess
+  #   networkAccess: true
 
 baseCommand: [Rscript, sleuth.R]