diff --git a/.gitattributes b/.gitattributes
index 07a4a56143d25a23ce6ab0320d147c3096caa5f6..574339b69b82d0008d4b3ffd2e7398ad5d82ed6d 100644
--- a/.gitattributes
+++ b/.gitattributes
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 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
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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
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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
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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/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