diff --git a/.gitattributes b/.gitattributes
index 07a4a56143d25a23ce6ab0320d147c3096caa5f6..574339b69b82d0008d4b3ffd2e7398ad5d82ed6d 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -32,4 +32,16 @@ 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/sleuth/kallisto_sleuthObject.RData filter=lfs diff=lfs merge=lfs -text
runs/sleuth/out/kallisto_sleuthObject.RData filter=lfs diff=lfs merge=lfs -text
-runs/kallisto/kallisto_results/** filter=lfs diff=lfs merge=lfs -text
\ No newline at end of file
+runs/kallisto/kallisto_results/** filter=lfs diff=lfs merge=lfs -text
+runs/fastqc/results/DB_097_CAMMD_CAGATC_L001_R1_001_fastqc.zip filter=lfs diff=lfs merge=lfs -text
+runs/fastqc/results/DB_163_reC3MD_GTGAAA_L001_R1_001_fastqc.html filter=lfs diff=lfs merge=lfs -text
+runs/fastqc/results/DB_097_CAMMD_CAGATC_L001_R1_001_fastqc.html filter=lfs diff=lfs merge=lfs -text
+runs/fastqc/results/DB_099_CAMMD_CTTGTA_L001_R1_001_fastqc.html filter=lfs diff=lfs merge=lfs -text
+runs/fastqc/results/DB_099_CAMMD_CTTGTA_L001_R1_001_fastqc.zip filter=lfs diff=lfs merge=lfs -text
+runs/fastqc/results/DB_103_CAMMD_AGTCAA_L001_R1_001_fastqc.html filter=lfs diff=lfs merge=lfs -text
+runs/fastqc/results/DB_103_CAMMD_AGTCAA_L001_R1_001_fastqc.zip filter=lfs diff=lfs merge=lfs -text
+runs/fastqc/results/DB_161_reC3MD_GTCCGC_L001_R1_001_fastqc.html filter=lfs diff=lfs merge=lfs -text
+runs/fastqc/results/DB_161_reC3MD_GTCCGC_L001_R1_001_fastqc.zip filter=lfs diff=lfs merge=lfs -text
+runs/fastqc/results/DB_163_reC3MD_GTGAAA_L001_R1_001_fastqc.zip filter=lfs diff=lfs merge=lfs -text
+runs/fastqc/results/DB_165_re-C3MD_GTGAAA_L002_R1_001_fastqc.html filter=lfs diff=lfs merge=lfs -text
+runs/fastqc/results/DB_165_re-C3MD_GTGAAA_L002_R1_001_fastqc.zip filter=lfs diff=lfs merge=lfs -text
diff --git a/assays/Talinum_RNASeq_minimal/dataset/.gitkeep b/assays/Talinum_RNASeq_minimal/dataset/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/runs/fastqc/results/DB_097_CAMMD_CAGATC_L001_R1_001_fastqc.html b/runs/fastqc/results/DB_097_CAMMD_CAGATC_L001_R1_001_fastqc.html
new file mode 100644
index 0000000000000000000000000000000000000000..51bd550d5177f5d8001e285b9e3b186f22a7206a
--- /dev/null
+++ b/runs/fastqc/results/DB_097_CAMMD_CAGATC_L001_R1_001_fastqc.html
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:496b053b05cdbff7213e1ce93e168c9aae01830b875ba4f140f0445add3a4c9d
+size 608772
diff --git a/runs/fastqc/results/DB_097_CAMMD_CAGATC_L001_R1_001_fastqc.zip b/runs/fastqc/results/DB_097_CAMMD_CAGATC_L001_R1_001_fastqc.zip
new file mode 100644
index 0000000000000000000000000000000000000000..9cf6ee9b211654b1618a018cfd9d8328430bb381
--- /dev/null
+++ b/runs/fastqc/results/DB_097_CAMMD_CAGATC_L001_R1_001_fastqc.zip
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:453098e0f3046efe2317023867e5859e92ee91b254da02f4c84c6a569a12c358
+size 423523
diff --git a/runs/fastqc/results/DB_099_CAMMD_CTTGTA_L001_R1_001_fastqc.html b/runs/fastqc/results/DB_099_CAMMD_CTTGTA_L001_R1_001_fastqc.html
new file mode 100644
index 0000000000000000000000000000000000000000..141b06f5d05da67b23731dd73f70df429c516163
--- /dev/null
+++ b/runs/fastqc/results/DB_099_CAMMD_CTTGTA_L001_R1_001_fastqc.html
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:6d20c29bba7d056d66f6a6516c4d1044cdb26184971499eb8814de46ebcbaf6c
+size 610809
diff --git a/runs/fastqc/results/DB_099_CAMMD_CTTGTA_L001_R1_001_fastqc.zip b/runs/fastqc/results/DB_099_CAMMD_CTTGTA_L001_R1_001_fastqc.zip
new file mode 100644
index 0000000000000000000000000000000000000000..3424223ad1bc8913bfc56dfbc320daeea46c538e
--- /dev/null
+++ b/runs/fastqc/results/DB_099_CAMMD_CTTGTA_L001_R1_001_fastqc.zip
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:c51133d51ff8d98ddaf9df5373e5dc832a66de48b603fc1fca788b75fc9314f8
+size 425882
diff --git a/runs/fastqc/results/DB_103_CAMMD_AGTCAA_L001_R1_001_fastqc.html b/runs/fastqc/results/DB_103_CAMMD_AGTCAA_L001_R1_001_fastqc.html
new file mode 100644
index 0000000000000000000000000000000000000000..1bbad97077bfab908d6766c70e34915a5988f5e7
--- /dev/null
+++ b/runs/fastqc/results/DB_103_CAMMD_AGTCAA_L001_R1_001_fastqc.html
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:462d62cb603020068aff4606f26b62d818d2bfb56eb1894dc993638a5763c7ae
+size 611722
diff --git a/runs/fastqc/results/DB_103_CAMMD_AGTCAA_L001_R1_001_fastqc.zip b/runs/fastqc/results/DB_103_CAMMD_AGTCAA_L001_R1_001_fastqc.zip
new file mode 100644
index 0000000000000000000000000000000000000000..3ebe7614ff4e82ecc20df2d88ff803c94f888c8e
--- /dev/null
+++ b/runs/fastqc/results/DB_103_CAMMD_AGTCAA_L001_R1_001_fastqc.zip
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:6e7d78a994d307c6a57adbb4b41d22207d0ae7ebf2ace568f9fbe70aa606da03
+size 424835
diff --git a/runs/fastqc/results/DB_161_reC3MD_GTCCGC_L001_R1_001_fastqc.html b/runs/fastqc/results/DB_161_reC3MD_GTCCGC_L001_R1_001_fastqc.html
new file mode 100644
index 0000000000000000000000000000000000000000..25b6a558790028b0b6654d8cc85efe226691ea9f
--- /dev/null
+++ b/runs/fastqc/results/DB_161_reC3MD_GTCCGC_L001_R1_001_fastqc.html
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:9e689e4f749d29fff8ec52ada03471255579e43f04e49191bb8b19896348e576
+size 608061
diff --git a/runs/fastqc/results/DB_161_reC3MD_GTCCGC_L001_R1_001_fastqc.zip b/runs/fastqc/results/DB_161_reC3MD_GTCCGC_L001_R1_001_fastqc.zip
new file mode 100644
index 0000000000000000000000000000000000000000..545e4bacd602bfbef83d7df68ac96811c098ff2b
--- /dev/null
+++ b/runs/fastqc/results/DB_161_reC3MD_GTCCGC_L001_R1_001_fastqc.zip
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:1772958d490994dabde1091c2506c634b78d12698027b37e9d8e15d20a72fbc1
+size 420951
diff --git a/runs/fastqc/results/DB_163_reC3MD_GTGAAA_L001_R1_001_fastqc.html b/runs/fastqc/results/DB_163_reC3MD_GTGAAA_L001_R1_001_fastqc.html
new file mode 100644
index 0000000000000000000000000000000000000000..9df68457865e1dd583b6ae2c5a6b2b18536feb53
--- /dev/null
+++ b/runs/fastqc/results/DB_163_reC3MD_GTGAAA_L001_R1_001_fastqc.html
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:4f54fd0ae336e95fa780a9b0fb097beb1f50cdbbc24610d6247066eba3b0454a
+size 610537
diff --git a/runs/fastqc/results/DB_163_reC3MD_GTGAAA_L001_R1_001_fastqc.zip b/runs/fastqc/results/DB_163_reC3MD_GTGAAA_L001_R1_001_fastqc.zip
new file mode 100644
index 0000000000000000000000000000000000000000..d94d2956abb44ef6071f5d4e888d4fe0396f10fd
--- /dev/null
+++ b/runs/fastqc/results/DB_163_reC3MD_GTGAAA_L001_R1_001_fastqc.zip
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:be44017bdb5956ac2b479115fd26a5f605b493b3224050bb0a0af6deb53786ac
+size 424179
diff --git a/runs/fastqc/results/DB_165_re-C3MD_GTGAAA_L002_R1_001_fastqc.html b/runs/fastqc/results/DB_165_re-C3MD_GTGAAA_L002_R1_001_fastqc.html
new file mode 100644
index 0000000000000000000000000000000000000000..5c6ddb761ce58660638ba16115b6d5dd8823b9b1
--- /dev/null
+++ b/runs/fastqc/results/DB_165_re-C3MD_GTGAAA_L002_R1_001_fastqc.html
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:24474916df5d793336d0806f8ae28754e3ce1c03c3c3979f91a37550f26eb126
+size 609445
diff --git a/runs/fastqc/results/DB_165_re-C3MD_GTGAAA_L002_R1_001_fastqc.zip b/runs/fastqc/results/DB_165_re-C3MD_GTGAAA_L002_R1_001_fastqc.zip
new file mode 100644
index 0000000000000000000000000000000000000000..1e9c80dd29f9e25c31b0a5eeb1cae36f5c46e214
--- /dev/null
+++ b/runs/fastqc/results/DB_165_re-C3MD_GTGAAA_L002_R1_001_fastqc.zip
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:6c7efe5eb2d68cb409f26228692e0b0d19da26787a2a3716faafd6f88722fdb0
+size 426039
diff --git a/runs/fastqc/run.cwl b/runs/fastqc/run.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..974e99274b8fab4201a548c27fdda57f059544b4
--- /dev/null
+++ b/runs/fastqc/run.cwl
@@ -0,0 +1,24 @@
+cwlVersion: v1.2
+class: Workflow
+
+requirements:
+ SubworkflowFeatureRequirement: {}
+ ScatterFeatureRequirement: {}
+ MultipleInputFeatureRequirement: {}
+
+inputs:
+ fastq: File[]
+ finaloutdir: string
+
+steps:
+ fastqc:
+ run: ../../workflows/fastqc/workflow.cwl
+ in:
+ fastq: fastq
+ finaloutdir: finaloutdir
+ out: [outdir]
+
+outputs:
+ outdir:
+ type: Directory
+ outputSource: fastqc/outdir
\ No newline at end of file
diff --git a/runs/fastqc/run.yml b/runs/fastqc/run.yml
new file mode 100644
index 0000000000000000000000000000000000000000..d9744cf09a5b541d9497c4831f5a81055fdc996d
--- /dev/null
+++ b/runs/fastqc/run.yml
@@ -0,0 +1,14 @@
+finaloutdir: "results"
+fastq:
+ - class: File
+ path: ../../assays/Talinum_RNASeq_minimal/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
+ - class: File
+ path: ../../assays/Talinum_RNASeq_minimal/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
+ - class: File
+ path: ../../assays/Talinum_RNASeq_minimal/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
diff --git a/runs/kallisto/run.cwl b/runs/kallisto/run.cwl
index 7ab4d83630e9cacda2b7da8c7a9b3ac804c5f12e..3ec2a22fd3d933361182dff470de94caf611a092 100644
--- a/runs/kallisto/run.cwl
+++ b/runs/kallisto/run.cwl
@@ -4,16 +4,20 @@ class: Workflow
requirements:
SubworkflowFeatureRequirement: {}
+ MultipleInputFeatureRequirement: {}
inputs:
IndexInput: File[]
- InputReadsMultipleSamples:
- type:
+ sampleRecord:
+ type:
type: array
- items:
- type: array
- items: File
- numUnderscoresFileName: int
+ items:
+ type: record
+ fields:
+ readsOfOneSample:
+ type: File[]
+ sampleName:
+ type: string?
isSingle: boolean
FragmentLength: double?
StandardDeviation: double?
@@ -25,8 +29,7 @@ steps:
run: ../../workflows/kallisto/workflow.cwl
in:
IndexInput: IndexInput
- InputReadsMultipleSamples: InputReadsMultipleSamples
- numUnderscoresFileName: numUnderscoresFileName
+ sampleRecord: sampleRecord
isSingle: isSingle
FragmentLength: FragmentLength
StandardDeviation: StandardDeviation
diff --git a/runs/kallisto/run.yml b/runs/kallisto/run.yml
index 1d147f9882253552f871d417b493cb2cf9ca5c17..541e17004c6844c012e70922d7bc4470a59b8963 100644
--- a/runs/kallisto/run.yml
+++ b/runs/kallisto/run.yml
@@ -5,44 +5,47 @@ IndexInput:
format: edam:format_1929 # FASTA
## Fastq files to be mapped
-# The `InputReadsMultipleSamples` looks more complicated than needed
-# It's an array of File arrays to generically allow multiple fastq files per sample
+# The `readsOfOneSample` looks more complicated than needed
+# It's an array of records (each with one or mupltiple files and a sample name) to generically allow multiple fastq files per sample
-InputReadsMultipleSamples:
- -
+sampleRecord:
+ - readsOfOneSample:
- class: File
path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
- format: edam:format_1930 # FASTQ
- -
+ 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
+ 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
- format: edam:format_1930 # FASTQ
- # -
- # - class: File
- # path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz
- # format: edam:format_1930 # FASTQ
- # -
- # - class: File
- # path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz
- # format: edam:format_1930 # FASTQ
- # -
- # - class: File
- # path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz
- # format: edam:format_1930 # FASTQ
- # -
- # - class: File
- # path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz
- # format: edam:format_1930 # FASTQ
-
-numUnderscoresFileName: 2
+ 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
+ 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
+ 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
+ format: edam:format_1930
+ sampleName: 'DB_165'
### Kallisto quant Parameters
isSingle: true
FragmentLength: 200
StandardDeviation: 20
BootstrapSamples: 30
-
-resultsFolder: test
+resultsFolder: kallisto_results
$namespaces:
edam: https://edamontology.org/
\ No newline at end of file
diff --git a/workflows/fastqc/collectFilesInDir.cwl b/workflows/fastqc/collectFilesInDir.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..39f9ff8ae5a33d939136c081a9cd79533972eddc
--- /dev/null
+++ b/workflows/fastqc/collectFilesInDir.cwl
@@ -0,0 +1,20 @@
+cwlVersion: v1.2
+class: ExpressionTool
+label: Collect files in a directory
+doc: |
+ Takes Files (e.g. from a workflow step) and yields them in a desired directory.
+requirements:
+ - class: InlineJavascriptRequirement
+inputs:
+ files: File[]
+ destination: string
+expression: |
+ ${
+ return {"outDir": {
+ "class": "Directory",
+ "basename": inputs.destination,
+ "listing": inputs.files
+ } };
+ }
+outputs:
+ outDir: Directory
\ No newline at end of file
diff --git a/workflows/fastqc/fastqc.cwl b/workflows/fastqc/fastqc.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..a2e408db732fa6913af001c6349dda4ac30a116e
--- /dev/null
+++ b/workflows/fastqc/fastqc.cwl
@@ -0,0 +1,48 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+class: CommandLineTool
+
+label: Run fastqc on raw reads in FASTQ format (single or paired end) or aligned reads in BAM.
+
+doc: |
+ simplified from: https://github.com/common-workflow-library/bio-cwl-tools/blob/66f620da5b0a11e934a6da83272205a2516bcd91/fastqc/fastqc_1.cwl
+
+ Run fastqc on raw reads in FASTQ format (single or paired end) or aligned reads in BAM.
+
+hints:
+ ResourceRequirement:
+ coresMin: 1
+ ramMin: 5000
+ DockerRequirement:
+ dockerPull: quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1
+ SoftwareRequirement:
+ packages:
+ fastqc:
+ specs: [ https://identifiers.org/biotools/fastqc ]
+ version: [ "0.11.9" ]
+
+
+baseCommand: "fastqc"
+arguments:
+ - valueFrom: $(runtime.outdir)
+ prefix: "-o"
+ - valueFrom: "--noextract"
+
+inputs:
+ fastq:
+ type: File
+ inputBinding:
+ position: 1
+
+outputs:
+ fastqc_zip:
+ doc: all data e.g. figures
+ type: File
+ outputBinding:
+ glob: "*_fastqc.zip"
+ fastqc_html:
+ doc: html report showing results from zip
+ type: File
+ outputBinding:
+ glob: "*_fastqc.html"
+
diff --git a/workflows/fastqc/workflow.cwl b/workflows/fastqc/workflow.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..d80a7eaafc7c6f530d3c43ca21716b005e7d1f4e
--- /dev/null
+++ b/workflows/fastqc/workflow.cwl
@@ -0,0 +1,32 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+class: Workflow
+
+requirements:
+ ScatterFeatureRequirement: {}
+ SubworkflowFeatureRequirement: {}
+
+inputs:
+ fastq: File[]
+ finaloutdir: string
+
+steps:
+ fastqc:
+ run: fastqc.cwl
+ scatter: fastq
+ in:
+ fastq: fastq
+ out: [fastqc_zip, fastqc_html]
+ collectFiles:
+ run: ./collectFilesInDir.cwl
+ in:
+ destination: finaloutdir
+ files:
+ source: [fastqc/fastqc_html, fastqc/fastqc_zip]
+ linkMerge: merge_flattened
+ out: [outDir]
+
+outputs:
+ outdir:
+ type: Directory
+ outputSource: collectFiles/outDir
\ No newline at end of file
diff --git a/workflows/kallisto/README.md b/workflows/kallisto/README.md
deleted file mode 100644
index 244a3c13bfec41dce6d7e5e892b1b5e37fe55d2f..0000000000000000000000000000000000000000
--- a/workflows/kallisto/README.md
+++ /dev/null
@@ -1,12 +0,0 @@
-
-# Kallisto
-
-CWL adapted from: https://github.com/common-workflow-library/bio-cwl-tools/commit/91c42fb809ce18eafe16155cca0abf362270c0fe
-
-## Workflow graph
-
-```bash
-cwltool --print-dot kallisto-workflow.cwl | dot -Tsvg > kallisto_workflow_graph.svg
-```
-
-
\ No newline at end of file
diff --git a/workflows/kallisto/kallisto-help.cwl b/workflows/kallisto/kallisto-test.cwl
similarity index 100%
rename from workflows/kallisto/kallisto-help.cwl
rename to workflows/kallisto/kallisto-test.cwl
diff --git a/workflows/kallisto/kallisto_workflow_graph.svg b/workflows/kallisto/kallisto_workflow_graph.svg
deleted file mode 100644
index a9083cee1ed9f5c8f89da0ff9cfcd795b28818aa..0000000000000000000000000000000000000000
--- a/workflows/kallisto/kallisto_workflow_graph.svg
+++ /dev/null
@@ -1,173 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
- "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
-<!-- Generated by graphviz version 2.50.0 (20220117.2223)
- -->
-<!-- Title: G Pages: 1 -->
-<svg width="1313pt" height="395pt"
- viewBox="0.00 0.00 1313.00 395.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
-<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 391)">
-<title>G</title>
-<polygon fill="#eeeeee" stroke="transparent" points="-4,4 -4,-391 1309,-391 1309,4 -4,4"/>
-<g id="clust1" class="cluster">
-<title>cluster_inputs</title>
-<polygon fill="#eeeeee" stroke="black" stroke-dasharray="5,2" points="8,-303 8,-379 1297,-379 1297,-303 8,-303"/>
-<text text-anchor="middle" x="1230" y="-310.8" font-family="Times,serif" font-size="14.00">Workflow Inputs</text>
-</g>
-<g id="clust2" class="cluster">
-<title>cluster_outputs</title>
-<polygon fill="#eeeeee" stroke="black" stroke-dasharray="5,2" points="310,-8 310,-84 456,-84 456,-8 310,-8"/>
-<text text-anchor="middle" x="383" y="-15.8" font-family="Times,serif" font-size="14.00">Workflow Outputs</text>
-</g>
-<!-- quant -->
-<g id="node1" class="node">
-<title>quant</title>
-<polygon fill="lightgoldenrodyellow" stroke="black" points="647,-185.5 647,-221.5 705,-221.5 705,-185.5 647,-185.5"/>
-<text text-anchor="middle" x="676" y="-199.8" font-family="Times,serif" font-size="14.00">quant</text>
-</g>
-<!-- collectResults -->
-<g id="node2" class="node">
-<title>collectResults</title>
-<polygon fill="lightgoldenrodyellow" stroke="black" points="325,-112.5 325,-148.5 441,-148.5 441,-112.5 325,-112.5"/>
-<text text-anchor="middle" x="383" y="-126.8" font-family="Times,serif" font-size="14.00">collectResults</text>
-</g>
-<!-- quant->collectResults -->
-<g id="edge1" class="edge">
-<title>quant->collectResults</title>
-<path fill="none" stroke="black" d="M646.83,-195.43C601.59,-184.47 513.24,-163.06 451.29,-148.05"/>
-<polygon fill="black" stroke="black" points="451.75,-144.56 441.2,-145.6 450.1,-151.36 451.75,-144.56"/>
-</g>
-<!-- finalOut -->
-<g id="node12" class="node">
-<title>finalOut</title>
-<polygon fill="#94ddf4" stroke="black" points="346,-39.5 346,-75.5 420,-75.5 420,-39.5 346,-39.5"/>
-<text text-anchor="middle" x="383" y="-53.8" font-family="Times,serif" font-size="14.00">finalOut</text>
-</g>
-<!-- collectResults->finalOut -->
-<g id="edge13" class="edge">
-<title>collectResults->finalOut</title>
-<path fill="none" stroke="black" d="M383,-112.31C383,-104.29 383,-94.55 383,-85.57"/>
-<polygon fill="black" stroke="black" points="386.5,-85.53 383,-75.53 379.5,-85.53 386.5,-85.53"/>
-</g>
-<!-- index -->
-<g id="node3" class="node">
-<title>index</title>
-<polygon fill="lightgoldenrodyellow" stroke="black" points="166,-258.5 166,-294.5 222,-294.5 222,-258.5 166,-258.5"/>
-<text text-anchor="middle" x="194" y="-272.8" font-family="Times,serif" font-size="14.00">index</text>
-</g>
-<!-- index->quant -->
-<g id="edge2" class="edge">
-<title>index->quant</title>
-<path fill="none" stroke="black" d="M222.35,-271.32C304.43,-259.23 542.41,-224.18 636.78,-210.28"/>
-<polygon fill="black" stroke="black" points="637.39,-213.73 646.77,-208.81 636.37,-206.8 637.39,-213.73"/>
-</g>
-<!-- resultsFolder -->
-<g id="node4" class="node">
-<title>resultsFolder</title>
-<polygon fill="#94ddf4" stroke="black" points="16,-334.5 16,-370.5 128,-370.5 128,-334.5 16,-334.5"/>
-<text text-anchor="middle" x="72" y="-348.8" font-family="Times,serif" font-size="14.00">resultsFolder</text>
-</g>
-<!-- resultsFolder->collectResults -->
-<g id="edge3" class="edge">
-<title>resultsFolder->collectResults</title>
-<path fill="none" stroke="black" d="M84.72,-334.44C100.23,-314.43 127.98,-281.07 157,-258 213.1,-213.41 286.94,-175.31 334.69,-152.9"/>
-<polygon fill="black" stroke="black" points="336.29,-156.02 343.88,-148.63 333.34,-149.67 336.29,-156.02"/>
-</g>
-<!-- IndexInput -->
-<g id="node5" class="node">
-<title>IndexInput</title>
-<polygon fill="#94ddf4" stroke="black" points="146.5,-334.5 146.5,-370.5 241.5,-370.5 241.5,-334.5 146.5,-334.5"/>
-<text text-anchor="middle" x="194" y="-348.8" font-family="Times,serif" font-size="14.00">IndexInput</text>
-</g>
-<!-- IndexInput->index -->
-<g id="edge4" class="edge">
-<title>IndexInput->index</title>
-<path fill="none" stroke="black" d="M188.2,-334.34C187.27,-325.56 187.02,-314.66 187.46,-304.77"/>
-<polygon fill="black" stroke="black" points="190.97,-304.8 188.21,-294.57 183.99,-304.29 190.97,-304.8"/>
-</g>
-<!-- IndexInput->index -->
-<g id="edge5" class="edge">
-<title>IndexInput->index</title>
-<path fill="none" stroke="black" d="M199.8,-334.34C200.73,-325.56 200.98,-314.66 200.54,-304.77"/>
-<polygon fill="black" stroke="black" points="204.01,-304.29 199.79,-294.57 197.03,-304.8 204.01,-304.29"/>
-</g>
-<!-- BootstrapSamples -->
-<g id="node6" class="node">
-<title>BootstrapSamples</title>
-<polygon fill="#94ddf4" stroke="black" points="260,-334.5 260,-370.5 408,-370.5 408,-334.5 260,-334.5"/>
-<text text-anchor="middle" x="334" y="-348.8" font-family="Times,serif" font-size="14.00">BootstrapSamples</text>
-</g>
-<!-- BootstrapSamples->quant -->
-<g id="edge6" class="edge">
-<title>BootstrapSamples->quant</title>
-<path fill="none" stroke="black" d="M361.03,-334.43C377.21,-324.58 398.38,-312.33 418,-303 493.49,-267.08 585.84,-234.39 637.06,-217.2"/>
-<polygon fill="black" stroke="black" points="638.36,-220.46 646.74,-213.97 636.15,-213.81 638.36,-220.46"/>
-</g>
-<!-- FragmentLength -->
-<g id="node7" class="node">
-<title>FragmentLength</title>
-<polygon fill="#94ddf4" stroke="black" points="426.5,-334.5 426.5,-370.5 563.5,-370.5 563.5,-334.5 426.5,-334.5"/>
-<text text-anchor="middle" x="495" y="-348.8" font-family="Times,serif" font-size="14.00">FragmentLength</text>
-</g>
-<!-- FragmentLength->quant -->
-<g id="edge7" class="edge">
-<title>FragmentLength->quant</title>
-<path fill="none" stroke="black" d="M516.12,-334.35C548.54,-308.02 610.66,-257.56 647.19,-227.9"/>
-<polygon fill="black" stroke="black" points="649.46,-230.56 655.02,-221.54 645.05,-225.13 649.46,-230.56"/>
-</g>
-<!-- StandardDeviation -->
-<g id="node8" class="node">
-<title>StandardDeviation</title>
-<polygon fill="#94ddf4" stroke="black" points="581.5,-334.5 581.5,-370.5 732.5,-370.5 732.5,-334.5 581.5,-334.5"/>
-<text text-anchor="middle" x="657" y="-348.8" font-family="Times,serif" font-size="14.00">StandardDeviation</text>
-</g>
-<!-- StandardDeviation->quant -->
-<g id="edge8" class="edge">
-<title>StandardDeviation->quant</title>
-<path fill="none" stroke="black" d="M659.22,-334.35C662.48,-309.12 668.6,-261.76 672.48,-231.74"/>
-<polygon fill="black" stroke="black" points="675.99,-231.91 673.8,-221.54 669.04,-231.01 675.99,-231.91"/>
-</g>
-<!-- isSingle -->
-<g id="node9" class="node">
-<title>isSingle</title>
-<polygon fill="#94ddf4" stroke="black" points="751,-334.5 751,-370.5 825,-370.5 825,-334.5 751,-334.5"/>
-<text text-anchor="middle" x="788" y="-348.8" font-family="Times,serif" font-size="14.00">isSingle</text>
-</g>
-<!-- isSingle->quant -->
-<g id="edge9" class="edge">
-<title>isSingle->quant</title>
-<path fill="none" stroke="black" d="M775.14,-334.23C766.7,-323.94 754.87,-311.31 742,-303 732.91,-297.13 727.06,-302.23 719,-295 700.25,-278.19 688.96,-251.45 682.68,-231.39"/>
-<polygon fill="black" stroke="black" points="685.99,-230.23 679.84,-221.59 679.26,-232.17 685.99,-230.23"/>
-</g>
-<!-- numUnderscoresFileName -->
-<g id="node10" class="node">
-<title>numUnderscoresFileName</title>
-<polygon fill="#94ddf4" stroke="black" points="843,-334.5 843,-370.5 1051,-370.5 1051,-334.5 843,-334.5"/>
-<text text-anchor="middle" x="947" y="-348.8" font-family="Times,serif" font-size="14.00">numUnderscoresFileName</text>
-</g>
-<!-- numUnderscoresFileName->quant -->
-<g id="edge10" class="edge">
-<title>numUnderscoresFileName->quant</title>
-<path fill="none" stroke="black" d="M914.31,-334.34C892.23,-323.54 862.1,-310.31 834,-303 800.7,-294.34 787.64,-310.65 757,-295 749.29,-291.06 718.14,-254.93 696.79,-229.53"/>
-<polygon fill="black" stroke="black" points="699.35,-227.14 690.25,-221.72 693.99,-231.63 699.35,-227.14"/>
-</g>
-<!-- InputReadsMultipleSamples -->
-<g id="node11" class="node">
-<title>InputReadsMultipleSamples</title>
-<polygon fill="#94ddf4" stroke="black" points="1069.5,-334.5 1069.5,-370.5 1288.5,-370.5 1288.5,-334.5 1069.5,-334.5"/>
-<text text-anchor="middle" x="1179" y="-348.8" font-family="Times,serif" font-size="14.00">InputReadsMultipleSamples</text>
-</g>
-<!-- InputReadsMultipleSamples->quant -->
-<g id="edge11" class="edge">
-<title>InputReadsMultipleSamples->quant</title>
-<path fill="none" stroke="black" d="M1133.09,-334.43C1108.8,-324.46 1078.54,-312.1 1051,-303 930.41,-263.16 784.15,-229.58 715.25,-213.93"/>
-<polygon fill="black" stroke="black" points="715.79,-210.46 705.27,-211.66 714.25,-217.29 715.79,-210.46"/>
-</g>
-<!-- InputReadsMultipleSamples->quant -->
-<g id="edge12" class="edge">
-<title>InputReadsMultipleSamples->quant</title>
-<path fill="none" stroke="black" d="M1148.73,-334.43C1126.8,-324.46 1096.54,-312.1 1069,-303 941.93,-261.02 786.37,-225.99 714.95,-211.57"/>
-<polygon fill="black" stroke="black" points="715.53,-208.11 705.04,-209.59 714.16,-214.98 715.53,-208.11"/>
-</g>
-</g>
-</svg>
diff --git a/workflows/kallisto/workflow.cwl b/workflows/kallisto/workflow.cwl
index 1d020e1110afc46d500e96eef07a1f7282164219..4ce56173769787379dddf9cd977d60b18e6ff9c1 100644
--- a/workflows/kallisto/workflow.cwl
+++ b/workflows/kallisto/workflow.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
cwlVersion: v1.2
class: Workflow
@@ -7,62 +8,58 @@ requirements:
InlineJavascriptRequirement: {}
inputs:
- IndexInput: File[]
- InputReadsMultipleSamples:
- type:
- type: array
- items:
- type: array
- items: File
- # numCharsFileName:
- # type: int
- # default: 6
- numUnderscoresFileName:
- type: int
- default: 2
- isSingle: boolean
- FragmentLength: double?
- StandardDeviation: double?
- BootstrapSamples: int?
- resultsFolder: string
+ IndexInput: File[]
+ sampleRecord:
+ type:
+ type: array
+ items:
+ type: record
+ fields:
+ readsOfOneSample:
+ type: File[]
+ sampleName:
+ type: string?
+ isSingle: boolean
+ FragmentLength: double?
+ StandardDeviation: double?
+ BootstrapSamples: int?
+ resultsFolder: string
steps:
- index:
- run: kallisto-index.cwl
- in:
- InputFiles: IndexInput
- IndexName:
- source: IndexInput
- valueFrom: $(self[0].nameroot)
- out: [index]
- quant:
- run: kallisto-quant.cwl
- scatter:
- - InputReads
- - QuantOutfolder
- scatterMethod: dotproduct
- in:
- InputReads: InputReadsMultipleSamples
- # numChars:
- # source: numCharsFileName
- numUnderscores: numUnderscoresFileName
- QuantOutfolder:
- source: InputReadsMultipleSamples
- # valueFrom: $(self[0].nameroot.substring(0, inputs.numChars))
- valueFrom: $(self[0].nameroot.split('_').slice(0, inputs.numUnderscores).join('_'))
- Index: index/index
- isSingle: isSingle
- FragmentLength: FragmentLength
- StandardDeviation: StandardDeviation
- BootstrapSamples: BootstrapSamples
- out: [outFolder]
- collectResults:
- run: ./yield-dirInDestination.cwl
- scatter: inDir
- in:
- inDir: quant/outFolder
- destinationDir: resultsFolder
- out: [outDir]
+ index:
+ run: kallisto-index.cwl
+ in:
+ InputFiles: IndexInput
+ IndexName:
+ source: IndexInput
+ valueFrom: $(self[0].nameroot)
+ out: [index]
+
+ quant:
+ run: kallisto-quant.cwl
+ scatter: [InputReads, QuantOutfolder]
+ scatterMethod: dotproduct
+ in:
+ InputReads:
+ source: sampleRecord
+ valueFrom: $(self.readsOfOneSample)
+ QuantOutfolder:
+ source: sampleRecord
+ valueFrom: $(self.sampleName)
+ Index: index/index
+ isSingle: isSingle
+ FragmentLength: FragmentLength
+ StandardDeviation: StandardDeviation
+ BootstrapSamples: BootstrapSamples
+ out: [outFolder]
+
+ collectResults:
+ run: ./yield-dirInDestination.cwl
+ scatter: inDir
+ in:
+ inDir: quant/outFolder
+ destinationDir: resultsFolder
+ out: [outDir]
outputs:
finalOut:
diff --git a/workflows/kallisto/yield-dirInDestination.cwl b/workflows/kallisto/yield-dirInDestination.cwl
index c2a20eabcd7bfc412238d74a99aedb6eac468008..bc90cb81f1a907735bd433d6117c55872c213f92 100644
--- a/workflows/kallisto/yield-dirInDestination.cwl
+++ b/workflows/kallisto/yield-dirInDestination.cwl
@@ -1,7 +1,7 @@
cwlVersion: v1.2
class: ExpressionTool
doc: |
- Takes a directory (e.g. from a workflow step) and yield it in a desired directory.
+ Takes a directory (e.g. from a workflow step) and yields it in a desired directory.
requirements:
- class: InlineJavascriptRequirement
inputs: