From a75819671005a95e8b48a656144637d0bdcf5414 Mon Sep 17 00:00:00 2001
From: Adrian Zimmer <z.adrian1995@gmail.com>
Date: Fri, 12 Aug 2022 15:42:14 +0200
Subject: [PATCH] Upeate structure, dockerize kallisto_index
---
.gitattributes | 2 +-
runs/kallisto_index/README.md | 10 +------
runs/kallisto_index/kallisto_index.yml | 8 +++---
runs/kallisto_index/{ => out}/kallisto_index | 0
runs/kallisto_index/run.cwl | 21 +++++++++++++++
.../{ => kallisto_collect}/kallisto_collect.R | 0
.../workflow.cwl} | 0
.../{ => kallisto_index}/kallisto_index.sh | 10 +++----
.../workflow.cwl} | 26 ++++++++++---------
.../{ => kallisto_quant}/kallisto_quant.sh | 0
.../workflow.cwl} | 0
.../{ => kallisto_sleuth}/kallisto_sleuth.R | 0
.../workflow.cwl} | 0
.../merge_isa_metadata.R | 0
.../workflow.cwl} | 0
workflows/{ => shiny_prep}/shiny_plots.Rmd | 0
workflows/{ => shiny_prep}/shiny_prep.R | 0
.../workflow.cwl} | 0
18 files changed, 44 insertions(+), 33 deletions(-)
rename runs/kallisto_index/{ => out}/kallisto_index (100%)
create mode 100644 runs/kallisto_index/run.cwl
rename workflows/{ => kallisto_collect}/kallisto_collect.R (100%)
rename workflows/{kallisto_collect.cwl => kallisto_collect/workflow.cwl} (100%)
rename workflows/{ => kallisto_index}/kallisto_index.sh (85%)
mode change 100755 => 100644
rename workflows/{kallisto_index.cwl => kallisto_index/workflow.cwl} (55%)
rename workflows/{ => kallisto_quant}/kallisto_quant.sh (100%)
mode change 100755 => 100644
rename workflows/{kallisto_quant.cwl => kallisto_quant/workflow.cwl} (100%)
rename workflows/{ => kallisto_sleuth}/kallisto_sleuth.R (100%)
rename workflows/{kallisto_sleuth.cwl => kallisto_sleuth/workflow.cwl} (100%)
rename workflows/{ => merge_isa_metadata}/merge_isa_metadata.R (100%)
rename workflows/{merge_isa_metadata.cwl => merge_isa_metadata/workflow.cwl} (100%)
rename workflows/{ => shiny_prep}/shiny_plots.Rmd (100%)
rename workflows/{ => shiny_prep}/shiny_prep.R (100%)
rename workflows/{shiny_prep.cwl => shiny_prep/workflow.cwl} (100%)
diff --git a/.gitattributes b/.gitattributes
index 9992776..7c3cf77 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_index/README.md b/runs/kallisto_index/README.md
index 16475f8..577a1e4 100644
--- a/runs/kallisto_index/README.md
+++ b/runs/kallisto_index/README.md
@@ -8,14 +8,6 @@ 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
-
+cwltool --enable-dev run.cwl kallisto_index.yml
```
diff --git a/runs/kallisto_index/kallisto_index.yml b/runs/kallisto_index/kallisto_index.yml
index 60f3a27..37c6681 100644
--- a/runs/kallisto_index/kallisto_index.yml
+++ b/runs/kallisto_index/kallisto_index.yml
@@ -1,7 +1,5 @@
cores: 1
-sh_script:
+in_genome_ref:
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
+ path: ../../studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa
+out_folder: ./out
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/runs/kallisto_index/run.cwl b/runs/kallisto_index/run.cwl
new file mode 100644
index 0000000..efca83d
--- /dev/null
+++ b/runs/kallisto_index/run.cwl
@@ -0,0 +1,21 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2.0-dev1
+class: Workflow
+inputs:
+ in_genome_ref:
+ type: File
+ out_folder:
+ type: string
+outputs:
+ out_dir:
+ type:
+ type: array
+ items: Directory
+ outputSource: kallisto_index/outdir
+steps:
+ kallisto_index:
+ run: ../../workflows/kallisto_index/workflow.cwl
+ in:
+ in_genome_ref: in_genome_ref
+ out_folder: out_folder
+ out: [outdir]
\ No newline at end of file
diff --git a/workflows/kallisto_collect.R b/workflows/kallisto_collect/kallisto_collect.R
similarity index 100%
rename from workflows/kallisto_collect.R
rename to workflows/kallisto_collect/kallisto_collect.R
diff --git a/workflows/kallisto_collect.cwl b/workflows/kallisto_collect/workflow.cwl
similarity index 100%
rename from workflows/kallisto_collect.cwl
rename to workflows/kallisto_collect/workflow.cwl
diff --git a/workflows/kallisto_index.sh b/workflows/kallisto_index/kallisto_index.sh
old mode 100755
new mode 100644
similarity index 85%
rename from workflows/kallisto_index.sh
rename to workflows/kallisto_index/kallisto_index.sh
index 6cd3e17..c7cb12d
--- a/workflows/kallisto_index.sh
+++ b/workflows/kallisto_index/kallisto_index.sh
@@ -16,9 +16,8 @@
#### Read arguments from CLI
################################################
-arc_root=$1
-in_genome_ref=$2
-out_folder=$3
+in_genome_ref=$1
+out_folder=$2
################################################
#### Print version and citation to test kallisto
@@ -31,11 +30,10 @@ kallisto cite
#### If it does not exist, create out dir
################################################
-mkdir -p "$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_index.cwl b/workflows/kallisto_index/workflow.cwl
similarity index 55%
rename from workflows/kallisto_index.cwl
rename to workflows/kallisto_index/workflow.cwl
index a6389de..a91a17c 100644
--- a/workflows/kallisto_index.cwl
+++ b/workflows/kallisto_index/workflow.cwl
@@ -1,25 +1,27 @@
#!/usr/bin/env cwl-runner
-cwlVersion: v1.2
+cwlVersion: v1.2.0-dev1
class: CommandLineTool
-
+hints:
+ DockerRequirement:
+ dockerPull: zlskidmore/kallisto:0.48.0
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - class: File
+ location: kallisto_index.sh
+arguments:
+ - position: 0
+ valueFrom: ./kallisto_index.sh
inputs:
-- id: sh_script
+- id: in_genome_ref
type: File
- inputBinding:
- position: 0
-- id: arc_root
- type: string
inputBinding:
position: 1
-- id: in_genome_ref
- type: string
- inputBinding:
- position: 2
- id: out_folder
type: string
inputBinding:
- position: 3
+ position: 2
outputs:
- id: outdir
diff --git a/workflows/kallisto_quant.sh b/workflows/kallisto_quant/kallisto_quant.sh
old mode 100755
new mode 100644
similarity index 100%
rename from workflows/kallisto_quant.sh
rename to workflows/kallisto_quant/kallisto_quant.sh
diff --git a/workflows/kallisto_quant.cwl b/workflows/kallisto_quant/workflow.cwl
similarity index 100%
rename from workflows/kallisto_quant.cwl
rename to workflows/kallisto_quant/workflow.cwl
diff --git a/workflows/kallisto_sleuth.R b/workflows/kallisto_sleuth/kallisto_sleuth.R
similarity index 100%
rename from workflows/kallisto_sleuth.R
rename to workflows/kallisto_sleuth/kallisto_sleuth.R
diff --git a/workflows/kallisto_sleuth.cwl b/workflows/kallisto_sleuth/workflow.cwl
similarity index 100%
rename from workflows/kallisto_sleuth.cwl
rename to workflows/kallisto_sleuth/workflow.cwl
diff --git a/workflows/merge_isa_metadata.R b/workflows/merge_isa_metadata/merge_isa_metadata.R
similarity index 100%
rename from workflows/merge_isa_metadata.R
rename to workflows/merge_isa_metadata/merge_isa_metadata.R
diff --git a/workflows/merge_isa_metadata.cwl b/workflows/merge_isa_metadata/workflow.cwl
similarity index 100%
rename from workflows/merge_isa_metadata.cwl
rename to workflows/merge_isa_metadata/workflow.cwl
diff --git a/workflows/shiny_plots.Rmd b/workflows/shiny_prep/shiny_plots.Rmd
similarity index 100%
rename from workflows/shiny_plots.Rmd
rename to workflows/shiny_prep/shiny_plots.Rmd
diff --git a/workflows/shiny_prep.R b/workflows/shiny_prep/shiny_prep.R
similarity index 100%
rename from workflows/shiny_prep.R
rename to workflows/shiny_prep/shiny_prep.R
diff --git a/workflows/shiny_prep.cwl b/workflows/shiny_prep/workflow.cwl
similarity index 100%
rename from workflows/shiny_prep.cwl
rename to workflows/shiny_prep/workflow.cwl
--
GitLab