diff --git a/.gitattributes b/.gitattributes
index 9992776affeb3d3878119e09bd8176a7fd14fcb0..7c3cf7781734b30a8e0cfccc6bdf9857f38f05a5 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -5,4 +5,4 @@
/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_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
-/runs/kallisto_index/kallisto_index filter=lfs diff=lfs merge=lfs -text
+/runs/kallisto_index/out/kallisto_index filter=lfs diff=lfs merge=lfs -text
diff --git a/runs/kallisto_collect/README.md b/runs/kallisto_collect/README.md
deleted file mode 100644
index 574080e009fc120d02514c5dfa15b6b6c602f00b..0000000000000000000000000000000000000000
--- a/runs/kallisto_collect/README.md
+++ /dev/null
@@ -1,21 +0,0 @@
-
-# cwltool README
-
-## First cd into the (runs) folder, with the .yml file
-
-cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_collect
-
-## Let it flow
-
-```bash
-### store arc root (two levels up from here) as variable
-arc_root=$(echo ${PWD%/*/*})
-
-### replace arc root line in yml (specific to the machine from where this is run)
-### not sure, if this works on linux...
-sed -i '' "s|^arc_root:.*|arc_root: $arc_root|g" kallisto_collect.yml
-
-### run with cwltool
-cwltool ../../workflows/kallisto_collect.cwl kallisto_collect.yml
-
-```
diff --git a/runs/kallisto_collect/kallisto_collect.yml b/runs/kallisto_collect/kallisto_collect.yml
deleted file mode 100644
index 1b300513c1481db8c9c0188d7dbd09f3acae4ad3..0000000000000000000000000000000000000000
--- a/runs/kallisto_collect/kallisto_collect.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-cores: 1
-r_script:
- class: File
- path: ../../workflows/kallisto_collect.R
-in_kallisto_results: "runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results"
-in_metadata_file: "runs/merged_isa_metadata/merged_isa.tsv"
-in_metadata_sample: "Sample.Name.2"
-in_metadata_factor: "Factor..Photosynthesis.mode."
-out_folder: runs/kallisto_collect
-arc_root: /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq
\ No newline at end of file
diff --git a/runs/kallisto_collect/isa.dataset.xlsx b/runs/kallisto_collect/out/isa.dataset.xlsx
similarity index 100%
rename from runs/kallisto_collect/isa.dataset.xlsx
rename to runs/kallisto_collect/out/isa.dataset.xlsx
diff --git a/runs/kallisto_collect/kallisto_mappingStats.csv b/runs/kallisto_collect/out/kallisto_mappingStats.csv
similarity index 100%
rename from runs/kallisto_collect/kallisto_mappingStats.csv
rename to runs/kallisto_collect/out/kallisto_mappingStats.csv
diff --git a/runs/kallisto_collect/kallisto_tpmMatrix.csv b/runs/kallisto_collect/out/kallisto_tpmMatrix.csv
similarity index 100%
rename from runs/kallisto_collect/kallisto_tpmMatrix.csv
rename to runs/kallisto_collect/out/kallisto_tpmMatrix.csv
diff --git a/workflows/kallisto_collect.cwl b/runs/kallisto_collect/run.cwl
similarity index 85%
rename from workflows/kallisto_collect.cwl
rename to runs/kallisto_collect/run.cwl
index 8e3064c8dae6adb671d4daa9bded1894915f32e4..eaee053d15b5358ec2e125861995edda2004e684 100644
--- a/workflows/kallisto_collect.cwl
+++ b/runs/kallisto_collect/run.cwl
@@ -8,30 +8,26 @@ inputs:
type: File
inputBinding:
position: 0
-- id: arc_root
- type: string
- inputBinding:
- position: 1
- id: in_kallisto_results
- type: string
+ type: Directory
inputBinding:
- position: 2
+ position: 1
- id: in_metadata_file
- type: string
+ type: File
inputBinding:
- position: 3
+ position: 2
- id: in_metadata_sample
type: string
inputBinding:
- position: 4
+ position: 3
- id: in_metadata_factor
type: string
inputBinding:
- position: 5
+ position: 4
- id: out_folder
type: string
inputBinding:
- position: 6
+ position: 5
outputs:
- id: outdir
@@ -42,4 +38,4 @@ outputs:
glob: $(runtime.outdir)/$(inputs.out_folder)
baseCommand:
-- Rscript
\ No newline at end of file
+- Rscript
diff --git a/runs/kallisto_collect/run.yml b/runs/kallisto_collect/run.yml
new file mode 100644
index 0000000000000000000000000000000000000000..2a4197c55b150b9c73030aac479a6ecbc2ec0edf
--- /dev/null
+++ b/runs/kallisto_collect/run.yml
@@ -0,0 +1,13 @@
+cores: 1
+r_script:
+ class: File
+ path: ../../workflows/kallisto_collect/kallisto_collect.R
+in_kallisto_results:
+ class: Directory
+ path: ../kallisto_sleuth/out
+in_metadata_file:
+ class: File
+ path: ../merged_isa_metadata/out/merged_isa.tsv
+in_metadata_sample: "Sample.Name.2"
+in_metadata_factor: "Factor..Photosynthesis.mode."
+out_folder: out
diff --git a/runs/kallisto_index/README.md b/runs/kallisto_index/README.md
deleted file mode 100644
index 16475f8b77405c2dbb0e3b86c84bda9db3d4ccdd..0000000000000000000000000000000000000000
--- a/runs/kallisto_index/README.md
+++ /dev/null
@@ -1,21 +0,0 @@
-
-# cwltool README
-
-## First cd into the (runs) folder, with the .yml file
-
-cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_index
-
-## Let it flow
-
-```bash
-### store arc root (two levels up from here) as variable
-arc_root=$(echo ${PWD%/*/*})
-
-### replace arc root line in yml (specific to the machine from where this is run)
-### not sure, if this works on linux...
-sed -i '' "s|^arc_root:.*|arc_root: $arc_root|g" kallisto_index.yml
-
-### run with cwltool
-cwltool ../../workflows/kallisto_index.cwl kallisto_index.yml
-
-```
diff --git a/runs/kallisto_index/kallisto_index.yml b/runs/kallisto_index/kallisto_index.yml
deleted file mode 100644
index 60f3a27f69a426983d158a83029b18693cf30c0c..0000000000000000000000000000000000000000
--- a/runs/kallisto_index/kallisto_index.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-cores: 1
-sh_script:
- class: File
- path: ../../workflows/kallisto_index.sh
-in_genome_ref: studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa
-out_folder: runs/kallisto_index
-arc_root: /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq
diff --git a/runs/kallisto_index/kallisto_index b/runs/kallisto_index/out/kallisto_index
similarity index 100%
rename from runs/kallisto_index/kallisto_index
rename to runs/kallisto_index/out/kallisto_index
diff --git a/workflows/kallisto_index.cwl b/runs/kallisto_index/run.cwl
similarity index 82%
rename from workflows/kallisto_index.cwl
rename to runs/kallisto_index/run.cwl
index a6389de36bedc4d46d297b71c7dabd50ed07e200..a8665ac38a52da961f0dc10751bedaef0451c8bd 100644
--- a/workflows/kallisto_index.cwl
+++ b/runs/kallisto_index/run.cwl
@@ -8,12 +8,8 @@ inputs:
type: File
inputBinding:
position: 0
-- id: arc_root
- type: string
- inputBinding:
- position: 1
- id: in_genome_ref
- type: string
+ type: File
inputBinding:
position: 2
- id: out_folder
@@ -30,4 +26,4 @@ outputs:
glob: $(runtime.outdir)/$(inputs.out_folder)
baseCommand:
-- bash
\ No newline at end of file
+- bash
diff --git a/runs/kallisto_index/run.yml b/runs/kallisto_index/run.yml
new file mode 100644
index 0000000000000000000000000000000000000000..df0c0706df4bcbda3746868761ef252449eb736c
--- /dev/null
+++ b/runs/kallisto_index/run.yml
@@ -0,0 +1,8 @@
+cores: 1
+sh_script:
+ class: File
+ path: ../../workflows/kallisto_index/kallisto_index.sh
+in_genome_ref:
+ class: File
+ path: ../../studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa
+out_folder: ./out
diff --git a/runs/kallisto_quant/README.md b/runs/kallisto_quant/README.md
deleted file mode 100644
index 7e0399169b09ac01f90709bcec1dd8d6e2e9694a..0000000000000000000000000000000000000000
--- a/runs/kallisto_quant/README.md
+++ /dev/null
@@ -1,21 +0,0 @@
-
-# cwltool README
-
-## First cd into the (runs) folder, with the .yml file
-
-cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_quant
-
-## Let it flow
-
-```bash
-### store arc root (two levels up from here) as variable
-arc_root=$(echo ${PWD%/*/*})
-
-### replace arc root line in yml (specific to the machine from where this is run)
-### not sure, if this works on linux...
-sed -i '' "s|^arc_root:.*|arc_root: $arc_root|g" kallisto_quant.yml
-
-### run with cwltool
-cwltool ../../workflows/kallisto_quant.cwl kallisto_quant.yml
-
-```
diff --git a/runs/kallisto_quant/kallisto_quant.yml b/runs/kallisto_quant/kallisto_quant.yml
deleted file mode 100644
index 3a700dde637416106f587147d1a6104ecdd6326d..0000000000000000000000000000000000000000
--- a/runs/kallisto_quant/kallisto_quant.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-cores: 4
-sh_script:
- class: File
- path: ../../workflows/kallisto_quant.sh
-arc_root: /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq
-out_folder: runs/kallisto_quant/kallisto_results
-in_kallisto_index: runs/kallisto_index/kallisto_index
-in_fastq_folder: assays/Talinum_RNASeq_minimal/dataset
-kallisto_bootstrap: 100
-kallisto_threads: 4
-kallisto_fragmentLength: 200
-kallisto_stdDev: 20
\ No newline at end of file
diff --git a/workflows/kallisto_quant.cwl b/runs/kallisto_quant/run.cwl
similarity index 86%
rename from workflows/kallisto_quant.cwl
rename to runs/kallisto_quant/run.cwl
index 9259357a2df7043a94a49eba13d0d1b1f534db28..980dc14143bab29a391bfbffc7040a6323df4b4a 100644
--- a/workflows/kallisto_quant.cwl
+++ b/runs/kallisto_quant/run.cwl
@@ -8,38 +8,34 @@ inputs:
type: File
inputBinding:
position: 0
-- id: arc_root
+- id: out_folder
type: string
inputBinding:
position: 1
-- id: out_folder
- type: string
+- id: in_kallisto_index
+ type: File
inputBinding:
position: 2
-- id: in_kallisto_index
- type: string
+- id: in_fastq_dir
+ type: Directory
inputBinding:
position: 3
-- id: in_fastq_folder
- type: string
- inputBinding:
- position: 4
- id: kallisto_bootstrap
type: int
inputBinding:
- position: 5
+ position: 4
- id: kallisto_threads
type: int
inputBinding:
- position: 6
+ position: 5
- id: kallisto_fragmentLength
type: int
inputBinding:
- position: 7
+ position: 6
- id: kallisto_stdDev
type: int
inputBinding:
- position: 8
+ position: 7
outputs:
- id: outdir
diff --git a/runs/kallisto_quant/run.yml b/runs/kallisto_quant/run.yml
new file mode 100644
index 0000000000000000000000000000000000000000..09afef48ab9d86fcdc40a041f12c78635c47bd18
--- /dev/null
+++ b/runs/kallisto_quant/run.yml
@@ -0,0 +1,15 @@
+cores: 4
+sh_script:
+ class: File
+ path: ../../workflows/kallisto_quant/kallisto_quant.sh
+out_folder: ./kallisto_results
+in_kallisto_index:
+ class: File
+ path: ../kallisto_index/out/kallisto_index
+in_fastq_dir:
+ class: Directory
+ path: ../../assays/Talinum_RNASeq_minimal/dataset
+kallisto_bootstrap: 100
+kallisto_threads: 4
+kallisto_fragmentLength: 200
+kallisto_stdDev: 20
diff --git a/runs/kallisto_sleuth/README.md b/runs/kallisto_sleuth/README.md
deleted file mode 100644
index 05639e7e53b53e81a9f51f01627e43af130fec9c..0000000000000000000000000000000000000000
--- a/runs/kallisto_sleuth/README.md
+++ /dev/null
@@ -1,21 +0,0 @@
-
-# cwltool README
-
-## First cd into the (runs) folder, with the .yml file
-
-cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_sleuth
-
-## Let it flow
-
-```bash
-### store arc root (two levels up from here) as variable
-arc_root=$(echo ${PWD%/*/*})
-
-### replace arc root line in yml (specific to the machine from where this is run)
-### not sure, if this works on linux...
-sed -i '' "s|^arc_root:.*|arc_root: $arc_root|g" kallisto_sleuth.yml
-
-### run with cwltool
-cwltool ../../workflows/kallisto_sleuth.cwl kallisto_sleuth.yml
-
-```
diff --git a/runs/kallisto_sleuth/kallisto_sleuth.yml b/runs/kallisto_sleuth/kallisto_sleuth.yml
deleted file mode 100644
index 34364fd1b8f453cf2ec511b2549f890fd06442ba..0000000000000000000000000000000000000000
--- a/runs/kallisto_sleuth/kallisto_sleuth.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-cores: 1
-r_script:
- class: File
- path: ../../workflows/kallisto_sleuth.R
-in_sleuth: runs/kallisto_collect/kallisto_sleuthObject.RData
-out_folder: runs/kallisto_sleuth
-arc_root: /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq
\ No newline at end of file
diff --git a/runs/kallisto_sleuth/sleuth_dge.csv b/runs/kallisto_sleuth/out/sleuth_dge.csv
similarity index 100%
rename from runs/kallisto_sleuth/sleuth_dge.csv
rename to runs/kallisto_sleuth/out/sleuth_dge.csv
diff --git a/workflows/merge_isa_metadata.cwl b/runs/kallisto_sleuth/run.cwl
similarity index 70%
rename from workflows/merge_isa_metadata.cwl
rename to runs/kallisto_sleuth/run.cwl
index d812914728833fca5140a2b9347c5e6994aa52ce..60a4475f53945dbe96e9499d6bf46859d3273b4d 100644
--- a/workflows/merge_isa_metadata.cwl
+++ b/runs/kallisto_sleuth/run.cwl
@@ -8,22 +8,14 @@ inputs:
type: File
inputBinding:
position: 0
-- id: arc_root
- type: string
+- id: in_sleuth
+ type: File
inputBinding:
position: 1
-- id: in_isa_study
- type: string
- inputBinding:
- position: 2
-- id: in_isa_assay
- type: string
- inputBinding:
- position: 3
- id: out_folder
type: string
inputBinding:
- position: 4
+ position: 2
outputs:
- id: outdir
diff --git a/runs/kallisto_sleuth/run.yml b/runs/kallisto_sleuth/run.yml
new file mode 100644
index 0000000000000000000000000000000000000000..7307a3537891c059bbbb4bea668f34678140f032
--- /dev/null
+++ b/runs/kallisto_sleuth/run.yml
@@ -0,0 +1,8 @@
+cores: 1
+r_script:
+ class: File
+ path: ../../workflows/kallisto_sleuth/kallisto_sleuth.R
+in_sleuth:
+ class: File
+ path: ../kallisto_collect/out/kallisto_sleuthObject.RData
+out_folder: out
diff --git a/runs/merged_isa_metadata/README.md b/runs/merged_isa_metadata/README.md
deleted file mode 100644
index 59c24ded29d2efa45432c30c827d84606161102c..0000000000000000000000000000000000000000
--- a/runs/merged_isa_metadata/README.md
+++ /dev/null
@@ -1,23 +0,0 @@
-
-# cwltool README
-
-## First cd into the (runs) folder, with the .yml file
-
-cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/merged_isa_metadata
-
-
-## Let it flow
-
-```bash
-
-### store arc root (two levels up from here) as variable
-arc_root=$(echo ${PWD%/*/*})
-
-### replace arc root line in yml (specific to the machine from where this is run)
-### not sure, if this works on linux...
-sed -i '' "s|^arc_root:.*|arc_root: $arc_root|g" merge_isa_metadata.yml
-
-### run with cwltool
-cwltool ../../workflows/merge_isa_metadata.cwl merge_isa_metadata.yml
-
-```
diff --git a/runs/merged_isa_metadata/merge_isa_metadata.yml b/runs/merged_isa_metadata/merge_isa_metadata.yml
deleted file mode 100644
index 0a52d038aaf9436fa63bd102e14eeb7066a4efb5..0000000000000000000000000000000000000000
--- a/runs/merged_isa_metadata/merge_isa_metadata.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-cores: 1
-r_script:
- class: File
- path: ../../workflows/merge_isa_metadata.R
-in_isa_study: studies/TalinumFacultativeCAM/isa.study.xlsx:plant_growth
-in_isa_assay: assays/Talinum_RNASeq_minimal/isa.assay.xlsx:2EXT01_RNA:3ASY01_RNASeq
-out_folder: runs/merged_isa_metadata
-arc_root: /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq
\ No newline at end of file
diff --git a/runs/merged_isa_metadata/merged_isa.tsv b/runs/merged_isa_metadata/out/merged_isa.tsv
similarity index 100%
rename from runs/merged_isa_metadata/merged_isa.tsv
rename to runs/merged_isa_metadata/out/merged_isa.tsv
diff --git a/workflows/kallisto_sleuth.cwl b/runs/merged_isa_metadata/run.cwl
similarity index 86%
rename from workflows/kallisto_sleuth.cwl
rename to runs/merged_isa_metadata/run.cwl
index 6f427261e5ec6da3dce2b916d2fcfc25659eff7a..859ac0b1c11de8981a582ea4bc1b12526c12c909 100644
--- a/workflows/kallisto_sleuth.cwl
+++ b/runs/merged_isa_metadata/run.cwl
@@ -1,26 +1,23 @@
#!/usr/bin/env cwl-runner
-
cwlVersion: v1.2
class: CommandLineTool
-
inputs:
- id: r_script
type: File
inputBinding:
position: 0
-- id: arc_root
- type: string
+- id: in_isa_study
+ type: File
inputBinding:
position: 1
-- id: in_sleuth
- type: string
+- id: in_isa_assay
+ type: File
inputBinding:
position: 2
- id: out_folder
type: string
inputBinding:
position: 3
-
outputs:
- id: outdir
type:
diff --git a/runs/merged_isa_metadata/run.yml b/runs/merged_isa_metadata/run.yml
new file mode 100644
index 0000000000000000000000000000000000000000..154dc89bd42c3a389aecb4a80ad8d3d868d167d4
--- /dev/null
+++ b/runs/merged_isa_metadata/run.yml
@@ -0,0 +1,11 @@
+cores: 1
+r_script:
+ class: File
+ path: ../../workflows/merge_isa_metadata/merge_isa_metadata.R
+in_isa_study:
+ class: File
+ path: ../../studies/TalinumFacultativeCAM/isa.study.xlsx
+in_isa_assay:
+ class: File
+ path: ../../assays/Talinum_RNASeq_minimal/isa.assay.xlsx
+out_folder: out
diff --git a/workflows/shiny_plots.Rmd b/runs/shiny_plots.Rmd
similarity index 96%
rename from workflows/shiny_plots.Rmd
rename to runs/shiny_plots.Rmd
index 8809a420c9cc539ff3b53988f40e09dc314f8715..3a1e99cf680cdd3c67d2d5d55397db7e39147d13 100644
--- a/workflows/shiny_plots.Rmd
+++ b/runs/shiny_plots.Rmd
@@ -11,9 +11,8 @@ knitr::opts_chunk$set(echo = TRUE)
```{r load_data, include=FALSE}
-# Load data
+load(file = "../runs/shiny_prep/out/shiny_prep.RData")
-load(file = "../runs/shiny_prep/shiny_prep.RData")
```
diff --git a/runs/shiny_prep/README.md b/runs/shiny_prep/README.md
deleted file mode 100644
index 05639e7e53b53e81a9f51f01627e43af130fec9c..0000000000000000000000000000000000000000
--- a/runs/shiny_prep/README.md
+++ /dev/null
@@ -1,21 +0,0 @@
-
-# cwltool README
-
-## First cd into the (runs) folder, with the .yml file
-
-cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_sleuth
-
-## Let it flow
-
-```bash
-### store arc root (two levels up from here) as variable
-arc_root=$(echo ${PWD%/*/*})
-
-### replace arc root line in yml (specific to the machine from where this is run)
-### not sure, if this works on linux...
-sed -i '' "s|^arc_root:.*|arc_root: $arc_root|g" kallisto_sleuth.yml
-
-### run with cwltool
-cwltool ../../workflows/kallisto_sleuth.cwl kallisto_sleuth.yml
-
-```
diff --git a/runs/shiny_prep/out/shiny_prep.RData b/runs/shiny_prep/out/shiny_prep.RData
new file mode 100644
index 0000000000000000000000000000000000000000..ae56a9cb309ac5e6b27e0c2a7c916035cbcc9dae
Binary files /dev/null and b/runs/shiny_prep/out/shiny_prep.RData differ
diff --git a/workflows/shiny_prep.cwl b/runs/shiny_prep/run.cwl
similarity index 82%
rename from workflows/shiny_prep.cwl
rename to runs/shiny_prep/run.cwl
index 918aaa0aefa401caed518703a64ac7fd6c333e3b..aa7ea15dbeb66f345b610edc8c2ba3b0043d7851 100644
--- a/workflows/shiny_prep.cwl
+++ b/runs/shiny_prep/run.cwl
@@ -8,18 +8,14 @@ inputs:
type: File
inputBinding:
position: 0
-- id: arc_root
- type: string
- inputBinding:
- position: 1
- id: out_folder
type: string
inputBinding:
- position: 2
+ position: 1
- id: in_kallisto_df
- type: string
+ type: File
inputBinding:
- position: 3
+ position: 2
outputs:
- id: outdir
@@ -30,4 +26,4 @@ outputs:
glob: $(runtime.outdir)/$(inputs.out_folder)
baseCommand:
-- Rscript
\ No newline at end of file
+- Rscript
diff --git a/runs/shiny_prep/run.yml b/runs/shiny_prep/run.yml
new file mode 100644
index 0000000000000000000000000000000000000000..7124f42d4bf3c475754e9f72ef0bddfd7c4d9dc7
--- /dev/null
+++ b/runs/shiny_prep/run.yml
@@ -0,0 +1,8 @@
+cores: 1
+r_script:
+ class: File
+ path: ../../workflows/shiny_prep/shiny_prep.R
+in_kallisto_df:
+ class: File
+ path: ../kallisto_collect/out/kallisto_df.csv
+out_folder: out
\ No newline at end of file
diff --git a/runs/shiny_prep/shiny_prep.RData b/runs/shiny_prep/shiny_prep.RData
deleted file mode 100644
index 258a091981fee5ee5389d9e76ca25e2a237768b8..0000000000000000000000000000000000000000
Binary files a/runs/shiny_prep/shiny_prep.RData and /dev/null differ
diff --git a/runs/shiny_prep/shiny_prep.yml b/runs/shiny_prep/shiny_prep.yml
deleted file mode 100644
index a8fec1d28132c8b86ab7e4264eae03acf7d79e2d..0000000000000000000000000000000000000000
--- a/runs/shiny_prep/shiny_prep.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-cores: 1
-r_script:
- class: File
- path: ../../workflows/shiny_prep.R
-in_kallisto_df: runs/kallisto_collect/kallisto_df.csv
-out_folder: runs/shiny_prep
-arc_root: /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq
diff --git a/workflows/install_dependencies/install_cwl.md b/workflows/install_dependencies/install_cwl.md
deleted file mode 100644
index d812962a3932a710221301d08205e47345bc95a2..0000000000000000000000000000000000000000
--- a/workflows/install_dependencies/install_cwl.md
+++ /dev/null
@@ -1,13 +0,0 @@
-
-# CWL Installation (MacOS)
-
-Docs: https://www.commonwl.org/
-GitHub: https://github.com/common-workflow-language/cwltool
-
-## Install CWL via conda
-
-> requires conda installation, which is a whole different story. Good luck.
-
-```bash
-conda install -c conda-forge cwltool
-```
diff --git a/workflows/install_dependencies/install_kallisto.md b/workflows/install_dependencies/install_kallisto.md
deleted file mode 100644
index 121b9f229d207352c3529e572286b3bd34b3f2f9..0000000000000000000000000000000000000000
--- a/workflows/install_dependencies/install_kallisto.md
+++ /dev/null
@@ -1,13 +0,0 @@
-
-# Kallisto Installation
-
-- Docs: http://pachterlab.github.io/kallisto/manual.html
-- GitHub: https://github.com/pachterlab/kallisto
-
-## MacOS Installation via conda
-
-see: https://anaconda.org/bioconda/kallisto
-
-```bash
-conda install -c bioconda kallisto
-```
diff --git a/workflows/install_dependencies/install_r_packages.R b/workflows/install_dependencies/install_r_packages.R
deleted file mode 100644
index fdb1eb1afb2ded3fb31d9f59a4487ce6a028163b..0000000000000000000000000000000000000000
--- a/workflows/install_dependencies/install_r_packages.R
+++ /dev/null
@@ -1,31 +0,0 @@
-#!/usr/bin/env Rscript
-
-################################################
-### Installation of R dependencies #############
-################################################
-
-### Default (CRAN)
-
-if(!"tidyverse" %in% row.names(installed.packages())){install.packages("tidyverse")}
-if(!"jsonlite" %in% row.names(installed.packages())){install.packages("jsonlite")}
-if(!"openxlsx" %in% row.names(installed.packages())){install.packages("openxlsx")}
-if(!"kableExtra" %in% row.names(installed.packages())){install.packages("kableExtra")}
-if(!"shiny" %in% row.names(installed.packages())){install.packages("shiny")}
-if(!"RColorBrewer" %in% row.names(installed.packages())){install.packages("RColorBrewer")}
-
-### From BiocManager
-
-if (!requireNamespace("BiocManager", quietly = TRUE)){install.packages("BiocManager")}
-if(!"BiocManager" %in% row.names(installed.packages())){BiocManager::install()}
-if(!"devtools" %in% row.names(installed.packages())){BiocManager::install("devtools")}
-if(!"sleuth" %in% row.names(installed.packages())){BiocManager::install("pachterlab/sleuth")}
-
-### Test load packages
-
-library(tidyverse)
-library(jsonlite)
-library(openxlsx)
-library(sleuth)
-library(kableExtra)
-library(shiny)
-library(RColorBrewer)
diff --git a/workflows/kallisto_collect.R b/workflows/kallisto_collect/kallisto_collect.R
similarity index 63%
rename from workflows/kallisto_collect.R
rename to workflows/kallisto_collect/kallisto_collect.R
index b52176342b317b3c38a0f1359c2d7ad171cd9fe1..6a24e7ee2b4cd5711ec8603ec9f19828a15565cb 100644
--- a/workflows/kallisto_collect.R
+++ b/workflows/kallisto_collect/kallisto_collect.R
@@ -1,16 +1,5 @@
#!/usr/bin/env Rscript
-################################################
-#### CWL-independent tests
-################################################
-
-# arc_root <- "~/gitlab_dataplant/samplearc_rnaseq/"
-# in_kallisto_results <- "runs/kallisto_quant/kallisto_results"
-# in_metadata_file <- "runs/merged_isa_metadata/merged_isa.tsv"
-# in_metadata_sample <- "Sample.Name.2"
-# in_metadata_factor <- "Factor..Photosynthesis.mode."
-# out_folder <- "runs/kallisto_collect"
-
################################################
#### Load required library
################################################
@@ -25,31 +14,30 @@ library(jsonlite)
args <- commandArgs(trailingOnly = T)
-arc_root <- args[1]
-in_kallisto_results <- args[2]
-in_metadata_file <- args[3]
-in_metadata_sample <- args[4]
-in_metadata_factor <- args[5]
-out_folder <- args[6]
+in_kallisto_results <- args[1]
+in_metadata_file <- args[2]
+in_metadata_sample <- args[3]
+in_metadata_factor <- args[4]
+out_folder <- args[5]
################################################
#### If it does not exist, create out dir
################################################
-dir.create(paste(arc_root, out_folder, sep = "/"), recursive = T, showWarnings = F)
+dir.create(out_folder, recursive = T, showWarnings = F)
################################################
#### Read ISA sample metadata
################################################
-samples <- read.table(file = paste(arc_root, in_metadata_file, sep = "/"), sep = "\t")
+samples <- read.table(file = in_metadata_file, sep = "\t")
################################################
#### Read Kallisto results
################################################
-base_dir <- paste(arc_root, in_kallisto_results, sep = "/")
+base_dir <- in_kallisto_results
# A list of paths to the kallisto results indexed by the sample IDs is collated with
kal_dirs <- dir(base_dir, full.names = T) ## Sleuth requires full paths
@@ -67,7 +55,7 @@ s2c <- merge(s2c, path_df, by = "out_name")
so <- sleuth_prep(s2c, full_model = ~condition, num_cores = 1)
-save(so, file = paste(arc_root, out_folder, "kallisto_sleuthObject.RData", sep = "/"))
+save(so, file = paste(out_folder, "kallisto_sleuthObject.RData", sep = "/"))
################################################
@@ -78,13 +66,13 @@ save(so, file = paste(arc_root, out_folder, "kallisto_sleuthObject.RData", sep =
expression_data <- kallisto_table(so)
## write to file
-write.csv(expression_data, paste(arc_root, out_folder, "/kallisto_df.csv", sep = "/"), row.names = F)
+write.csv(expression_data, paste(out_folder, "/kallisto_df.csv", sep = "/"), row.names = F)
## as tpm matrix (gene x sample)
tpm_table <- pivot_wider(expression_data, id_cols = target_id, names_from = sample, values_from = tpm)
## write to file
-write.csv(tpm_table, paste(arc_root, out_folder, "/kallisto_tpmMatrix.csv", sep = "/"), row.names = F)
+write.csv(tpm_table, paste(out_folder, "/kallisto_tpmMatrix.csv", sep = "/"), row.names = F)
################################################
#### Summarize mapping stats
@@ -99,4 +87,4 @@ for (i in dir(kal_dirs, pattern = ".json", full.names = T))
mapping_stats <- rbind(mapping_stats, z)
}
-write.csv(mapping_stats, paste(arc_root, out_folder, "/kallisto_mappingStats.csv", sep = "/"), row.names = F)
+write.csv(mapping_stats, paste(out_folder, "/kallisto_mappingStats.csv", sep = "/"), row.names = F)
diff --git a/workflows/kallisto_index.sh b/workflows/kallisto_index/kallisto_index.sh
old mode 100755
new mode 100644
similarity index 57%
rename from workflows/kallisto_index.sh
rename to workflows/kallisto_index/kallisto_index.sh
index 6cd3e178fa47e59af1e430a16e3def895dcefb37..c346206eca3c0d7ec2294deb2387573e8d7926f8
--- a/workflows/kallisto_index.sh
+++ b/workflows/kallisto_index/kallisto_index.sh
@@ -2,23 +2,12 @@
### Build kallisto index
-
-################################################
-#### CWL-independent tests
-################################################
-
-# in_genome_ref=studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa
-# out_folder=runs/kallisto_index
-# arc_root=/Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq
-
-
################################################
#### Read arguments from CLI
################################################
-arc_root=$1
-in_genome_ref=$2
-out_folder=$3
+in_genome_ref=$1
+out_folder=$2
################################################
#### Print version and citation to test kallisto
@@ -31,11 +20,10 @@ kallisto cite
#### If it does not exist, create out dir
################################################
-mkdir -p "$arc_root/$out_folder/"
-
+mkdir -p $out_folder
################################################
#### Build kallisto index
################################################
-kallisto index -i "$arc_root/$out_folder/kallisto_index" "$arc_root/$in_genome_ref"
+kallisto index -i $out_folder/kallisto_index $in_genome_ref
diff --git a/workflows/kallisto_quant.sh b/workflows/kallisto_quant.sh
deleted file mode 100755
index c1217416f77460b75944ccf50bb7cf9632a93ba8..0000000000000000000000000000000000000000
--- a/workflows/kallisto_quant.sh
+++ /dev/null
@@ -1,59 +0,0 @@
-#!/usr/bin/env bash
-
-### Map RNASeq reads via kallisto
-### Note, this is written for single-end mode only
-
-################################################
-#### CWL-independent tests
-################################################
-
-# arc_root=/Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq
-# out_folder=runs/kallisto_quant/kallisto_results_v48_anaconda
-# in_kallisto_index=runs/kallisto_index/kallisto_index
-# in_fastq_folder=assays/Talinum_RNASeq_minimal/dataset
-# kallisto_bootstrap=100
-# kallisto_threads=4
-# kallisto_fragmentLength=200
-# kallisto_stdDev=20
-
-################################################
-#### Read arguments from CLI
-################################################
-
-arc_root=$1
-out_folder=$2
-in_kallisto_index=$3
-in_fastq_folder=$4
-kallisto_bootstrap=$5
-kallisto_threads=$6
-kallisto_fragmentLength=$7
-kallisto_stdDev=$8
-
-################################################
-#### If it does not exist, create out dir
-################################################
-
-mkdir -p "$arc_root/$out_folder/"
-
-################################################
-#### Store fastq files in variable
-################################################
-
-fastq_files=$(ls "${arc_root}"/"${in_fastq_folder}"/*fastq*)
-
-################################################
-#### Loop over fastq files and quantify reads
-################################################
-
-for j in $fastq_files; do
-
- # cut away path. retain only first six chars of file name
- sampleName=$(echo $j | sed -e 's|.*/||' | sed -e 's|.fastq.*||')
-
- echo $sampleName
-
- kallisto quant --single -b $kallisto_bootstrap -t $kallisto_threads -l $kallisto_fragmentLength -s $kallisto_stdDev -i "$arc_root/$in_kallisto_index" -o "$arc_root/$out_folder/$sampleName" $j
-
- echo 'Kallisto done'
-
-done
diff --git a/workflows/kallisto_quant/kallisto_quant.sh b/workflows/kallisto_quant/kallisto_quant.sh
new file mode 100644
index 0000000000000000000000000000000000000000..63d0cb1af98ba421d835ceb9c6787e20be95d2d1
--- /dev/null
+++ b/workflows/kallisto_quant/kallisto_quant.sh
@@ -0,0 +1,44 @@
+#!/usr/bin/env bash
+
+### Map RNASeq reads via kallisto
+### Note, this is written for single-end mode only
+
+################################################
+#### Read arguments from CLI
+################################################
+
+out_folder=$1
+in_kallisto_index=$2
+in_fastq_folder=$3
+kallisto_bootstrap=$4
+kallisto_threads=$5
+kallisto_fragmentLength=$6
+kallisto_stdDev=$7
+
+################################################
+#### If it does not exist, create out dir
+################################################
+
+mkdir -p "$out_folder"
+
+################################################
+#### Store fastq files in variable
+################################################
+
+fastq_files=$(ls "${in_fastq_folder}"/*fastq*)
+
+################################################
+#### Loop over fastq files and quantify reads
+################################################
+
+for j in $fastq_files; do
+
+ sampleName=$(basename $j)
+
+ echo $sampleName
+
+ kallisto quant --single -b $kallisto_bootstrap -t $kallisto_threads -l $kallisto_fragmentLength -s $kallisto_stdDev -i "$in_kallisto_index" -o "$out_folder/$sampleName" $j
+
+ echo 'Kallisto done'
+
+done
diff --git a/workflows/kallisto_sleuth.R b/workflows/kallisto_sleuth/kallisto_sleuth.R
similarity index 59%
rename from workflows/kallisto_sleuth.R
rename to workflows/kallisto_sleuth/kallisto_sleuth.R
index ec3a84afe7aec0e9bab0b621c113e23e177a83bd..c4b599b5a0b99eae5b0026fd167ec6daaff93913 100644
--- a/workflows/kallisto_sleuth.R
+++ b/workflows/kallisto_sleuth/kallisto_sleuth.R
@@ -1,21 +1,10 @@
#!/usr/bin/env Rscript
-################################################
-### Diff. gene expression with sleuth ##########
-################################################
-
-################################################
-#### CWL-independent tests
-################################################
-
-# arc_root <- "~/gitlab_dataplant/samplearc_rnaseq/"
-# in_sleuth <- "runs/kallisto_collect/kallisto_sleuthObject.RData"
-# out_folder <- "runs/kallisto_sleuth"
+### Diff. gene expression with sleuth
################################################
#### Load required library
################################################
-
library(sleuth)
################################################
@@ -24,21 +13,20 @@ library(sleuth)
args <- commandArgs(trailingOnly = T)
-arc_root <- args[1]
-in_sleuth <- args[2]
-out_folder <- args[3]
+in_sleuth <- args[1]
+out_folder <- args[2]
################################################
#### If it does not exist, create out dir
################################################
-dir.create(paste(arc_root, out_folder, sep = "/"), recursive = T, showWarnings = F)
+dir.create(out_folder, recursive = T, showWarnings = F)
################################################
#### Load sleuth object
################################################
-load(file = paste(arc_root, in_sleuth, sep = "/"))
+load(file = in_sleuth)
################################################
#### Run sleuth fit
@@ -55,4 +43,4 @@ sleuth_table <- sleuth_results(so, "reduced:full", "lrt", show_all = FALSE)
#### write to file
################################################
-write.csv(sleuth_table, paste(arc_root, out_folder, "sleuth_dge.csv", sep = "/"), row.names = F)
+write.csv(sleuth_table, paste(out_folder, "sleuth_dge.csv", sep = "/"), row.names = F)
diff --git a/workflows/merge_isa_metadata.R b/workflows/merge_isa_metadata/merge_isa_metadata.R
similarity index 67%
rename from workflows/merge_isa_metadata.R
rename to workflows/merge_isa_metadata/merge_isa_metadata.R
index 5af105c569fe6b23a20b25e53e82ef80eb76b787..b4daca150962998854d9a3aaaf7d3f695a98b524 100644
--- a/workflows/merge_isa_metadata.R
+++ b/workflows/merge_isa_metadata/merge_isa_metadata.R
@@ -1,14 +1,5 @@
#!/usr/bin/env Rscript
-################################################
-#### CWL-independent tests
-################################################
-
-# arc_root <- "~/gitlab_dataplant/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"
-# out_folder <- "runs/merged_isa_metadata"
-
################################################
#### Load required library
################################################
@@ -21,17 +12,18 @@ library(openxlsx)
args <- commandArgs(trailingOnly = T)
-arc_root <- args[1]
-in_isa_study <- args[2]
-in_isa_assay <- args[3]
-out_folder <- args[4]
+in_isa_study <- paste(args[1], ":plant_growth", sep="")
+print(in_isa_study)
+in_isa_assay <- paste(args[2], ":2EXT01_RNA:3ASY01_RNASeq", sep="")
+print(in_isa_assay)
+out_folder <- args[3]
################################################
#### Read metadata from isa excel workbooks
################################################
-isa_study <- unlist(strsplit(paste(arc_root, in_isa_study, sep = "/"), split = ":"))
-isa_assay <- unlist(strsplit(paste(arc_root, in_isa_assay, sep = "/"), split = ":"))
+isa_study <- unlist(strsplit(in_isa_study, split = ":"))
+isa_assay <- unlist(strsplit(in_isa_assay, split = ":"))
isa_sheets <- list()
for (i in 2:length(isa_study))
@@ -76,12 +68,10 @@ isa_merged <- isa_merged[, !apply(isa_merged, 2, function(x) {
#### If it does not exist, create out dir
################################################
-
-dir.create(paste(arc_root, out_folder, sep = "/"), recursive = T, showWarnings = F)
-
+dir.create(out_folder, recursive = T, showWarnings = F)
################################################
#### Write table to file
################################################
-write.table(isa_merged, file = paste(arc_root, out_folder, "merged_isa.tsv", sep = "/"), sep = "\t")
+write.table(isa_merged, file = paste(out_folder, "merged_isa.tsv", sep = "/"), sep = "\t")
diff --git a/workflows/rnaseq_pipeline.drawio.svg b/workflows/rnaseq_pipeline.drawio.svg
deleted file mode 100644
index b9d487ccf97e05fda12d053e0324f68f6e7fd659..0000000000000000000000000000000000000000
--- a/workflows/rnaseq_pipeline.drawio.svg
+++ /dev/null
@@ -1,127 +0,0 @@
-<svg host="65bd71144e" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" version="1.1" width="602px" height="262px" viewBox="-0.5 -0.5 602 262" content="<mxfile><diagram id="xGNej_qxJKJTo4vCftfG" name="Page-1">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</diagram></mxfile>">
- <defs/>
- <g>
- <path d="M 380 60 L 380 93.63" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="stroke"/>
- <path d="M 380 98.88 L 376.5 91.88 L 380 93.63 L 383.5 91.88 Z" fill="rgb(0, 0, 0)" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="all"/>
- <rect x="320" y="0" width="120" height="60" rx="9" ry="9" fill="rgb(255, 255, 255)" stroke="rgb(0, 0, 0)" pointer-events="all"/>
- <g transform="translate(-0.5 -0.5)">
- <switch>
- <foreignObject pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility" style="overflow: visible; text-align: left;">
- <div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 30px; margin-left: 321px;">
- <div data-drawio-colors="color: rgb(0, 0, 0); " style="box-sizing: border-box; font-size: 0px; text-align: center;">
- <div style="display: inline-block; font-size: 12px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;">
- merge_isa_metadata
- </div>
- </div>
- </div>
- </foreignObject>
- <text x="380" y="34" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="12px" text-anchor="middle">
- merge_isa_metadata
- </text>
- </switch>
- </g>
- <path d="M 120 130 L 153.63 130" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="stroke"/>
- <path d="M 158.88 130 L 151.88 133.5 L 153.63 130 L 151.88 126.5 Z" fill="rgb(0, 0, 0)" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="all"/>
- <rect x="0" y="100" width="120" height="60" rx="9" ry="9" fill="rgb(255, 255, 255)" stroke="rgb(0, 0, 0)" pointer-events="all"/>
- <g transform="translate(-0.5 -0.5)">
- <switch>
- <foreignObject pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility" style="overflow: visible; text-align: left;">
- <div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 130px; margin-left: 1px;">
- <div data-drawio-colors="color: rgb(0, 0, 0); " style="box-sizing: border-box; font-size: 0px; text-align: center;">
- <div style="display: inline-block; font-size: 12px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;">
- kallisto_index
- </div>
- </div>
- </div>
- </foreignObject>
- <text x="60" y="134" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="12px" text-anchor="middle">
- kallisto_index
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- </g>
- <path d="M 280 130 L 313.63 130" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="stroke"/>
- <path d="M 318.88 130 L 311.88 133.5 L 313.63 130 L 311.88 126.5 Z" fill="rgb(0, 0, 0)" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="all"/>
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- <switch>
- <foreignObject pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility" style="overflow: visible; text-align: left;">
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- kallisto_quant
- </div>
- </div>
- </div>
- </foreignObject>
- <text x="220" y="134" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="12px" text-anchor="middle">
- kallisto_quant
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- </g>
- <path d="M 380 160 L 380 193.63" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="stroke"/>
- <path d="M 380 198.88 L 376.5 191.88 L 380 193.63 L 383.5 191.88 Z" fill="rgb(0, 0, 0)" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="all"/>
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- kallisto_collect
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\ No newline at end of file
diff --git a/workflows/shiny_prep.R b/workflows/shiny_prep.R
deleted file mode 100644
index a44796250a409d286eb330862a7cdb6c4b473036..0000000000000000000000000000000000000000
--- a/workflows/shiny_prep.R
+++ /dev/null
@@ -1,41 +0,0 @@
-#!/usr/bin/env Rscript
-
-################################################
-#### CWL-independent tests
-################################################
-
-# arc_root <- "~/gitlab_dataplant/samplearc_rnaseq/"
-# out_folder <- "runs/shiny_prep"
-# in_kallisto_df <- "runs/kallisto_collect/kallisto_df.csv"
-
-################################################
-#### Load required library
-################################################
-
-
-
-################################################
-#### Read arguments from CLI
-################################################
-
-args <- commandArgs(trailingOnly = T)
-
-arc_root <- args[1]
-out_folder <- args[2]
-in_kallisto_df <- args[3]
-
-################################################
-#### If it does not exist, create out dir
-################################################
-
-dir.create(paste(arc_root, out_folder, sep = "/"), recursive = T, showWarnings = F)
-
-################################################
-#### Prep data for shiny app
-################################################
-
-expression_data <- read.csv(file = paste(arc_root, in_kallisto_df, sep = "/"))
-
-available_genes <- unique(expression_data$target_id)
-
-save(expression_data, available_genes, file = paste(arc_root, out_folder, 'shiny_prep.RData', sep = "/"))
diff --git a/workflows/shiny_prep/shiny_prep.R b/workflows/shiny_prep/shiny_prep.R
new file mode 100644
index 0000000000000000000000000000000000000000..804ad85db72c912c214f19b868e6073316524bab
--- /dev/null
+++ b/workflows/shiny_prep/shiny_prep.R
@@ -0,0 +1,26 @@
+#!/usr/bin/env Rscript
+
+################################################
+#### Read arguments from CLI
+################################################
+
+args <- commandArgs(trailingOnly = T)
+
+out_folder <- args[1]
+in_kallisto_df <- args[2]
+
+################################################
+#### If it does not exist, create out dir
+################################################
+
+dir.create(out_folder, recursive = T, showWarnings = F)
+
+################################################
+#### Prep data for shiny app
+################################################
+
+expression_data <- read.csv(file = in_kallisto_df)
+
+available_genes <- unique(expression_data$target_id)
+
+save(expression_data, available_genes, file = paste(out_folder, 'shiny_prep.RData', sep = "/"))