diff --git a/.gitattributes b/.gitattributes
index 574339b69b82d0008d4b3ffd2e7398ad5d82ed6d..6668a8d572594430db45b791b0a5758f339a5aff 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 62ea32b962470601a6064a216c3121ca7983dafa..a0b47600f691b2402d98bfee41e34da7a0c1b704 100644
--- a/README.md
+++ b/README.md
@@ -9,11 +9,11 @@ The [Talinum Genome Draft](./studies/TalinumGenomeDraft) originates from <https:
2. [Publication](#publication)
3. Studies
- [TalinumGenomeDraft](#study--talinumgenomedraft)
- - [TalinumFacultativeCAM](#study--talinumfacultativecam)
+ - [TalinumSamples-STRI](#study--TalinumSamples-STRI)
4. Assays
- [MassHunter_targets](#assay--masshunter_targets)
- - [Talinum_RNASeq_minimal](#assay--talinum_rnaseq_minimal)
- [GCqTOF_targets](#assay--gcqtof_targets)
+ - [RNASeq](#assay--RNASeq)
### Description
@@ -32,15 +32,15 @@ flowchart TD
subgraph STUDY_TalinumGenomeDraft[Study:TalinumGenomeDraft]
TalinumGenomeDraft[TalinumGenomeDraft]
end
- Facultative-CAM-in-Talinum-->STUDY_TalinumFacultativeCAM
- subgraph STUDY_TalinumFacultativeCAM[Study:TalinumFacultativeCAM]
+ Facultative-CAM-in-Talinum-->STUDY_TalinumSamples-STRI
+ subgraph STUDY_TalinumSamples-STRI[Study:TalinumSamples-STRI]
plant_material[plant_material]
end
subgraph ASSAY_MassHunter_targets[Assay:MassHunter_targets]
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
@@ -62,8 +62,8 @@ classDef studyStyle fill:#62d4c1,color:#2d3e50,font-weight:bold;
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 STUDY_TalinumGenomeDraft,STUDY_TalinumSamples-STRI studyStyle;
+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;
```
@@ -73,9 +73,9 @@ class TalinumGenomeDraft,plant_material,mh-quant-results,mh-quant-report,rna_ext
| --------- | ----------- |
| Submission Date | July 07, 2015 |
| Public Release Date | Nov 05, 2015 |
-| Study identifiers | TalinumGenomeDraft , TalinumFacultativeCAM |
+| Study identifiers | TalinumGenomeDraft , TalinumSamples-STRI |
| Study Count | 2 |
-| Assay identifiers | MassHunter_targets , Talinum_RNASeq_minimal , GCqTOF_targets |
+| Assay identifiers | MassHunter_targets , RNASeq , GCqTOF_targets |
| Assay Count | 3 |
## Publication
@@ -103,7 +103,7 @@ class TalinumGenomeDraft,plant_material,mh-quant-results,mh-quant-report,rna_ext
### Annotation headers
-## Study : *TalinumFacultativeCAM*
+## Study : *TalinumSamples-STRI*
### Additional details
@@ -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
@@ -150,7 +150,7 @@ class TalinumGenomeDraft,plant_material,mh-quant-results,mh-quant-report,rna_ext
| Table Names | rna_extraction , illumina |
| Sample Count | 6 |
| Data File Count | 6 |
-| Associated studies | TalinumFacultativeCAM |
+| Associated studies | TalinumSamples-STRI |
### Annotation headers
@@ -167,7 +167,7 @@ class TalinumGenomeDraft,plant_material,mh-quant-results,mh-quant-report,rna_ext
| Table Names | metabolite_extraction , gas_chromatography , mass_spec |
| Sample Count | 20 |
| Data File Count | 20 |
-| Associated studies | TalinumFacultativeCAM |
+| Associated studies | TalinumSamples-STRI |
### Annotation headers
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
index 0000000000000000000000000000000000000000..eeb862e6cfd4ea9398952c532926bed2893afff9
Binary files /dev/null and b/assays/RNASeq/isa.assay.xlsx differ
diff --git a/assays/.gitkeep b/assays/RNASeq/protocols/.gitkeep
similarity index 100%
rename from assays/.gitkeep
rename to assays/RNASeq/protocols/.gitkeep
diff --git a/assays/Talinum_RNASeq_minimal/protocols/illumina.md b/assays/RNASeq/protocols/illumina.md
similarity index 100%
rename from assays/Talinum_RNASeq_minimal/protocols/illumina.md
rename to assays/RNASeq/protocols/illumina.md
diff --git a/assays/Talinum_RNASeq_minimal/protocols/rna_extraction.md b/assays/RNASeq/protocols/rna_extraction.md
similarity index 100%
rename from assays/Talinum_RNASeq_minimal/protocols/rna_extraction.md
rename to assays/RNASeq/protocols/rna_extraction.md
diff --git a/assays/Talinum_RNASeq_minimal/isa.assay.xlsx b/assays/Talinum_RNASeq_minimal/isa.assay.xlsx
deleted file mode 100644
index ca0e8a7a976d3764b8d7c3c75de6e7561c611eef..0000000000000000000000000000000000000000
Binary files a/assays/Talinum_RNASeq_minimal/isa.assay.xlsx and /dev/null differ
diff --git a/runs/fastqc/run.yml b/runs/fastqc/run.yml
index d9744cf09a5b541d9497c4831f5a81055fdc996d..e45e457ca4895f2addb91e2277d271bdab0a6ffe 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 375bb88317e61a873ad8b7cd9f2bf04f4ebfda4f..ff17e5db8a91496d92456c4a2632526174fdcd98 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 541e17004c6844c012e70922d7bc4470a59b8963..f7dd756fab5c1e1b6f5d9f85b0b8def87db194c3 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/studies/TalinumFacultativeCAM/isa.study.xlsx b/studies/TalinumFacultativeCAM/isa.study.xlsx
deleted file mode 100644
index 0a83fd2d7f6d0487f700abb76eac92200cf11a71..0000000000000000000000000000000000000000
Binary files a/studies/TalinumFacultativeCAM/isa.study.xlsx and /dev/null differ
diff --git a/studies/TalinumFacultativeCAM/resources/.gitkeep b/studies/TalinumFacultativeCAM/resources/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/studies/TalinumFacultativeCAM/README.md b/studies/TalinumSamples-STRI/README.md
similarity index 100%
rename from studies/TalinumFacultativeCAM/README.md
rename to studies/TalinumSamples-STRI/README.md
diff --git a/assays/Talinum_RNASeq_minimal/protocols/.gitkeep b/studies/TalinumSamples-STRI/protocols/.gitkeep
similarity index 100%
rename from assays/Talinum_RNASeq_minimal/protocols/.gitkeep
rename to studies/TalinumSamples-STRI/protocols/.gitkeep
diff --git a/studies/TalinumFacultativeCAM/protocols/plant_material.md b/studies/TalinumSamples-STRI/protocols/plant_material.md
similarity index 100%
rename from studies/TalinumFacultativeCAM/protocols/plant_material.md
rename to studies/TalinumSamples-STRI/protocols/plant_material.md
diff --git a/studies/TalinumFacultativeCAM/protocols/.gitkeep b/studies/TalinumSamples-STRI/resources/.gitkeep
similarity index 100%
rename from studies/TalinumFacultativeCAM/protocols/.gitkeep
rename to studies/TalinumSamples-STRI/resources/.gitkeep
diff --git a/studies/TalinumFacultativeCAM/resources/DB_097 b/studies/TalinumSamples-STRI/resources/DB_097
similarity index 100%
rename from studies/TalinumFacultativeCAM/resources/DB_097
rename to studies/TalinumSamples-STRI/resources/DB_097
diff --git a/studies/TalinumFacultativeCAM/resources/DB_099 b/studies/TalinumSamples-STRI/resources/DB_099
similarity index 100%
rename from studies/TalinumFacultativeCAM/resources/DB_099
rename to studies/TalinumSamples-STRI/resources/DB_099
diff --git a/studies/TalinumFacultativeCAM/resources/DB_103 b/studies/TalinumSamples-STRI/resources/DB_103
similarity index 100%
rename from studies/TalinumFacultativeCAM/resources/DB_103
rename to studies/TalinumSamples-STRI/resources/DB_103
diff --git a/studies/TalinumFacultativeCAM/resources/DB_161 b/studies/TalinumSamples-STRI/resources/DB_161
similarity index 100%
rename from studies/TalinumFacultativeCAM/resources/DB_161
rename to studies/TalinumSamples-STRI/resources/DB_161
diff --git a/studies/TalinumFacultativeCAM/resources/DB_163 b/studies/TalinumSamples-STRI/resources/DB_163
similarity index 100%
rename from studies/TalinumFacultativeCAM/resources/DB_163
rename to studies/TalinumSamples-STRI/resources/DB_163
diff --git a/studies/TalinumFacultativeCAM/resources/DB_165 b/studies/TalinumSamples-STRI/resources/DB_165
similarity index 100%
rename from studies/TalinumFacultativeCAM/resources/DB_165
rename to studies/TalinumSamples-STRI/resources/DB_165
diff --git a/workflows/deseq2/README.md b/workflows/deseq2/README.md
deleted file mode 100644
index 8b68f05954783ac9a6cc39c9861dadd38b90d05f..0000000000000000000000000000000000000000
--- a/workflows/deseq2/README.md
+++ /dev/null
@@ -1,35 +0,0 @@
-# DESeq2
-
-Workflow used for **differential gene expression analysis**
-
-## DESeq2 docs
-
-- https://bioconductor.org/packages/release/bioc/html/DESeq2.html
-
-## Importing kallisto output with tximport
-
-- https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html#kallisto
-
-## Run pure script (to test)
-
-### Install R dependencies for deseq2
-
-```R
-if (!require("BiocManager", quietly = TRUE))
- install.packages("BiocManager")
-
-BiocManager::install("DESeq2")
-library("DESeq2")
-
-BiocManager::install("tximport")
-library("tximport")
-
-BiocManager::install("rhdf5")
-library("rhdf5")
-```
-
-## Multi-package containers
-
-- R and combinations of library dependencies are available as multi-package containers from [BioContainers](https://github.com/BioContainers/multi-package-containers)
-- Searched for `repo:BioContainers/multi-package-containers deseq2 tximport rhdf5`
-- and found `quay.io/biocontainers/mulled-v2-05fd88b9ac812a9149da2f2d881d62f01cc49835:a10f0e3a7a70fc45494f8781d33901086d2214d0-0` :tada:
diff --git a/workflows/deseq2/workflow.cwl b/workflows/deseq2/workflow.cwl
index 993371903c5258fdc98b03740978714854530c22..0f1d68dfbb3bf401270f8f0b49a4706f0f571455 100644
--- a/workflows/deseq2/workflow.cwl
+++ b/workflows/deseq2/workflow.cwl
@@ -1,7 +1,8 @@
#!/usr/bin/env cwl-runner
doc: |
- DESeq2 example workflow
+ DESeq2 example workflow for **differential gene expression analysis**
+
This workflow runs DESeq2 on the output of the kallisto workflow
and the metadata file.
It runs an R script, deseq2.R, which ideally should be split into three sub scripts and accordingly three workflow steps
@@ -9,6 +10,17 @@ doc: |
2. Prep / run deseq2
3. Plot results
+ ## DESeq2 docs:
+ https://bioconductor.org/packages/release/bioc/html/DESeq2.html
+
+ ## Importing kallisto output with tximport
+ https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html#kallisto
+
+ ## Multi-package containers
+ - R and combinations of library dependencies are available as multi-package containers from [BioContainers](https://github.com/BioContainers/multi-package-containers)
+ - Searched for `repo:BioContainers/multi-package-containers deseq2 tximport rhdf5`
+ - and found `quay.io/biocontainers/mulled-v2-05fd88b9ac812a9149da2f2d881d62f01cc49835:a10f0e3a7a70fc45494f8781d33901086d2214d0-0` :tada:
+
cwlVersion: v1.2
class: CommandLineTool
hints:
diff --git a/workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.fsx b/workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.fsx
index c73f8d1634a81d2888baf39f021ca985d2c0951e..6fffb68e5283aae7cb0a95bab6e0c021c0245138 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 c2ef89de0657e40149af4c0419e5e21076c92cc6..9cace450b08381d8a8dc408daf6fab25489e8881 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:
diff --git a/workflows/shiny/Dockerfile b/workflows/shiny/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..01b85ffdf2b66e9bd1b90733ae43f980cb543749
--- /dev/null
+++ b/workflows/shiny/Dockerfile
@@ -0,0 +1,13 @@
+# Use an official R base image
+FROM rocker/shiny:4.4
+
+# Install R packages
+RUN R -q -e 'install.packages("ggplot2")'
+
+EXPOSE 3838
+
+# Set the working directory to /app
+WORKDIR /app
+
+# Default command to run when the container starts
+CMD ["R"]
diff --git a/workflows/shiny/shiny-app.R b/workflows/shiny/shiny-app.R
index 4c020248813f9dfe57180989361fa246103f07a7..4d4275f1d6d43a7f6ff232e5a2855e2791cce135 100644
--- a/workflows/shiny/shiny-app.R
+++ b/workflows/shiny/shiny-app.R
@@ -3,7 +3,6 @@
# Load libraries
library(shiny)
-library(RColorBrewer)
library(ggplot2)
# CLI arguments
@@ -65,4 +64,5 @@ server <- function(input, output, session) {
# Launch app
-shinyApp(ui, server)
+sa <- shinyApp(ui, server)
+runApp(sa, port = 3838)
diff --git a/workflows/shiny/workflow.cwl b/workflows/shiny/workflow.cwl
index 2e80423e1801af7875f5917f15ff4f704afa2c9e..00d0f26f62c10679c181f711ea54aa69f4f481ba 100644
--- a/workflows/shiny/workflow.cwl
+++ b/workflows/shiny/workflow.cwl
@@ -4,8 +4,9 @@ cwlVersion: v1.2
class: CommandLineTool
# hints:
-# DockerRequirement:
-# dockerPull:
+# DockerRequirement:
+# dockerImageId: "shiny"
+# dockerFile: {$include: "Dockerfile"}
requirements:
- class: InitialWorkDirRequirement
diff --git a/workflows/sleuth/Dockerfile b/workflows/sleuth/Dockerfile
deleted file mode 100644
index 39a6609301f9954da43bf426be379cfda98e5f85..0000000000000000000000000000000000000000
--- a/workflows/sleuth/Dockerfile
+++ /dev/null
@@ -1,29 +0,0 @@
-# Use an official R base image
-FROM rocker/r-ver:4.1.3
-
-# Install system dependencies for R packages and other utilities
-RUN apt-get update && apt-get install -y \
- libcurl4-openssl-dev \
- libssl-dev \
- libxml2-dev \
- git \
- build-essential \
- && rm -rf /var/lib/apt/lists/*
-
-# Install BiocManager
-RUN R -e "install.packages('BiocManager')"
-
-# Install Bioconductor version 3.14
-RUN R -e "BiocManager::install(version = '3.11')"
-
-# Install sleuth from Bioconductor
-RUN R -e "BiocManager::install('sleuth')"
-
-# Install other necessary CRAN packages
-RUN R -e "install.packages('jsonlite', repos='https://cran.r-project.org')"
-
-# Set the working directory to /app
-WORKDIR /app
-
-# Default command to run when the container starts
-CMD ["R"]
diff --git a/workflows/sleuth/workflow.cwl b/workflows/sleuth/workflow.cwl
index 8163e27b260d56b501b3e5f0ad8a95ffb4586649..4a8add08556780341d42af5b5488691ea8608107 100644
--- a/workflows/sleuth/workflow.cwl
+++ b/workflows/sleuth/workflow.cwl
@@ -4,9 +4,6 @@ cwlVersion: v1.2
class: CommandLineTool
hints:
- # DockerRequirement:
- # dockerImageId: "sleuth"
- # dockerFile: {$include: "Dockerfile"}
DockerRequirement:
dockerPull: quay.io/biocontainers/mulled-v2-fdd016122f200fdc6dc30f6ea2fd0000e8067dff:f9531f6ac1f44332eff70b5912d7d5f3ebe8df38-0