From 2e31eeda271e7d4197dcc8d27b7528c982f64672 Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <dominik.brilhaus@hhu.de>
Date: Tue, 9 Aug 2022 10:23:19 +0200
Subject: [PATCH] execute from runs folder
---
runs/merged_isa_metadata/README.md | 4 ++++
.../merged_isa_metadata}/merge_isa_metadata.yml | 3 ++-
workflows/merge_isa_metadata.R | 15 +++++++--------
3 files changed, 13 insertions(+), 9 deletions(-)
create mode 100644 runs/merged_isa_metadata/README.md
rename {workflows => runs/merged_isa_metadata}/merge_isa_metadata.yml (82%)
diff --git a/runs/merged_isa_metadata/README.md b/runs/merged_isa_metadata/README.md
new file mode 100644
index 0000000..ceeaf9b
--- /dev/null
+++ b/runs/merged_isa_metadata/README.md
@@ -0,0 +1,4 @@
+
+
+
+cwltool ../../workflows/merge_isa_metadata.cwl merge_isa_metadata.yml
\ No newline at end of file
diff --git a/workflows/merge_isa_metadata.yml b/runs/merged_isa_metadata/merge_isa_metadata.yml
similarity index 82%
rename from workflows/merge_isa_metadata.yml
rename to runs/merged_isa_metadata/merge_isa_metadata.yml
index 27806b3..0a2a9fd 100644
--- a/workflows/merge_isa_metadata.yml
+++ b/runs/merged_isa_metadata/merge_isa_metadata.yml
@@ -1,7 +1,8 @@
cores: 1
r_script:
class: File
- path: ./merge_isa_metadata.R
+ path: ../../workflows/merge_isa_metadata.R
+# arc_root: ../
arc_root: /Users/dominikbrilhaus/03_DataPLANT_gitlab/samplearc_rnaseq/
in_isa_study: studies/TalinumFacultativeCAM/isa.study.xlsx:plant_growth
in_isa_assay: assays/Talinum_RNASeq_minimal/isa.assay.xlsx:2EXT01_RNA:3ASY01_RNASeq
diff --git a/workflows/merge_isa_metadata.R b/workflows/merge_isa_metadata.R
index 4af0582..c629683 100644
--- a/workflows/merge_isa_metadata.R
+++ b/workflows/merge_isa_metadata.R
@@ -1,7 +1,7 @@
#!/usr/bin/env Rscript
################################################
-#### Test area
+#### Test area (Within R)
################################################
# arc_root <- "~/03_DataPLANT_gitlab/samplearc_rnaseq/"
@@ -14,7 +14,6 @@
################################################
library(openxlsx)
-# library(tidyverse)
################################################
#### Read arguments from CLI
@@ -77,15 +76,15 @@ isa_merged <- isa_merged[, !apply(isa_merged, 2, function(x) {
################################################
-#### Write to file
+#### If it does not exist, create out dir
################################################
-## Create directory
+
dir.create(paste(arc_root, out_folder, sep = "/"), recursive = T, showWarnings = F)
-# dir.create(out_folder, recursive = T, showWarnings = F)
-## Write
-write.table(isa_merged, file = paste(arc_root, out_folder, "merged_isa.tsv", sep = "/"), sep = "\t")
+################################################
+#### Write table to file
+################################################
-# View(read.csv(paste(arc_root, out_folder, "merged_isa.tsv", sep = "/"), sep = "\t"))
+write.table(isa_merged, file = paste(arc_root, out_folder, "merged_isa.tsv", sep = "/"), sep = "\t")
\ No newline at end of file
--
GitLab