From 142f85518f4ce2c1be17fdc18c2f42b6ed6ba330 Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Mon, 24 Mar 2025 09:21:34 +0100
Subject: [PATCH] add sleuth metadata
---
workflows/sleuth/sleuth.R | 2 +-
workflows/sleuth/workflow.cwl | 17 +++++++++++++++--
2 files changed, 16 insertions(+), 3 deletions(-)
diff --git a/workflows/sleuth/sleuth.R b/workflows/sleuth/sleuth.R
index 2c87d61..2b2283c 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 4a8add0..497533c 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]
--
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