diff --git a/workflows/sleuth/sleuth.R b/workflows/sleuth/sleuth.R index 2c87d6161cb691e17e222abd177150e261645fec..2b2283ccb69b6f8ee328c707646bc9c4a153684a 100644 --- a/workflows/sleuth/sleuth.R +++ b/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") diff --git a/workflows/sleuth/workflow.cwl b/workflows/sleuth/workflow.cwl index 4a8add08556780341d42af5b5488691ea8608107..497533cc151798d73ded9b32e829ba7d894970c5 100644 --- a/workflows/sleuth/workflow.cwl +++ b/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]