From 9214eb5eab1a3af1a5f52dcc6060ac9b4059a823 Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Fri, 2 Aug 2024 11:25:05 +0200
Subject: [PATCH] first steps re-design cwl based analysis
---
.gitattributes | 139 +++++++++---------
runs/kallisto/README.md | 8 +
runs/kallisto/run.yml | 21 ---
runs/kallisto/single-steps/README.md | 16 ++
runs/kallisto/single-steps/index.yml | 8 +
runs/kallisto/single-steps/quant.yml | 15 ++
runs/kallisto/workflow.yml | 15 ++
studies/TalinumGenomeDraft/resources/.gitkeep | 0
.../resources/Talinum.gm.CDS.nt.fa | 3 +
workflows/kallisto/kallisto-help.cwl | 18 +++
workflows/kallisto/kallisto-index.cwl | 16 +-
workflows/kallisto/kallisto-quant.cwl | 2 +-
workflows/kallisto/kallisto-workflow.cwl | 22 +--
13 files changed, 161 insertions(+), 122 deletions(-)
create mode 100644 runs/kallisto/README.md
delete mode 100644 runs/kallisto/run.yml
create mode 100644 runs/kallisto/single-steps/README.md
create mode 100644 runs/kallisto/single-steps/index.yml
create mode 100644 runs/kallisto/single-steps/quant.yml
create mode 100644 runs/kallisto/workflow.yml
delete mode 100644 studies/TalinumGenomeDraft/resources/.gitkeep
create mode 100755 studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa
create mode 100644 workflows/kallisto/kallisto-help.cwl
diff --git a/.gitattributes b/.gitattributes
index 3e11c7a..9be800a 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -1,84 +1,79 @@
**/dataset/** 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_163_reC3MD_GTGAAA_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_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
-/runs/kallisto_index/out/kallisto_index filter=lfs diff=lfs merge=lfs -text
-/assays/GCqTOF_targets/dataset/150112_55.D/AcqData/TDASpec.bin filter=lfs diff=lfs merge=lfs -text
+/assays/GCqTOF_targets/dataset/150112_03.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
+/assays/GCqTOF_targets/dataset/150112_15.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150112_55.D/AcqData/MSPeak.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150112_55.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
-/assays/GCqTOF_targets/dataset/150112_15.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
-/assays/GCqTOF_targets/dataset/150115_12.D/AcqData/TDA.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
-/assays/GCqTOF_targets/dataset/150115_11.D/AcqData/TDASpec.bin filter=lfs diff=lfs merge=lfs -text
+/assays/GCqTOF_targets/dataset/150112_55.D/AcqData/TDASpec.bin filter=lfs diff=lfs merge=lfs -text
+/assays/GCqTOF_targets/dataset/150112_61.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
+/assays/GCqTOF_targets/dataset/150112_65.D/AcqData/MSPeak.bin filter=lfs diff=lfs merge=lfs -text
+/assays/GCqTOF_targets/dataset/150112_65.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
+/assays/GCqTOF_targets/dataset/150112_65.D/AcqData/TDASpec.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150115_11.D/AcqData/MSPeak.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150115_11.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
-/assays/GCqTOF_targets/dataset/150115_15.D/AcqData/TDASpec.bin filter=lfs diff=lfs merge=lfs -text
-/assays/GCqTOF_targets/dataset/150115_15.D/AcqData/MSPeak.bin filter=lfs diff=lfs merge=lfs -text
-/assays/GCqTOF_targets/dataset/150115_15.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
-/assays/GCqTOF_targets/dataset/150115_14.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
-/assays/GCqTOF_targets/dataset/150112_03.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
-/assays/GCqTOF_targets/dataset/150115_13.D/AcqData/TDASpec.bin filter=lfs diff=lfs merge=lfs -text
+/assays/GCqTOF_targets/dataset/150115_11.D/AcqData/TDASpec.bin filter=lfs diff=lfs merge=lfs -text
+/assays/GCqTOF_targets/dataset/150115_12.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150115_13.D/AcqData/MSPeak.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150115_13.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
-/assays/GCqTOF_targets/dataset/150112_65.D/AcqData/TDASpec.bin filter=lfs diff=lfs merge=lfs -text
-/assays/GCqTOF_targets/dataset/150112_65.D/AcqData/MSPeak.bin filter=lfs diff=lfs merge=lfs -text
-/assays/GCqTOF_targets/dataset/150112_65.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
-/assays/GCqTOF_targets/dataset/150112_61.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
-studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa filter=lfs diff=lfs merge=lfs -text
-runs/run1/01_kallisto_results/DB_103/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_quant/kallisto_results_v48_anaconda/DB_163_reC3MD_GTGAAA_L001_R1_001/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/no_CWL_yet/kallisto_sleuth/run1/03_kallisto_sleuthObject.RData filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_sleuth/run1/01_kallisto_results/DB_099/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_quant/kallisto_results_v48_anaconda/DB_099_CAMMD_CTTGTA_L001_R1_001/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_103/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_sleuth/run1/01_kallisto_index filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_quant/kallisto_results/DB_097/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_sleuth/run1/03_kallisto_df.csv filter=lfs diff=lfs merge=lfs -text
-runs/no_CWL_yet/kallisto_sleuth/run2/03_kallisto_sleuthObject.RData filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_quant/kallisto_results/DB_163/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_sleuth/sleuth_dge.csv filter=lfs diff=lfs merge=lfs -text
+/assays/GCqTOF_targets/dataset/150115_13.D/AcqData/TDASpec.bin filter=lfs diff=lfs merge=lfs -text
+/assays/GCqTOF_targets/dataset/150115_14.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
+/assays/GCqTOF_targets/dataset/150115_15.D/AcqData/MSPeak.bin filter=lfs diff=lfs merge=lfs -text
+/assays/GCqTOF_targets/dataset/150115_15.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
+/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
+/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
runs/kallisto_collect/kallisto_df.csv filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_quant/kallisto_results_v48_anaconda/DB_165_re-C3MD_GTGAAA_L002_R1_001/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_163/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/run1/01_kallisto_results/DB_097/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_161/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_quant/kallisto_results/DB_161_reC3MD_GTCCGC_L001_R1_001/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/run1/01_kallisto_results/DB_161/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_quant/kallisto_results/DB_161/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_sleuth/run1/01_kallisto_results/DB_103/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/run1/01_kallisto_index filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_sleuth/run1/01_kallisto_results/DB_163/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/no_CWL_yet/kallisto_sleuth/run2/03_kallisto_df.csv filter=lfs diff=lfs merge=lfs -text
-runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_165/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_097/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/no_CWL_yet/kallisto_sleuth/run1/03_kallisto_df.csv filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_sleuth/run1/01_kallisto_results/DB_161/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_quant/kallisto_results/DB_099_CAMMD_CTTGTA_L001_R1_001/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_quant/kallisto_results_v48_anaconda/DB_103_CAMMD_AGTCAA_L001_R1_001/abundance.h5 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/run1/01_kallisto_results/DB_165/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_quant/kallisto_results/DB_099/abundance.h5 filter=lfs diff=lfs merge=lfs -text
+
+
runs/kallisto_collect/out/kallisto_sleuthObject.RData filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_quant/kallisto_results/DB_103/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_quant/kallisto_results/DB_165/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_099/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_quant/kallisto_results_v48_anaconda/DB_097_CAMMD_CAGATC_L001_R1_001/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_sleuth/run1/01_kallisto_results/DB_097/abundance.h5 filter=lfs diff=lfs merge=lfs -text
+
+
+
+
+
runs/kallisto_sleuth/run2/03_kallisto_df.csv filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_quant/kallisto_results/DB_165_re-C3MD_GTGAAA_L002_R1_001/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-externals/Talinum.gm.CDS.nt.fa filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_sleuth/run1/03_kallisto_sleuthObject.RData filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_sleuth/run1/01_kallisto_results/DB_165/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_quant/kallisto_results/DB_103_CAMMD_AGTCAA_L001_R1_001/abundance.h5 filter=lfs diff=lfs merge=lfs -text
+
+
+
+
runs/kallisto_sleuth/run2/03_kallisto_sleuthObject.RData filter=lfs diff=lfs merge=lfs -text
-runs/run1/01_kallisto_results/DB_099/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_quant/kallisto_results/DB_097_CAMMD_CAGATC_L001_R1_001/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/run1/03_kallisto_df.csv filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_quant/kallisto_results/DB_163_reC3MD_GTGAAA_L001_R1_001/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/run1/03_kallisto_sleuthObject.RData filter=lfs diff=lfs merge=lfs -text
-runs/run1/01_kallisto_results/DB_163/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_quant/kallisto_results_v48_anaconda/DB_161_reC3MD_GTCCGC_L001_R1_001/abundance.h5 filter=lfs diff=lfs merge=lfs -text
-runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_index filter=lfs diff=lfs merge=lfs -text
+
+
+
+
+
+
+
+
diff --git a/runs/kallisto/README.md b/runs/kallisto/README.md
new file mode 100644
index 0000000..f3a9d64
--- /dev/null
+++ b/runs/kallisto/README.md
@@ -0,0 +1,8 @@
+# Kallisto Workflow
+
+## Executing individual steps
+
+```bash
+cd runs/kallisto/
+cwltool ../../workflows/kallisto/kallisto-index.cwl index.yml
+```
\ No newline at end of file
diff --git a/runs/kallisto/run.yml b/runs/kallisto/run.yml
deleted file mode 100644
index 269c202..0000000
--- a/runs/kallisto/run.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-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
-
-
-
-in_genome_ref:
- class: File
- path: ../../studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa
\ No newline at end of file
diff --git a/runs/kallisto/single-steps/README.md b/runs/kallisto/single-steps/README.md
new file mode 100644
index 0000000..847851e
--- /dev/null
+++ b/runs/kallisto/single-steps/README.md
@@ -0,0 +1,16 @@
+# Kallisto
+
+## Executing individual steps
+
+### Create genome index
+
+```bash
+cwltool ../../../workflows/kallisto/kallisto-index.cwl index.yml
+
+```
+
+### Quantification of a single sample
+
+```bash
+cwltool ../../../workflows/kallisto/kallisto-quant.cwl quant.yml
+```
diff --git a/runs/kallisto/single-steps/index.yml b/runs/kallisto/single-steps/index.yml
new file mode 100644
index 0000000..70501a1
--- /dev/null
+++ b/runs/kallisto/single-steps/index.yml
@@ -0,0 +1,8 @@
+InputFiles:
+ - class: File
+ path: ../../../studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa
+ format: edam:format_1929 # FASTA
+IndexName: "Talinum.gm.CDS"
+
+$namespaces:
+ edam: https://edamontology.org/
\ No newline at end of file
diff --git a/runs/kallisto/single-steps/quant.yml b/runs/kallisto/single-steps/quant.yml
new file mode 100644
index 0000000..bd6cb6a
--- /dev/null
+++ b/runs/kallisto/single-steps/quant.yml
@@ -0,0 +1,15 @@
+InputReads:
+ - class: File
+ path: ../../../assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
+ format: edam:format_1930 # FASTA
+QuantOutfolder: DB_097
+Index:
+ class: File
+ path: ./Talinum.gm.CDS.kallistoIndex
+isSingle: true
+FragmentLength: 200
+StandardDeviation: 20
+BootstrapSamples: 30
+
+$namespaces:
+ edam: https://edamontology.org/
\ No newline at end of file
diff --git a/runs/kallisto/workflow.yml b/runs/kallisto/workflow.yml
new file mode 100644
index 0000000..b21cbe8
--- /dev/null
+++ b/runs/kallisto/workflow.yml
@@ -0,0 +1,15 @@
+InputReads:
+ - class: File
+ path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
+ format: edam:format_1930 # FASTQ
+InputFiles:
+ - class: File
+ path: ../../../studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa
+ format: edam:format_1929 # FASTA
+isSingle: true
+FragmentLength: 200
+StandardDeviation: 20
+BootstrapSamples: 30
+
+$namespaces:
+ edam: https://edamontology.org/
\ No newline at end of file
diff --git a/studies/TalinumGenomeDraft/resources/.gitkeep b/studies/TalinumGenomeDraft/resources/.gitkeep
deleted file mode 100644
index e69de29..0000000
diff --git a/studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa b/studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa
new file mode 100755
index 0000000..e91fe86
--- /dev/null
+++ b/studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:29dca7b3f0807548db82f227157cdea39427e700b348e9fb2266ee985a71e609
+size 38610478
diff --git a/workflows/kallisto/kallisto-help.cwl b/workflows/kallisto/kallisto-help.cwl
new file mode 100644
index 0000000..c0dc2d2
--- /dev/null
+++ b/workflows/kallisto/kallisto-help.cwl
@@ -0,0 +1,18 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+class: CommandLineTool
+
+hints:
+ DockerRequirement:
+ dockerPull: quay.io/biocontainers/kallisto:0.46.2--h4f7b962_1
+ SoftwareRequirement:
+ packages:
+ kallisto:
+ version: [ "0.46.0" ]
+ specs: [ https://identifiers.org/biotools/kallisto ]
+
+inputs: []
+
+baseCommand: [kallisto, index]
+
+outputs: []
\ No newline at end of file
diff --git a/workflows/kallisto/kallisto-index.cwl b/workflows/kallisto/kallisto-index.cwl
index 4e5b609..8813559 100644
--- a/workflows/kallisto/kallisto-index.cwl
+++ b/workflows/kallisto/kallisto-index.cwl
@@ -13,11 +13,6 @@ hints:
requirements:
- class: InlineJavascriptRequirement
- - class: InitialWorkDirRequirement
- listing:
- - entry: "$({class: 'Directory', listing: []})"
- entryname: $(inputs.IndexOutfolder)
- writable: true
inputs:
InputFiles:
@@ -25,15 +20,13 @@ inputs:
format: edam:format_1929 # FASTA
inputBinding:
position: 200
-
- IndexOutfolder:
- type: string
IndexName:
type: string
inputBinding:
prefix: "--index="
separate: false
+ valueFrom: $(self).kallistoIndex
#Optional arguments
@@ -51,13 +44,12 @@ inputs:
baseCommand: [kallisto, index]
outputs:
-
index:
- type: Directory
+ type: File
outputBinding:
- glob: $(runtime.outdir)/$(inputs.IndexOutfolder)
+ glob: $(inputs.IndexName).kallistoIndex
$namespaces:
- edam: http://edamontology.org/
+ edam: https://edamontology.org/
$schemas:
- https://edamontology.org/EDAM_1.18.owl
diff --git a/workflows/kallisto/kallisto-quant.cwl b/workflows/kallisto/kallisto-quant.cwl
index a5c3b3e..8267499 100755
--- a/workflows/kallisto/kallisto-quant.cwl
+++ b/workflows/kallisto/kallisto-quant.cwl
@@ -14,7 +14,7 @@ hints:
inputs:
InputReads:
type: File[]
- format: edam:format_1930 # FASTA
+ format: edam:format_1930 # FASTQ
inputBinding:
position: 200
diff --git a/workflows/kallisto/kallisto-workflow.cwl b/workflows/kallisto/kallisto-workflow.cwl
index 5f65dfc..08047cd 100644
--- a/workflows/kallisto/kallisto-workflow.cwl
+++ b/workflows/kallisto/kallisto-workflow.cwl
@@ -5,9 +5,7 @@ requirements:
ScatterFeatureRequirement: {}
inputs:
- parentDir: Directory
- dirNamePattern: string
- collectedOut: string
+ InputReads: []
Index: File
isSingle: boolean
FragmentLength: double?
@@ -17,28 +15,20 @@ inputs:
steps:
quant:
run: kallisto-quant.cwl
- scatter:
- - InputReads
- - QuantOutfolder
- scatterMethod: dotproduct
+ scatter: InputReads
in:
InputReads: listFiles/inDirFiles
- QuantOutfolder: listFiles/inDirBasename
+ QuantOutfolder:
+ source: InputReads
+ valueFrom: $(self.nameroot)
Index: Index
isSingle: isSingle
FragmentLength: FragmentLength
StandardDeviation: StandardDeviation
BootstrapSamples: BootstrapSamples
out: [outFolder]
- collect:
- run: ../_aux-tools/yield-dirInDestination.cwl
- scatter: inDir
- in:
- inDir: quant/outFolder
- destinationDir: collectedOut
- out: [outDir]
outputs:
finalOut:
type: Directory[]
- outputSource: collect/outDir
+ outputSource: quant/outFolder
--
GitLab