diff --git a/src/runner/main.nf b/src/runner/main.nf
index 731d11d..65f305e 100644
--- a/src/runner/main.nf
+++ b/src/runner/main.nf
@@ -9,6 +9,17 @@ workflow run_wf {
 
   main:
     output_ch = input_ch
+      | map { id, state -> 
+        // The argument names for this workflow and the demultiplex workflow may overlap
+        // here, we store a copy in order to make sure to not accidentally overwrite the state.
+        def new_state = state + [
+          "fastq_output_workflow": state.fastq_output,
+          "multiqc_output_workflow": state.multiqc_output,
+          "sample_qc_output_workflow": state.sample_qc_output,
+          "demultiplexer_logs_workflow": state.demultiplexer_logs,
+        ]
+        return [id, new_state]
+      }
       // Extract the ID from the input.
       // If the input is a tarball, strip the suffix.
       | map{ id, state ->
@@ -45,17 +56,16 @@ workflow run_wf {
           def id1 = (state.plain_output) ? id : "${state.run_id}/${date}"
           def id2 = (state.plain_output) ? id : "${id1}_demultiplex_${version}"
 
-          def fastq_output_1 = (id2 == "run") ? state.fastq_output : "${id2}/" + state.fastq_output
-          def sample_qc_output_1 = (id2 == "run") ? state.sample_qc_output : "${id2}/" + state.sample_qc_output
-          def multiqc_output_1 = (id2 == "run") ? state.multiqc_output : "${id2}/" + state.multiqc_output
-          def run_information_output_1 = (id2 == "run") ? "${state.output_run_information.getName()}" : "${id2}/${state.output_run_information.getName()}"
-          def demultiplexer_logs_output = (id2 == "run") ? state.demultiplexer_logs : "${id2}/${state.demultiplexer_logs.getName()}"
+          def prefix = (id2 == "run") ? "" : "${id2}/"
+          // These output names are determined by arguments.
+          def fastq_output_1 = "${prefix}${state.fastq_output_workflow}"
+          def sample_qc_output_1 = "${prefix}${state.sample_qc_output_workflow}"
+          def multiqc_output_1 = "${prefix}${state.multiqc_output_workflow}"
+          def demultiplexer_logs_output = "${prefix}${state.demultiplexer_logs_workflow}"
+          // The name of the output file for the run information is determined by the input file name.
+          def run_information_output_1 = "${prefix}${state.output_run_information.getName()}"
 
-          if (id2 == "run") {
-            println("Publising to ${params.publish_dir}")
-          } else {
-            println("Publising to ${params.publish_dir}/${id2}")
-          }
+          println("Publising to ${params.publish_dir}/${prefix}")
 
           [
             input: state.output,
diff --git a/src/runner/test.nf b/src/runner/test.nf
index fce5e39..6bbb2ff 100644
--- a/src/runner/test.nf
+++ b/src/runner/test.nf
@@ -1,25 +1,31 @@
 import java.nio.file.Files
+import nextflow.exception.WorkflowScriptErrorException
 
-// Create temporary directory
-def tempDir = Files.createTempDirectory("demultiplex_runner_integration_test")
-println "Created temp directory: $tempDir"
-// Register shutdown hook to delete it on JVM exit
-Runtime.runtime.addShutdownHook(new Thread({
-    try {
-        // Delete directory recursively
-        Files.walk(tempDir)
-            .sorted(Comparator.reverseOrder())
-            .forEach { Files.delete(it) }
-        println "Deleted temp directory: $tempDir"
-    } catch (Exception e) {
-        println "Failed to delete temp directory: $e"
-    }
-}))
+// Create temporary directory for the publish_dir if it is not defined
+if (!params.publish_dir && params.publishDir) {
+    params.publish_dir = params.publishDir
+}
 
+if (!params.publish_dir) {
+    def tempDir = Files.createTempDirectory("demultiplex_runner_integration_test")
+    println "Created temp directory: $tempDir"
+    // Register shutdown hook to delete it on JVM exit
+    Runtime.runtime.addShutdownHook(new Thread({
+        try {
+            // Delete directory recursively
+            Files.walk(tempDir)
+                .sorted(Comparator.reverseOrder())
+                .forEach { Files.delete(it) }
+            println "Deleted temp directory: $tempDir"
+        } catch (Exception e) {
+            println "Failed to delete temp directory: $e"
+        }
+    }))
+    params.publish_dir = tempDir
+}
 // The module inherits the parameters defined before the include statement, 
 // therefore any parameters set afterwards will not be used by the module.
 
-params.publish_dir = tempDir
 include { runner } from params.rootDir + "/target/nextflow/runner/main.nf"
 params.resources_test = params.rootDir + "/testData/"
 
@@ -35,41 +41,51 @@ workflow test {
         fromState: {id, state -> state }
     )
     workflow.onComplete = {
-        def all_files = file("${tempDir}/200624_A00834_0183_BHMTFYDRXX").listFiles()
-        assert all_files.size() == 1
-        def publish_dir = file(all_files[0])
-        assert publish_dir.name.endsWith("_demultiplex_unknown_version")
-        def published_items = publish_dir.listFiles()
-        assert published_items.size() == 4
-        assert published_items.collect{it.name}.toSet() == ["demultiplexer_logs", "fastq", "qc", "SampleSheet.csv"].toSet()
-        def fastqc_files = publish_dir.resolve("qc/fastqc").listFiles()
-        assert fastqc_files.collect{it.name}.toSet() == [
-            "Sample1_S1_L001_R1_001_fastqc_data.txt",
-            "Sample1_S1_L001_R1_001_fastqc_report.html",
-            "Sample1_S1_L001_R1_001_summary.txt",
-            "Sample23_S3_L001_R1_001_fastqc_data.txt",
-            "Sample23_S3_L001_R1_001_fastqc_report.html",
-            "Sample23_S3_L001_R1_001_summary.txt",
-            "SampleA_S2_L001_R1_001_fastqc_data.txt",
-            "SampleA_S2_L001_R1_001_fastqc_report.html",
-            "SampleA_S2_L001_R1_001_summary.txt",
-            "sampletest_S4_L001_R1_001_fastqc_data.txt",
-            "sampletest_S4_L001_R1_001_fastqc_report.html",
-            "sampletest_S4_L001_R1_001_summary.txt",
-            "Undetermined_S0_L001_R1_001_fastqc_data.txt",
-            "Undetermined_S0_L001_R1_001_fastqc_report.html",
-            "Undetermined_S0_L001_R1_001_summary.txt"
-        ].toSet()
-        assert publish_dir.resolve("qc/multiqc_report.html").exists()
-        def fastq_files = publish_dir.resolve("fastq").listFiles()
-        fastq_files.collect{it.name}.toSet() == [
-            "Sample1_S1_L001_R1_001.fastq.gz",
-            "Sample23_S3_L001_R1_001.fastq.gz",
-            "SampleA_S2_L001_R1_001.fastq.gz",
-            "sampletest_S4_L001_R1_001.fastq.gz",
-            "Undetermined_S0_L001_R1_001.fastq.gz"
-        ].toSet()
-        assert publish_dir.resolve("SampleSheet.csv").exists()
+        try {
+            // Nexflow only allows exceptions generated using the 'error' function (which throws WorkflowScriptErrorException).
+            // So in order for the assert statement to work (or allow other errors to let the tests to fail)
+            // We need to wrap these in WorkflowScriptErrorException. See https://github.com/nextflow-io/nextflow/pull/4458/files
+            // The error message will show up in .nextflow.log
+            def publish_subdir = file("${params.publish_dir}/200624_A00834_0183_BHMTFYDRXX")
+            assert publish_subdir.isDirectory() 
+            def all_files = publish_subdir.listFiles()
+            assert all_files.size() == 1
+            def publish_dir = file(all_files[0])
+            assert publish_dir.name.endsWith("_demultiplex_unknown_version")
+            def published_items = publish_dir.listFiles()
+            assert published_items.size() == 4
+            assert published_items.collect{it.name}.toSet() == ["demultiplexer_logs", "fastq", "qc", "SampleSheet.csv"].toSet()
+            def fastqc_files = publish_dir.resolve("qc/fastqc").listFiles()
+            assert fastqc_files.collect{it.name}.toSet() == [
+                "Sample1_S1_L001_R1_001_fastqc_data.txt",
+                "Sample1_S1_L001_R1_001_fastqc_report.html",
+                "Sample1_S1_L001_R1_001_summary.txt",
+                "Sample23_S3_L001_R1_001_fastqc_data.txt",
+                "Sample23_S3_L001_R1_001_fastqc_report.html",
+                "Sample23_S3_L001_R1_001_summary.txt",
+                "SampleA_S2_L001_R1_001_fastqc_data.txt",
+                "SampleA_S2_L001_R1_001_fastqc_report.html",
+                "SampleA_S2_L001_R1_001_summary.txt",
+                "sampletest_S4_L001_R1_001_fastqc_data.txt",
+                "sampletest_S4_L001_R1_001_fastqc_report.html",
+                "sampletest_S4_L001_R1_001_summary.txt",
+                "Undetermined_S0_L001_R1_001_fastqc_data.txt",
+                "Undetermined_S0_L001_R1_001_fastqc_report.html",
+                "Undetermined_S0_L001_R1_001_summary.txt"
+            ].toSet()
+            assert publish_dir.resolve("qc/multiqc_report.html").exists()
+            def fastq_files = publish_dir.resolve("fastq").listFiles()
+            assert fastq_files.collect{it.name}.toSet() == [
+                "Sample1_S1_L001_R1_001.fastq.gz",
+                "Sample23_S3_L001_R1_001.fastq.gz",
+                "SampleA_S2_L001_R1_001.fastq.gz",
+                "sampletest_S4_L001_R1_001.fastq.gz",
+                "Undetermined_S0_L001_R1_001.fastq.gz"
+            ].toSet()
+            assert publish_dir.resolve("SampleSheet.csv").exists()
+        } catch (Exception e) {
+            throw new WorkflowScriptErrorException("Integration test failed!", e)
+        }
     }
 
 }
diff --git a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
index c27bcff..9eb0147 100644
--- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
@@ -157,9 +157,9 @@ build_info:
   output: "target/executable/io/interop_summary_to_csv"
   executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
   viash_version: "0.9.4"
-  git_commit: "b964c6be513b030c07afa48bfd3e4e6bb80644ed"
+  git_commit: "05f865da660a3eb3ada0d4a15c515afdcfe8c087"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-35-gb964c6b"
+  git_tag: "v0.1.1-39-g05f865d"
 package_config:
   name: "demultiplex"
   version: "replace_falco_with_fastqc"
diff --git a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
index ad9fa74..d5b716c 100755
--- a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
+++ b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
@@ -454,9 +454,9 @@ 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/
 
 LABEL org.opencontainers.image.description="Companion container for running component io interop_summary_to_csv"
-LABEL org.opencontainers.image.created="2025-05-27T20:00:48Z"
+LABEL org.opencontainers.image.created="2025-05-28T09:38:56Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="b964c6be513b030c07afa48bfd3e4e6bb80644ed"
+LABEL org.opencontainers.image.revision="05f865da660a3eb3ada0d4a15c515afdcfe8c087"
 LABEL org.opencontainers.image.version="replace_falco_with_fastqc"
 
 VIASHDOCKER
diff --git a/target/executable/io/publish/.config.vsh.yaml b/target/executable/io/publish/.config.vsh.yaml
index cea87fe..8636f5b 100644
--- a/target/executable/io/publish/.config.vsh.yaml
+++ b/target/executable/io/publish/.config.vsh.yaml
@@ -219,9 +219,9 @@ build_info:
   output: "target/executable/io/publish"
   executable: "target/executable/io/publish/publish"
   viash_version: "0.9.4"
-  git_commit: "b964c6be513b030c07afa48bfd3e4e6bb80644ed"
+  git_commit: "05f865da660a3eb3ada0d4a15c515afdcfe8c087"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-35-gb964c6b"
+  git_tag: "v0.1.1-39-g05f865d"
 package_config:
   name: "demultiplex"
   version: "replace_falco_with_fastqc"
diff --git a/target/executable/io/publish/publish b/target/executable/io/publish/publish
index 6ebac80..badf08f 100755
--- a/target/executable/io/publish/publish
+++ b/target/executable/io/publish/publish
@@ -450,9 +450,9 @@ RUN apt-get update && \
   rm -rf /var/lib/apt/lists/*
 
 LABEL org.opencontainers.image.description="Companion container for running component io publish"
-LABEL org.opencontainers.image.created="2025-05-27T20:00:48Z"
+LABEL org.opencontainers.image.created="2025-05-28T09:38:55Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="b964c6be513b030c07afa48bfd3e4e6bb80644ed"
+LABEL org.opencontainers.image.revision="05f865da660a3eb3ada0d4a15c515afdcfe8c087"
 LABEL org.opencontainers.image.version="replace_falco_with_fastqc"
 
 VIASHDOCKER
diff --git a/target/executable/io/untar/.config.vsh.yaml b/target/executable/io/untar/.config.vsh.yaml
index 820137a..e955bd9 100644
--- a/target/executable/io/untar/.config.vsh.yaml
+++ b/target/executable/io/untar/.config.vsh.yaml
@@ -156,9 +156,9 @@ build_info:
   output: "target/executable/io/untar"
   executable: "target/executable/io/untar/untar"
   viash_version: "0.9.4"
-  git_commit: "b964c6be513b030c07afa48bfd3e4e6bb80644ed"
+  git_commit: "05f865da660a3eb3ada0d4a15c515afdcfe8c087"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-35-gb964c6b"
+  git_tag: "v0.1.1-39-g05f865d"
 package_config:
   name: "demultiplex"
   version: "replace_falco_with_fastqc"
diff --git a/target/executable/io/untar/untar b/target/executable/io/untar/untar
index be21633..5422a40 100755
--- a/target/executable/io/untar/untar
+++ b/target/executable/io/untar/untar
@@ -450,9 +450,9 @@ RUN apt-get update && \
   rm -rf /var/lib/apt/lists/*
 
 LABEL org.opencontainers.image.description="Companion container for running component io untar"
-LABEL org.opencontainers.image.created="2025-05-27T20:00:48Z"
+LABEL org.opencontainers.image.created="2025-05-28T09:38:55Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="b964c6be513b030c07afa48bfd3e4e6bb80644ed"
+LABEL org.opencontainers.image.revision="05f865da660a3eb3ada0d4a15c515afdcfe8c087"
 LABEL org.opencontainers.image.version="replace_falco_with_fastqc"
 
 VIASHDOCKER
diff --git a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
index 8b306ad..9f30a5f 100644
--- a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
+++ b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
@@ -165,9 +165,9 @@ build_info:
   output: "target/nextflow/dataflow/combine_samples"
   executable: "target/nextflow/dataflow/combine_samples/main.nf"
   viash_version: "0.9.4"
-  git_commit: "b964c6be513b030c07afa48bfd3e4e6bb80644ed"
+  git_commit: "05f865da660a3eb3ada0d4a15c515afdcfe8c087"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-35-gb964c6b"
+  git_tag: "v0.1.1-39-g05f865d"
 package_config:
   name: "demultiplex"
   version: "replace_falco_with_fastqc"
diff --git a/target/nextflow/dataflow/combine_samples/main.nf b/target/nextflow/dataflow/combine_samples/main.nf
index 8dd5caa..5550dfc 100644
--- a/target/nextflow/dataflow/combine_samples/main.nf
+++ b/target/nextflow/dataflow/combine_samples/main.nf
@@ -3230,9 +3230,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/dataflow/combine_samples",
     "viash_version" : "0.9.4",
-    "git_commit" : "b964c6be513b030c07afa48bfd3e4e6bb80644ed",
+    "git_commit" : "05f865da660a3eb3ada0d4a15c515afdcfe8c087",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-35-gb964c6b"
+    "git_tag" : "v0.1.1-39-g05f865d"
   },
   "package_config" : {
     "name" : "demultiplex",
diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
index ac57e5b..4d98dde 100644
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
@@ -156,9 +156,9 @@ build_info:
   output: "target/nextflow/dataflow/gather_fastqs_and_validate"
   executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
   viash_version: "0.9.4"
-  git_commit: "b964c6be513b030c07afa48bfd3e4e6bb80644ed"
+  git_commit: "05f865da660a3eb3ada0d4a15c515afdcfe8c087"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-35-gb964c6b"
+  git_tag: "v0.1.1-39-g05f865d"
 package_config:
   name: "demultiplex"
   version: "replace_falco_with_fastqc"
diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
index 79efc8b..95b6b78 100644
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
@@ -3227,9 +3227,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
     "viash_version" : "0.9.4",
-    "git_commit" : "b964c6be513b030c07afa48bfd3e4e6bb80644ed",
+    "git_commit" : "05f865da660a3eb3ada0d4a15c515afdcfe8c087",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-35-gb964c6b"
+    "git_tag" : "v0.1.1-39-g05f865d"
   },
   "package_config" : {
     "name" : "demultiplex",
diff --git a/target/nextflow/demultiplex/.config.vsh.yaml b/target/nextflow/demultiplex/.config.vsh.yaml
index 1c6242a..a1a5a0d 100644
--- a/target/nextflow/demultiplex/.config.vsh.yaml
+++ b/target/nextflow/demultiplex/.config.vsh.yaml
@@ -262,9 +262,9 @@ build_info:
   output: "target/nextflow/demultiplex"
   executable: "target/nextflow/demultiplex/main.nf"
   viash_version: "0.9.4"
-  git_commit: "b964c6be513b030c07afa48bfd3e4e6bb80644ed"
+  git_commit: "05f865da660a3eb3ada0d4a15c515afdcfe8c087"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-35-gb964c6b"
+  git_tag: "v0.1.1-39-g05f865d"
   dependencies:
   - "target/nextflow/io/untar"
   - "target/nextflow/dataflow/gather_fastqs_and_validate"
diff --git a/target/nextflow/demultiplex/main.nf b/target/nextflow/demultiplex/main.nf
index 4d00e68..564903e 100644
--- a/target/nextflow/demultiplex/main.nf
+++ b/target/nextflow/demultiplex/main.nf
@@ -3369,9 +3369,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/demultiplex",
     "viash_version" : "0.9.4",
-    "git_commit" : "b964c6be513b030c07afa48bfd3e4e6bb80644ed",
+    "git_commit" : "05f865da660a3eb3ada0d4a15c515afdcfe8c087",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-35-gb964c6b"
+    "git_tag" : "v0.1.1-39-g05f865d"
   },
   "package_config" : {
     "name" : "demultiplex",
diff --git a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
index 89ec11c..a1b8278 100644
--- a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
@@ -157,9 +157,9 @@ build_info:
   output: "target/nextflow/io/interop_summary_to_csv"
   executable: "target/nextflow/io/interop_summary_to_csv/main.nf"
   viash_version: "0.9.4"
-  git_commit: "b964c6be513b030c07afa48bfd3e4e6bb80644ed"
+  git_commit: "05f865da660a3eb3ada0d4a15c515afdcfe8c087"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-35-gb964c6b"
+  git_tag: "v0.1.1-39-g05f865d"
 package_config:
   name: "demultiplex"
   version: "replace_falco_with_fastqc"
diff --git a/target/nextflow/io/interop_summary_to_csv/main.nf b/target/nextflow/io/interop_summary_to_csv/main.nf
index 1997839..c8c13b1 100644
--- a/target/nextflow/io/interop_summary_to_csv/main.nf
+++ b/target/nextflow/io/interop_summary_to_csv/main.nf
@@ -3228,9 +3228,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/interop_summary_to_csv",
     "viash_version" : "0.9.4",
-    "git_commit" : "b964c6be513b030c07afa48bfd3e4e6bb80644ed",
+    "git_commit" : "05f865da660a3eb3ada0d4a15c515afdcfe8c087",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-35-gb964c6b"
+    "git_tag" : "v0.1.1-39-g05f865d"
   },
   "package_config" : {
     "name" : "demultiplex",
diff --git a/target/nextflow/io/publish/.config.vsh.yaml b/target/nextflow/io/publish/.config.vsh.yaml
index 7de5eb8..b390876 100644
--- a/target/nextflow/io/publish/.config.vsh.yaml
+++ b/target/nextflow/io/publish/.config.vsh.yaml
@@ -219,9 +219,9 @@ build_info:
   output: "target/nextflow/io/publish"
   executable: "target/nextflow/io/publish/main.nf"
   viash_version: "0.9.4"
-  git_commit: "b964c6be513b030c07afa48bfd3e4e6bb80644ed"
+  git_commit: "05f865da660a3eb3ada0d4a15c515afdcfe8c087"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-35-gb964c6b"
+  git_tag: "v0.1.1-39-g05f865d"
 package_config:
   name: "demultiplex"
   version: "replace_falco_with_fastqc"
diff --git a/target/nextflow/io/publish/main.nf b/target/nextflow/io/publish/main.nf
index b5ed540..2de7bf9 100644
--- a/target/nextflow/io/publish/main.nf
+++ b/target/nextflow/io/publish/main.nf
@@ -3297,9 +3297,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/publish",
     "viash_version" : "0.9.4",
-    "git_commit" : "b964c6be513b030c07afa48bfd3e4e6bb80644ed",
+    "git_commit" : "05f865da660a3eb3ada0d4a15c515afdcfe8c087",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-35-gb964c6b"
+    "git_tag" : "v0.1.1-39-g05f865d"
   },
   "package_config" : {
     "name" : "demultiplex",
diff --git a/target/nextflow/io/untar/.config.vsh.yaml b/target/nextflow/io/untar/.config.vsh.yaml
index 4d3a13c..5bf585e 100644
--- a/target/nextflow/io/untar/.config.vsh.yaml
+++ b/target/nextflow/io/untar/.config.vsh.yaml
@@ -156,9 +156,9 @@ build_info:
   output: "target/nextflow/io/untar"
   executable: "target/nextflow/io/untar/main.nf"
   viash_version: "0.9.4"
-  git_commit: "b964c6be513b030c07afa48bfd3e4e6bb80644ed"
+  git_commit: "05f865da660a3eb3ada0d4a15c515afdcfe8c087"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-35-gb964c6b"
+  git_tag: "v0.1.1-39-g05f865d"
 package_config:
   name: "demultiplex"
   version: "replace_falco_with_fastqc"
diff --git a/target/nextflow/io/untar/main.nf b/target/nextflow/io/untar/main.nf
index 5116cb0..80c4578 100644
--- a/target/nextflow/io/untar/main.nf
+++ b/target/nextflow/io/untar/main.nf
@@ -3227,9 +3227,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/untar",
     "viash_version" : "0.9.4",
-    "git_commit" : "b964c6be513b030c07afa48bfd3e4e6bb80644ed",
+    "git_commit" : "05f865da660a3eb3ada0d4a15c515afdcfe8c087",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-35-gb964c6b"
+    "git_tag" : "v0.1.1-39-g05f865d"
   },
   "package_config" : {
     "name" : "demultiplex",
diff --git a/target/nextflow/runner/.config.vsh.yaml b/target/nextflow/runner/.config.vsh.yaml
index caa700c..9d70acc 100644
--- a/target/nextflow/runner/.config.vsh.yaml
+++ b/target/nextflow/runner/.config.vsh.yaml
@@ -211,9 +211,9 @@ build_info:
   output: "target/nextflow/runner"
   executable: "target/nextflow/runner/main.nf"
   viash_version: "0.9.4"
-  git_commit: "b964c6be513b030c07afa48bfd3e4e6bb80644ed"
+  git_commit: "05f865da660a3eb3ada0d4a15c515afdcfe8c087"
   git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-35-gb964c6b"
+  git_tag: "v0.1.1-39-g05f865d"
   dependencies:
   - "target/nextflow/demultiplex"
   - "target/nextflow/io/publish"
diff --git a/target/nextflow/runner/main.nf b/target/nextflow/runner/main.nf
index fa7edd7..7069179 100644
--- a/target/nextflow/runner/main.nf
+++ b/target/nextflow/runner/main.nf
@@ -3291,9 +3291,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/runner",
     "viash_version" : "0.9.4",
-    "git_commit" : "b964c6be513b030c07afa48bfd3e4e6bb80644ed",
+    "git_commit" : "05f865da660a3eb3ada0d4a15c515afdcfe8c087",
     "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-35-gb964c6b"
+    "git_tag" : "v0.1.1-39-g05f865d"
   },
   "package_config" : {
     "name" : "demultiplex",
@@ -3350,6 +3350,17 @@ workflow run_wf {
 
   main:
     output_ch = input_ch
+      | map { id, state -> 
+        // The argument names for this workflow and the demultiplex workflow may overlap
+        // here, we store a copy in order to make sure to not accidentally overwrite the state.
+        def new_state = state + [
+          "fastq_output_workflow": state.fastq_output,
+          "multiqc_output_workflow": state.multiqc_output,
+          "sample_qc_output_workflow": state.sample_qc_output,
+          "demultiplexer_logs_workflow": state.demultiplexer_logs,
+        ]
+        return [id, new_state]
+      }
       // Extract the ID from the input.
       // If the input is a tarball, strip the suffix.
       | map{ id, state ->
@@ -3386,17 +3397,16 @@ workflow run_wf {
           def id1 = (state.plain_output) ? id : "${state.run_id}/${date}"
           def id2 = (state.plain_output) ? id : "${id1}_demultiplex_${version}"
 
-          def fastq_output_1 = (id2 == "run") ? state.fastq_output : "${id2}/" + state.fastq_output
-          def sample_qc_output_1 = (id2 == "run") ? state.sample_qc_output : "${id2}/" + state.sample_qc_output
-          def multiqc_output_1 = (id2 == "run") ? state.multiqc_output : "${id2}/" + state.multiqc_output
-          def run_information_output_1 = (id2 == "run") ? "${state.output_run_information.getName()}" : "${id2}/${state.output_run_information.getName()}"
-          def demultiplexer_logs_output = (id2 == "run") ? state.demultiplexer_logs : "${id2}/${state.demultiplexer_logs.getName()}"
+          def prefix = (id2 == "run") ? "" : "${id2}/"
+          // These output names are determined by arguments.
+          def fastq_output_1 = "${prefix}${state.fastq_output_workflow}"
+          def sample_qc_output_1 = "${prefix}${state.sample_qc_output_workflow}"
+          def multiqc_output_1 = "${prefix}${state.multiqc_output_workflow}"
+          def demultiplexer_logs_output = "${prefix}${state.demultiplexer_logs_workflow}"
+          // The name of the output file for the run information is determined by the input file name.
+          def run_information_output_1 = "${prefix}${state.output_run_information.getName()}"
 
-          if (id2 == "run") {
-            println("Publising to ${params.publish_dir}")
-          } else {
-            println("Publising to ${params.publish_dir}/${id2}")
-          }
+          println("Publising to ${params.publish_dir}/${prefix}")
 
           [
             input: state.output,