From c572b83d00933a260e97dc5ba990f518d5b0e83e Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Fri, 14 Mar 2025 15:49:17 +0100
Subject: [PATCH] rename workflow to sleuth
---
.gitattributes | 6 +++---
runs/shiny_prep/run.yml | 2 +-
.../results/kallisto_df.csv | 0
.../results/kallisto_mappingStats.csv | 0
.../results/kallisto_sleuthObject.RData | Bin
.../results/kallisto_tpmMatrix.csv | 0
.../results/sleuth_dge.csv | 0
runs/{kallisto_collect => sleuth}/run.cwl | 2 +-
runs/{kallisto_collect => sleuth}/run.yml | 0
workflows/{kallisto_collect => sleuth}/Dockerfile | 0
.../kallisto_collect.R => sleuth/sleuth.R} | 0
workflows/{kallisto_collect => sleuth}/workflow.cwl | 6 +++---
12 files changed, 8 insertions(+), 8 deletions(-)
rename runs/{kallisto_collect => sleuth}/results/kallisto_df.csv (100%)
rename runs/{kallisto_collect => sleuth}/results/kallisto_mappingStats.csv (100%)
rename runs/{kallisto_collect => sleuth}/results/kallisto_sleuthObject.RData (100%)
rename runs/{kallisto_collect => sleuth}/results/kallisto_tpmMatrix.csv (100%)
rename runs/{kallisto_collect => sleuth}/results/sleuth_dge.csv (100%)
rename runs/{kallisto_collect => sleuth}/run.cwl (91%)
rename runs/{kallisto_collect => sleuth}/run.yml (100%)
rename workflows/{kallisto_collect => sleuth}/Dockerfile (100%)
rename workflows/{kallisto_collect/kallisto_collect.R => sleuth/sleuth.R} (100%)
rename workflows/{kallisto_collect => sleuth}/workflow.cwl (89%)
diff --git a/.gitattributes b/.gitattributes
index 9c9b391..07a4a56 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -27,9 +27,9 @@
/assays/Talinum_RNASeq_minimal/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
/assays/Talinum_RNASeq_minimal/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
/assays/Talinum_RNASeq_minimal/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_collect/kallisto_df.csv filter=lfs diff=lfs merge=lfs -text
+runs/sleuth/kallisto_df.csv filter=lfs diff=lfs merge=lfs -text
runs/kallisto_sleuth/sleuth_dge.csv filter=lfs diff=lfs merge=lfs -text
studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_collect/kallisto_sleuthObject.RData filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_collect/out/kallisto_sleuthObject.RData filter=lfs diff=lfs merge=lfs -text
+runs/sleuth/kallisto_sleuthObject.RData filter=lfs diff=lfs merge=lfs -text
+runs/sleuth/out/kallisto_sleuthObject.RData filter=lfs diff=lfs merge=lfs -text
runs/kallisto/kallisto_results/** filter=lfs diff=lfs merge=lfs -text
\ No newline at end of file
diff --git a/runs/shiny_prep/run.yml b/runs/shiny_prep/run.yml
index 7124f42..8e7954b 100644
--- a/runs/shiny_prep/run.yml
+++ b/runs/shiny_prep/run.yml
@@ -4,5 +4,5 @@ r_script:
path: ../../workflows/shiny_prep/shiny_prep.R
in_kallisto_df:
class: File
- path: ../kallisto_collect/out/kallisto_df.csv
+ path: ../sleuth/out/kallisto_df.csv
out_folder: out
\ No newline at end of file
diff --git a/runs/kallisto_collect/results/kallisto_df.csv b/runs/sleuth/results/kallisto_df.csv
similarity index 100%
rename from runs/kallisto_collect/results/kallisto_df.csv
rename to runs/sleuth/results/kallisto_df.csv
diff --git a/runs/kallisto_collect/results/kallisto_mappingStats.csv b/runs/sleuth/results/kallisto_mappingStats.csv
similarity index 100%
rename from runs/kallisto_collect/results/kallisto_mappingStats.csv
rename to runs/sleuth/results/kallisto_mappingStats.csv
diff --git a/runs/kallisto_collect/results/kallisto_sleuthObject.RData b/runs/sleuth/results/kallisto_sleuthObject.RData
similarity index 100%
rename from runs/kallisto_collect/results/kallisto_sleuthObject.RData
rename to runs/sleuth/results/kallisto_sleuthObject.RData
diff --git a/runs/kallisto_collect/results/kallisto_tpmMatrix.csv b/runs/sleuth/results/kallisto_tpmMatrix.csv
similarity index 100%
rename from runs/kallisto_collect/results/kallisto_tpmMatrix.csv
rename to runs/sleuth/results/kallisto_tpmMatrix.csv
diff --git a/runs/kallisto_collect/results/sleuth_dge.csv b/runs/sleuth/results/sleuth_dge.csv
similarity index 100%
rename from runs/kallisto_collect/results/sleuth_dge.csv
rename to runs/sleuth/results/sleuth_dge.csv
diff --git a/runs/kallisto_collect/run.cwl b/runs/sleuth/run.cwl
similarity index 91%
rename from runs/kallisto_collect/run.cwl
rename to runs/sleuth/run.cwl
index 302db8d..b214342 100644
--- a/runs/kallisto_collect/run.cwl
+++ b/runs/sleuth/run.cwl
@@ -13,7 +13,7 @@ inputs:
steps:
collectResults:
- run: ../../workflows/kallisto_collect/workflow.cwl
+ run: ../../workflows/sleuth/workflow.cwl
in:
inKallistoResults: inKallistoResults
inMetadataFile: inMetadataFile
diff --git a/runs/kallisto_collect/run.yml b/runs/sleuth/run.yml
similarity index 100%
rename from runs/kallisto_collect/run.yml
rename to runs/sleuth/run.yml
diff --git a/workflows/kallisto_collect/Dockerfile b/workflows/sleuth/Dockerfile
similarity index 100%
rename from workflows/kallisto_collect/Dockerfile
rename to workflows/sleuth/Dockerfile
diff --git a/workflows/kallisto_collect/kallisto_collect.R b/workflows/sleuth/sleuth.R
similarity index 100%
rename from workflows/kallisto_collect/kallisto_collect.R
rename to workflows/sleuth/sleuth.R
diff --git a/workflows/kallisto_collect/workflow.cwl b/workflows/sleuth/workflow.cwl
similarity index 89%
rename from workflows/kallisto_collect/workflow.cwl
rename to workflows/sleuth/workflow.cwl
index 1b182ea..8163e27 100644
--- a/workflows/kallisto_collect/workflow.cwl
+++ b/workflows/sleuth/workflow.cwl
@@ -13,13 +13,13 @@ hints:
requirements:
- class: InitialWorkDirRequirement
listing:
- - entryname: kallisto_collect.R
+ - entryname: sleuth.R
entry:
- $include: kallisto_collect.R
+ $include: sleuth.R
- class: NetworkAccess
networkAccess: true
-baseCommand: [Rscript, kallisto_collect.R]
+baseCommand: [Rscript, sleuth.R]
inputs:
inKallistoResults:
--
GitLab