From 12952600d165426df1abddfd05063bbc4f0bc98c Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Tue, 18 Mar 2025 16:14:39 +0100
Subject: [PATCH] rename assay rnaseq
---
.gitattributes | 12 ++++++------
README.md | 12 ++++++------
.../README.md | 0
.../DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz | 0
.../DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz | 0
.../DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz | 0
.../DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz | 0
.../DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz | 0
.../DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz | 0
assays/RNASeq/isa.assay.xlsx | Bin 0 -> 14275 bytes
assays/{ => RNASeq/protocols}/.gitkeep | 0
.../protocols/illumina.md | 0
.../protocols/rna_extraction.md | 0
assays/Talinum_RNASeq_minimal/isa.assay.xlsx | Bin 14034 -> 0 bytes
.../Talinum_RNASeq_minimal/protocols/.gitkeep | 0
runs/fastqc/run.yml | 12 ++++++------
runs/isaSampleToRawDataSeq/run.yml | 2 +-
runs/kallisto/run.yml | 12 ++++++------
.../isaSampleToRawDataSeq.fsx | 2 +-
workflows/isaSampleToRawDataSeq/workflow.cwl | 2 +-
20 files changed, 27 insertions(+), 27 deletions(-)
rename assays/{Talinum_RNASeq_minimal => RNASeq}/README.md (100%)
rename assays/{Talinum_RNASeq_minimal => RNASeq}/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz (100%)
rename assays/{Talinum_RNASeq_minimal => RNASeq}/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz (100%)
rename assays/{Talinum_RNASeq_minimal => RNASeq}/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz (100%)
rename assays/{Talinum_RNASeq_minimal => RNASeq}/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz (100%)
rename assays/{Talinum_RNASeq_minimal => RNASeq}/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz (100%)
rename assays/{Talinum_RNASeq_minimal => RNASeq}/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz (100%)
create mode 100644 assays/RNASeq/isa.assay.xlsx
rename assays/{ => RNASeq/protocols}/.gitkeep (100%)
rename assays/{Talinum_RNASeq_minimal => RNASeq}/protocols/illumina.md (100%)
rename assays/{Talinum_RNASeq_minimal => RNASeq}/protocols/rna_extraction.md (100%)
delete mode 100644 assays/Talinum_RNASeq_minimal/isa.assay.xlsx
delete mode 100644 assays/Talinum_RNASeq_minimal/protocols/.gitkeep
diff --git a/.gitattributes b/.gitattributes
index 574339b..6668a8d 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -21,12 +21,12 @@
/assays/GCqTOF_targets/dataset/150115_15.D/AcqData/TDASpec.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150115_16.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
*fastq.gz filter=lfs diff=lfs merge=lfs -text
-/assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
-/assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
-/assays/Talinum_RNASeq_minimal/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
-/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
+/assays/RNASeq/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
+/assays/RNASeq/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
+/assays/RNASeq/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
+/assays/RNASeq/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
+/assays/RNASeq/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
+/assays/RNASeq/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz 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
diff --git a/README.md b/README.md
index 62ea32b..60d41c9 100644
--- a/README.md
+++ b/README.md
@@ -12,8 +12,8 @@ The [Talinum Genome Draft](./studies/TalinumGenomeDraft) originates from <https:
- [TalinumFacultativeCAM](#study--talinumfacultativecam)
4. Assays
- [MassHunter_targets](#assay--masshunter_targets)
- - [Talinum_RNASeq_minimal](#assay--talinum_rnaseq_minimal)
- [GCqTOF_targets](#assay--gcqtof_targets)
+ - [RNASeq](#assay--RNASeq)
### Description
@@ -40,7 +40,7 @@ flowchart TD
mh-quant-results[mh-quant-results]
mh-quant-report[mh-quant-report]
end
- subgraph ASSAY_Talinum_RNASeq_minimal[Assay:Talinum_RNASeq_minimal]
+ subgraph ASSAY_RNASeq[Assay:RNASeq]
rna_extraction[rna_extraction]
illumina[illumina]
end
@@ -63,7 +63,7 @@ classDef assayStyle fill:#ffd34d,color:#2d3e50,font-weight:bold;
classDef processStyle fill:#D46275,color:#2d3e50,font-weight:;
class Facultative-CAM-in-Talinum investigationStyle;
class STUDY_TalinumGenomeDraft,STUDY_TalinumFacultativeCAM studyStyle;
-class ASSAY_MassHunter_targets,ASSAY_Talinum_RNASeq_minimal,ASSAY_GCqTOF_targets assayStyle;
+class ASSAY_MassHunter_targets,ASSAY_RNASeq,ASSAY_GCqTOF_targets assayStyle;
class TalinumGenomeDraft,plant_material,mh-quant-results,mh-quant-report,rna_extraction,illumina,metabolite_extraction,gas_chromatography,mass_spec processStyle;
```
@@ -75,7 +75,7 @@ class TalinumGenomeDraft,plant_material,mh-quant-results,mh-quant-report,rna_ext
| Public Release Date | Nov 05, 2015 |
| Study identifiers | TalinumGenomeDraft , TalinumFacultativeCAM |
| Study Count | 2 |
-| Assay identifiers | MassHunter_targets , Talinum_RNASeq_minimal , GCqTOF_targets |
+| Assay identifiers | MassHunter_targets , RNASeq , GCqTOF_targets |
| Assay Count | 3 |
## Publication
@@ -113,7 +113,7 @@ class TalinumGenomeDraft,plant_material,mh-quant-results,mh-quant-report,rna_ext
| Table Names | plant_material |
| Sample Count | 6 |
| Data File Count | 0 |
-| Associated assays | Talinum_RNASeq_minimal , GCqTOF_targets |
+| Associated assays | RNASeq , GCqTOF_targets |
| Biological replicates | 0 |
### Annotation headers
@@ -138,7 +138,7 @@ class TalinumGenomeDraft,plant_material,mh-quant-results,mh-quant-report,rna_ext
### Annotation headers
-## Assay : *Talinum_RNASeq_minimal*
+## Assay : *RNASeq*
### Additional details
diff --git a/assays/Talinum_RNASeq_minimal/README.md b/assays/RNASeq/README.md
similarity index 100%
rename from assays/Talinum_RNASeq_minimal/README.md
rename to assays/RNASeq/README.md
diff --git a/assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz b/assays/RNASeq/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
similarity index 100%
rename from assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
rename to assays/RNASeq/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
diff --git a/assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz b/assays/RNASeq/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz
similarity index 100%
rename from assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz
rename to assays/RNASeq/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz
diff --git a/assays/Talinum_RNASeq_minimal/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz b/assays/RNASeq/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz
similarity index 100%
rename from assays/Talinum_RNASeq_minimal/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz
rename to assays/RNASeq/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz
diff --git a/assays/Talinum_RNASeq_minimal/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz b/assays/RNASeq/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz
similarity index 100%
rename from assays/Talinum_RNASeq_minimal/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz
rename to assays/RNASeq/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz
diff --git a/assays/Talinum_RNASeq_minimal/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz b/assays/RNASeq/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz
similarity index 100%
rename from assays/Talinum_RNASeq_minimal/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz
rename to assays/RNASeq/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz
diff --git a/assays/Talinum_RNASeq_minimal/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz b/assays/RNASeq/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz
similarity index 100%
rename from assays/Talinum_RNASeq_minimal/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz
rename to assays/RNASeq/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz
diff --git a/assays/RNASeq/isa.assay.xlsx b/assays/RNASeq/isa.assay.xlsx
new file mode 100644
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diff --git a/assays/Talinum_RNASeq_minimal/protocols/.gitkeep b/assays/Talinum_RNASeq_minimal/protocols/.gitkeep
deleted file mode 100644
index e69de29..0000000
diff --git a/runs/fastqc/run.yml b/runs/fastqc/run.yml
index d9744cf..e45e457 100644
--- a/runs/fastqc/run.yml
+++ b/runs/fastqc/run.yml
@@ -1,14 +1,14 @@
finaloutdir: "results"
fastq:
- class: File
- path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
+ path: ../../assays/RNASeq/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
- class: File
- path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz
+ path: ../../assays/RNASeq/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz
- class: File
- path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz
+ path: ../../assays/RNASeq/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz
- class: File
- path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz
+ path: ../../assays/RNASeq/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz
- class: File
- path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz
+ path: ../../assays/RNASeq/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz
- class: File
- path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz
\ No newline at end of file
+ path: ../../assays/RNASeq/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz
\ No newline at end of file
diff --git a/runs/isaSampleToRawDataSeq/run.yml b/runs/isaSampleToRawDataSeq/run.yml
index 375bb88..ff17e5d 100644
--- a/runs/isaSampleToRawDataSeq/run.yml
+++ b/runs/isaSampleToRawDataSeq/run.yml
@@ -1,6 +1,6 @@
arcPath:
class: Directory
path: ../../
-assayName: "Talinum_RNASeq_minimal"
+assayName: "RNASeq"
outName: rnaseq-samples
startingNodeNum: 0
diff --git a/runs/kallisto/run.yml b/runs/kallisto/run.yml
index 541e170..f7dd756 100644
--- a/runs/kallisto/run.yml
+++ b/runs/kallisto/run.yml
@@ -11,32 +11,32 @@ IndexInput:
sampleRecord:
- readsOfOneSample:
- class: File
- path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
+ path: ../../assays/RNASeq/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
format: edam:format_1930
sampleName: 'DB_097'
- readsOfOneSample:
- class: File
- path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz
+ path: ../../assays/RNASeq/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz
format: edam:format_1930
sampleName: 'DB_163'
- readsOfOneSample:
- class: File
- path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz
+ path: ../../assays/RNASeq/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz
format: edam:format_1930
sampleName: 'DB_099'
- readsOfOneSample:
- class: File
- path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz
+ path: ../../assays/RNASeq/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz
format: edam:format_1930
sampleName: 'DB_103'
- readsOfOneSample:
- class: File
- path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz
+ path: ../../assays/RNASeq/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz
format: edam:format_1930
sampleName: 'DB_161'
- readsOfOneSample:
- class: File
- path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz
+ path: ../../assays/RNASeq/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz
format: edam:format_1930
sampleName: 'DB_165'
diff --git a/workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.fsx b/workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.fsx
index c73f8d1..6fffb68 100644
--- a/workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.fsx
+++ b/workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.fsx
@@ -16,7 +16,7 @@ open FsSpreadsheet.CsvIO
// test parameters
// let source = __SOURCE_DIRECTORY__
// let arcPath = System.IO.Path.Combine(source, "../../")
-// let assayName = "Talinum_RNASeq_minimal"
+// let assayName = "RNASeq"
// let startingNodeNum = 0
// let outName = "rnaseq-samples"
diff --git a/workflows/isaSampleToRawDataSeq/workflow.cwl b/workflows/isaSampleToRawDataSeq/workflow.cwl
index c2ef89d..9cace45 100644
--- a/workflows/isaSampleToRawDataSeq/workflow.cwl
+++ b/workflows/isaSampleToRawDataSeq/workflow.cwl
@@ -2,7 +2,7 @@ cwlVersion: v1.2
class: CommandLineTool
doc: |
- Run script with `dotnet fsi isaSampleToRawDataSeq.fsx ../../ Talinum_RNASeq_minimal 1 rnaseq-samples`
+ Run script with `dotnet fsi isaSampleToRawDataSeq.fsx ../../ RNASeq 1 rnaseq-samples`
hints:
DockerRequirement:
--
GitLab