diff --git a/.gitignore b/.gitignore
index 9e379c7..78db699 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,4 +3,5 @@ testData
 
 # Nextflow related files
 .nextflow
+.nextflow.log*
 work
\ No newline at end of file
diff --git a/src/config/tests.config b/src/config/tests.config
index a49d658..3473a3d 100644
--- a/src/config/tests.config
+++ b/src/config/tests.config
@@ -1,5 +1,6 @@
-profiles {
 
+process.container = 'nextflow/bash:latest'
+profiles {
   // detect tempdir
   tempDir = java.nio.file.Paths.get(
     System.getenv('NXF_TEMP') ?:
@@ -26,6 +27,7 @@ profiles {
   }
 
   docker {
+    docker.fixOwnership    = true
     docker.enabled         = true
     // docker.userEmulation   = true
     singularity.enabled    = false
diff --git a/src/dataflow/combine_samples/config.vsh.yaml b/src/dataflow/combine_samples/config.vsh.yaml
new file mode 100644
index 0000000..d82717e
--- /dev/null
+++ b/src/dataflow/combine_samples/config.vsh.yaml
@@ -0,0 +1,38 @@
+name: combine_samples
+namespace: dataflow
+description: Combine fastq files from across samples into one event with a list of fastq files per orientation.
+argument_groups:
+  - name: Input arguments
+    arguments:
+      - name: "--id"
+        description: "ID of the new event"
+        type: string
+        required: true
+      - name: --forward_input
+        type: file
+        required: true
+      - name: --reverse_input
+        type: file
+        required: false
+  - name: Output arguments
+    arguments:
+      - name: --output_forward
+        type: file
+        direction: output
+        multiple: true
+        required: true
+      - name: --output_reverse
+        type: file
+        direction: output
+        multiple: true
+        required: false
+resources:
+  - type: nextflow_script
+    path: main.nf
+    entrypoint: run_wf
+
+runners:
+  - type: nextflow
+
+engines:
+  - type: native
diff --git a/src/dataflow/combine_samples/main.nf b/src/dataflow/combine_samples/main.nf
new file mode 100644
index 0000000..1a16fa6
--- /dev/null
+++ b/src/dataflow/combine_samples/main.nf
@@ -0,0 +1,28 @@
+workflow run_wf {
+  take:
+    input_ch
+
+  main:
+    output_ch = input_ch
+      | map { id, state ->
+        def newEvent = [state.id, state + ["_meta": ["join_id": id]]]
+        newEvent
+      }
+      | groupTuple(by: 0, sort: "hash")
+      | map {run_id, states ->
+        // Gather the following state for all samples
+        def forward_fastqs = states.collect{it.forward_input}
+        def reverse_fastqs = states.collect{it.reverse_input}.findAll{it != null}
+        
+        def resultState = [
+          "output_forward": forward_fastqs,
+          "output_reverse": reverse_fastqs,
+          // The join ID is the same across all samples from the same run
+          "_meta": ["join_id": states[0]._meta.join_id]
+        ]
+        return [run_id, resultState]
+      }
+  
+  emit:
+    output_ch
+}
\ No newline at end of file
diff --git a/src/dataflow/gather_fastqs_and_validate/config.vsh.yaml b/src/dataflow/gather_fastqs_and_validate/config.vsh.yaml
new file mode 100644
index 0000000..e0b7733
--- /dev/null
+++ b/src/dataflow/gather_fastqs_and_validate/config.vsh.yaml
@@ -0,0 +1,36 @@
+name: gather_fastqs_and_validate
+namespace: dataflow
+description: |
+  From a directory containing fastq files, gather the files per sample 
+  and validate according to the contents of the sample sheet.
+argument_groups:
+  - name: Input arguments
+    arguments:
+      - name: --input
+        description: Directory containing .fastq files
+        type: file
+        required: true
+      - name: --sample_sheet
+        description: Sample sheet
+        type: file
+        required: true
+  - name: Output arguments
+    arguments:
+      - name: --fastq_forward
+        type: file
+        direction: output
+        required: true
+      - name: "--fastq_reverse"
+        type: file
+        direction: output
+        required: false
+resources:
+  - type: nextflow_script
+    path: main.nf
+    entrypoint: run_wf
+
+runners:
+  - type: nextflow
+
+engines:
+  - type: native
diff --git a/src/dataflow/gather_fastqs_and_validate/main.nf b/src/dataflow/gather_fastqs_and_validate/main.nf
new file mode 100644
index 0000000..e6afd77
--- /dev/null
+++ b/src/dataflow/gather_fastqs_and_validate/main.nf
@@ -0,0 +1,73 @@
+workflow run_wf {
+  take:
+    input_ch
+
+  main:
+    output_ch = input_ch
+      // Gather input files from BCL convert output folder
+      | flatMap { id, state ->
+        println "Processing sample sheet: $state.sample_sheet"
+        def sample_sheet = state.sample_sheet
+        def start_parsing = false
+        def sample_id_column_index = null
+        def samples = ["Undetermined"]
+        def original_id = id
+
+        // Parse sample sheet for sample IDs
+        csv_lines = sample_sheet.splitCsv(header: false, sep: ',')
+        csv_lines.any { csv_items ->
+          if (csv_items.isEmpty()) {
+            return
+          }
+          def possible_header = csv_items[0]
+          def header = possible_header.find(/\[(.*)\]/){fullmatch, header_name -> header_name}
+          if (header) {
+            if (start_parsing) {
+              // Stop parsing when encountering the next header
+              return true
+            }
+            if (header == "Data") {
+              start_parsing = true
+            }
+          }
+          if (start_parsing) {
+            if ( !sample_id_column_index ) {
+              sample_id_column_index = csv_items.findIndexValues{it == "Sample_ID"}
+              assert sample_id_column_index != -1:
+              "Could not find column 'Sample_ID' in sample sheet!"
+              return
+            }
+            samples += csv_items[sample_id_column_index]
+          }
+        }
+        println "Looking for fastq files in ${state.input}."
+        def allfastqs = state.input.listFiles().findAll{it.isFile() && it.name ==~ /^.+\.fastq.gz$/}
+        println "Found ${allfastqs.size()} fastq files, matching them to the following samples: ${samples}."
+        processed_samples = samples.collect { sample_id ->
+          def forward_regex = ~/^${sample_id}_S(\d+)_(L(\d+)_)?R1_(\d+)\.fastq\.gz$/
+          def reverse_regex = ~/^${sample_id}_S(\d+)_(L(\d+)_)?R2_(\d+)\.fastq\.gz$/
+          def forward_fastq = state.input.listFiles().findAll{it.isFile() && it.name ==~ forward_regex}
+          def reverse_fastq = state.input.listFiles().findAll{it.isFile() && it.name ==~ reverse_regex}
+          assert forward_fastq : "No forward fastq files were found for sample ${sample_id}"
+          assert forward_fastq.size() < 2:
+          "Found multiple forward fastq files corresponding to sample ${sample_id}: ${forward_fastq}"
+          assert reverse_fastq.size() < 2:
+          "Found multiple reverse fastq files corresponding to sample ${sample_id}: ${reverse_fastq}."
+          assert !forward_fastq.isEmpty():
+          "Expected a forward fastq file to have been created correspondig to sample ${sample_id}."
+          // TODO: if one sample had reverse reads, the others must as well.
+          reverse_fastq = !reverse_fastq.isEmpty() ? reverse_fastq[0] : null
+          def fastqs_state = [
+            "fastq_forward": forward_fastq[0],
+            "fastq_reverse": reverse_fastq,
+            "_meta": [ "join_id": original_id ],
+          ]
+          [sample_id, fastqs_state]
+        }
+        println "Finished processing sample sheet."
+        return processed_samples
+      }
+
+  emit:
+    output_ch
+}
\ No newline at end of file
diff --git a/src/demultiplex/config.vsh.yaml b/src/demultiplex/config.vsh.yaml
index f840a76..1f005e1 100644
--- a/src/demultiplex/config.vsh.yaml
+++ b/src/demultiplex/config.vsh.yaml
@@ -8,9 +8,11 @@ argument_groups:
         type: file
         required: true
       - name: --sample_sheet
-        description: Sample sheet
+        description: |
+          Sample sheet as input for BCL Convert. If not specified,
+          will try to autodetect the sample sheet in the input directory
         type: file
-        required: true
+        required: false
   - name: Output arguments
     arguments:
       - name: --output
@@ -18,6 +20,18 @@ argument_groups:
         type: file
         direction: output
         required: true
+      - name: "--output_falco"
+        description: Directory to write falco output to
+        type: file
+        direction: output
+        required: false
+        default: "$id/falco"
+      - name: "--output_multiqc"
+        description: Directory to write falco output to
+        type: file
+        direction: output
+        required: false
+        default: "$id/multiqc_report.html"
 resources:
   - type: nextflow_script
     path: main.nf
@@ -31,14 +45,22 @@ test_resources:
 dependencies:
   - name: io/untar
     repository: local
+  - name: dataflow/gather_fastqs_and_validate
+    repository: local
+  - name: io/interop_summary_to_csv
+    repository: local
+  - name: dataflow/combine_samples
+    repository: local
   - name: bcl_convert
     repository: bb
-
+  - name: falco
+    repository: bb
+  - name: multiqc
+    repository: bb
 repositories:
   - name: bb
     type: vsh
     repo: viash-hub/biobase
-    tag: main
 
 runners:
   - type: nextflow
diff --git a/src/demultiplex/integration_tests.sh b/src/demultiplex/integration_tests.sh
index d327e36..1042753 100755
--- a/src/demultiplex/integration_tests.sh
+++ b/src/demultiplex/integration_tests.sh
@@ -6,10 +6,11 @@ REPO_ROOT=$(git rev-parse --show-toplevel)
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-viash ns build -q 'untar|demultiplex' --setup cb
+viash ns build --setup cb
 
 nextflow run . \
   -main-script src/demultiplex/test.nf \
   -profile docker,no_publish \
   -entry test_wf \
-  -c src/config/tests.config
+  -c src/config/tests.config \
+  -resume
diff --git a/src/demultiplex/main.nf b/src/demultiplex/main.nf
index 2cae23b..4c401da 100644
--- a/src/demultiplex/main.nf
+++ b/src/demultiplex/main.nf
@@ -3,30 +3,129 @@ workflow run_wf {
     input_ch
 
   main:
-    output_ch = input_ch
+    samples_ch = input_ch
       // untar input if needed
       | untar.run(
-        runIf: {id, state -> 
+        runIf: {id, state ->
           def inputStr = state.input.toString()
-          inputStr.endsWith(".tar.gz") || inputStr.endsWith(".tar") || inputStr.endsWith(".tgz") ? true : false
+          inputStr.endsWith(".tar.gz") || \
+          inputStr.endsWith(".tar") || \
+          inputStr.endsWith(".tgz") ? true : false
         },
         fromState: [
           "input": "input",
         ],
         toState: { id, result, state ->
-          state + [ input: result.output ]
+          state + ["input": result.output]
         },
       )
+      // Gather input files from folder
+      | map {id, state ->
+        def newState = [:]
+        if (!state.sample_sheet) {
+          def sample_sheet = state.input.resolve("SampleSheet.csv")
+          assert (sample_sheet && sample_sheet.isFile()): "Could not find 'SampleSheet.csv' file in input directory."
+          newState["sample_sheet"] = sample_sheet
+        }
+
+        // Do not add InterOp to state because we generate the summary csv's in the next
+        // step based on the run dir, not the InterOp dir.
+        def interop_dir = state.input.resolve("InterOp")
+        assert interop_dir.isDirectory(): "Expected InterOp directory to be present."
+
+        def resultState = state + newState
+        [id, resultState]
+      }
+
+      | interop_summary_to_csv.run(
+        fromState: [
+          "input": "input", 
+        ],
+        toState: [
+          "interop_run_summary": "output_run_summary",
+          "interop_index_summary": "output_index_summary",
+        ]
+      )
       // run bcl_convert
       | bcl_convert.run(
-          fromState: { id, state ->
-            [
-              bcl_input_directory: state.input,
-              sample_sheet: state.sample_sheet,
-            ]
-          },
-          toState: { id, result, state -> [ output: result.output_directory ] }
-        )
+        fromState: [
+          "bcl_input_directory": "input",
+          "sample_sheet": "sample_sheet",
+          "output_directory": "output",
+        ],
+        toState: {id, result, state -> 
+          def toAdd = [
+            "output_bclconvert" : result.output_directory,
+            "bclconvert_reports": result.reports,
+            "run_id": id,
+          ]
+          def newState = state + toAdd
+          return newState
+        }
+      )
+      | gather_fastqs_and_validate.run(
+        fromState: [
+          "input": "output_bclconvert",
+          "sample_sheet": "sample_sheet",
+        ],
+        toState: [
+          "fastq_forward": "fastq_forward",
+          "fastq_reverse": "fastq_reverse",
+        ],
+      )
+
+    output_ch = samples_ch 
+      | combine_samples.run(
+        fromState: { id, state ->
+          [
+            "id": state.run_id,
+            "forward_input": state.fastq_forward,
+            "reverse_input": state.fastq_reverse, 
+          ]
+        },
+        toState: [
+          "forward_fastqs": "output_forward",
+          "reverse_fastqs": "output_reverse",
+        ]
+      )
+      | falco.run(
+        fromState: {id, state ->
+          reverse_fastqs_list = state.reverse_fastqs ? state.reverse_fastqs : []
+          [
+            "input": state.forward_fastqs + reverse_fastqs_list,
+            "outdir": "${state.output_falco}",
+            "summary_filename": null,
+            "report_filename": null,
+            "data_filename": null,
+          ]
+        },
+        toState: { id, result, state ->
+          state + [ "output_falco" : result.outdir ]
+        },
+      )
+      | multiqc.run(
+        fromState: {id, state ->
+          [
+            "input": [
+              state.output_falco,
+              state.interop_run_summary.getParent(),
+              state.interop_index_summary.getParent()
+            ],
+            "output_report": state.output_multiqc,
+            "cl_config": 'sp: {fastqc/data: {fn: "*_fastqc_data.txt"}}',
+          ]
+        },
+        toState: { id, result, state ->
+          state + [ "output_multiqc" : result.output_report ]
+        },
+      )
+      | setState(
+        [
+          "output": "output_bclconvert",
+          "output_falco": "output_falco",
+          "output_multiqc": "output_multiqc"
+        ]
+      )
 
   emit:
     output_ch
diff --git a/src/demultiplex/test.nf b/src/demultiplex/test.nf
index 51a5e03..c46a438 100644
--- a/src/demultiplex/test.nf
+++ b/src/demultiplex/test.nf
@@ -7,7 +7,7 @@ workflow test_wf {
         [
           // sample_sheet: resources_test.resolve("bcl_convert_samplesheet.csv"),
           // input: resources_test.resolve("iseq-DI/"),
-          sample_sheet: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/SampleSheet.csv",
+          //sample_sheet: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/SampleSheet.csv",
           input: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz",
           publish_dir: "output_dir/",
         ]
@@ -21,4 +21,9 @@ workflow test_wf {
         assert output.size() == 2 : "outputs should contain two elements; [id, file]"
         "Output: $output"
       }
+    | map {id, state ->
+      assert state.output.isDirectory(): "Expected bclconvert output to be a directory"
+      assert state.output_falco.isDirectory(): "Expected falco output to be a directory"
+      assert state.output_multiqc.isFile(): "Expected multiQC output to be a file"
+    }
 }
diff --git a/src/io/interop_summary_to_csv/config.vsh.yaml b/src/io/interop_summary_to_csv/config.vsh.yaml
new file mode 100644
index 0000000..2d74808
--- /dev/null
+++ b/src/io/interop_summary_to_csv/config.vsh.yaml
@@ -0,0 +1,41 @@
+name: interop_summary_to_csv
+namespace: io
+argument_groups:
+  - name: Input arguments
+    arguments:
+      - name: --input
+        description: Sequencing run folder (*not* InterOp folder).
+        type: file
+        required: true
+  - name: Output arguments
+    arguments:
+      - name: --output_run_summary
+        type: file
+        direction: output
+        required: true
+      - name: --output_index_summary
+        type: file
+        direction: output
+        required: true
+requirements:
+  - commands: ["summary", "index-summary"]
+resources:
+  - type: bash_script
+    path: script.sh
+engines:
+  - type: docker
+    image: debian:stable-slim
+    setup:
+      - type: apt
+        packages:
+          - procps
+          - wget
+      - type: docker
+        run: |
+          wget https://github.com/Illumina/interop/releases/download/v1.3.1/interop-1.3.1-Linux-GNU.tar.gz -O /tmp/interop.tar.gz && \
+          tar -C /tmp/ --no-same-owner --no-same-permissions -xvf /tmp/interop.tar.gz && \
+          mv /tmp/interop-1.3.1-Linux-GNU/bin/index-summary /tmp/interop-1.3.1-Linux-GNU/bin/summary /usr/local/bin/
+
+runners:
+  - type: executable
+  - type: nextflow
\ No newline at end of file
diff --git a/src/io/interop_summary_to_csv/script.sh b/src/io/interop_summary_to_csv/script.sh
new file mode 100644
index 0000000..e4a37fb
--- /dev/null
+++ b/src/io/interop_summary_to_csv/script.sh
@@ -0,0 +1,10 @@
+#!/usr/bin/env bash
+
+set -eo pipefail
+
+if [ ! -d "$par_input" ]; then
+    echo "Input directory does not exist or is not a directory"
+    exit 1
+fi
+$(which summary) --csv=1 "$par_input" 1> "$par_output_run_summary"
+$(which index-summary) --csv=1 "$par_input" 1> "$par_output_index_summary"