Build branch runner_multiple_input_directories with version runner_multiple_input_directories (ed94807)

Build pipeline: viash-hub.htrnaseq.runner-multiple-input-directories-z22c4 Source commit: ed9480768e Source message: Fix lanes
2025-02-13 12:35:46 +00:00
parent 0477efa887
commit caa6cec4e2
62 changed files with 145 additions and 98 deletions
--- a/src/utils/listInputDir/config.vsh.yaml
+++ b/src/utils/listInputDir/config.vsh.yaml
@@ -24,6 +24,10 @@ arguments:
    type: string
    description: Sample nr
    direction: output
+  - name: "--sample_id"
+    type: string
+    description: Sample name
+    direction: output

 resources:
  - type: nextflow_script
--- a/src/utils/listInputDir/main.nf
+++ b/src/utils/listInputDir/main.nf
@@ -18,7 +18,7 @@ workflow run_wf {

        println("Extracting information from fastq/fasta filenames")
        def processed_fastqs = allFastqs.collect { f ->
-          def regex = ~/^(\w+)_S(\d+)_(L(\d+)_)?R(\d)_(\d+)\.fast[qa](\.gz)?$/
+          def regex = ~/^(\w+)_S(\d+)_(L(\d+))_?R(\d)_(\d+)\.fast[qa](\.gz)?$/
          def validFastq = f.name ==~ regex

          assert validFastq: "${f} does not match the regex ${regex}"
@@ -36,20 +36,27 @@ workflow run_wf {

        println("Group paired fastq/fasta files")
        def grouped = processed_fastqs
-          .groupBy({it.sample_id})
-          .collect{ k, vs ->
-            def r1 = vs.find{it.read == "1"}
-            def r2 = vs.find{it.read == "2"}
-            def newState = [
-              r1_output: r1.fastq,
-              r2_output: r2.fastq
-            ]
-            def updtState = newState + vs[0].findAll{ it.key in ["sample", "lane"] }
-            return [k, updtState]
-          }
+          .groupBy({it.sample_id}, {it.lane})
+          .collectMany{ sample_id, states_per_lane ->
+            def result = states_per_lane.collect{lane, lane_states ->
+              assert lane_states.size() == 2, "Expected to find two fastq files per lane! " +
+                "Found ${lane_states.size()}. State: ${states_per_lane}"
+              def r1_state = lane_states.find({it.read == "1"})
+              def r2_state = lane_states.find({it.read == "2"})
+              def fastq_state = [
+                "r1_output": r1_state.fastq,
+                "r2_output": r2_state.fastq
+              ]
+              def new_state = fastq_state +
+                r1_state.findAll{it.key in ["sample_id", "sample", "lane"]} + 
+                ["_meta": ["join_id": id]]
+              return ["${sample_id}_${lane}".toString(), new_state]
+            }
+            return result
+
+          }
+          return grouped

-        grouped
-          .collect{ [ it[0], it[1] + [ _meta: [ join_id: id ] ] ] }
      }

  emit: out_
--- a/src/workflows/runner/main.nf
+++ b/src/workflows/runner/main.nf
@@ -35,6 +35,7 @@ workflow run_wf {
      // there might be multiple FASTQs for a single sample that correspond to the
      // lanes. So the fastq files must be gathered across lanes and input folders
      // in order to create an input lists for R1 and R2.
+      | map {id, state -> [state.sample_id, state]}
      | groupTuple(by: 0, sort: { state1, state2 ->
        if (state1.index == state2.index) {
          return state1.lane <=> state2.lane
--- a/target/executable/eset/create_eset/.config.vsh.yaml
+++ b/target/executable/eset/create_eset/.config.vsh.yaml
@@ -198,7 +198,7 @@ build_info:
  output: "target/executable/eset/create_eset"
  executable: "target/executable/eset/create_eset/create_eset"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/eset/create_eset/create_eset
+++ b/target/executable/eset/create_eset/create_eset
@@ -477,9 +477,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag

 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_eset"
-LABEL org.opencontainers.image.created="2025-02-13T08:19:03Z"
+LABEL org.opencontainers.image.created="2025-02-13T11:46:10Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59"
 LABEL org.opencontainers.image.version="runner_multiple_input_directories"

 VIASHDOCKER
--- a/target/executable/eset/create_fdata/.config.vsh.yaml
+++ b/target/executable/eset/create_fdata/.config.vsh.yaml
@@ -177,7 +177,7 @@ build_info:
  output: "target/executable/eset/create_fdata"
  executable: "target/executable/eset/create_fdata/create_fdata"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/eset/create_fdata/create_fdata
+++ b/target/executable/eset/create_fdata/create_fdata
@@ -478,9 +478,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_fdata"
-LABEL org.opencontainers.image.created="2025-02-13T08:19:03Z"
+LABEL org.opencontainers.image.created="2025-02-13T11:46:11Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59"
 LABEL org.opencontainers.image.version="runner_multiple_input_directories"

 VIASHDOCKER
--- a/target/executable/eset/create_pdata/.config.vsh.yaml
+++ b/target/executable/eset/create_pdata/.config.vsh.yaml
@@ -191,7 +191,7 @@ build_info:
  output: "target/executable/eset/create_pdata"
  executable: "target/executable/eset/create_pdata/create_pdata"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/eset/create_pdata/create_pdata
+++ b/target/executable/eset/create_pdata/create_pdata
@@ -488,9 +488,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_pdata"
-LABEL org.opencontainers.image.created="2025-02-13T08:19:03Z"
+LABEL org.opencontainers.image.created="2025-02-13T11:46:10Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59"
 LABEL org.opencontainers.image.version="runner_multiple_input_directories"

 VIASHDOCKER
--- a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
+++ b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
@@ -148,7 +148,7 @@ build_info:
  output: "target/executable/integration_test_components/htrnaseq/check_eset"
  executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
+++ b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
@@ -470,9 +470,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag

 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/htrnaseq check_eset"
-LABEL org.opencontainers.image.created="2025-02-13T08:19:03Z"
+LABEL org.opencontainers.image.created="2025-02-13T11:46:11Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59"
 LABEL org.opencontainers.image.version="runner_multiple_input_directories"

 VIASHDOCKER
--- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
+++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
@@ -158,7 +158,7 @@ build_info:
  output: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output"
  executable: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output
+++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output
@@ -476,9 +476,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/well_demultiplexing check_cutadapt_output"
-LABEL org.opencontainers.image.created="2025-02-13T08:19:03Z"
+LABEL org.opencontainers.image.created="2025-02-13T11:46:10Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59"
 LABEL org.opencontainers.image.version="runner_multiple_input_directories"

 VIASHDOCKER
--- a/target/executable/io/publish_fastqs/.config.vsh.yaml
+++ b/target/executable/io/publish_fastqs/.config.vsh.yaml
@@ -143,7 +143,7 @@ build_info:
  output: "target/executable/io/publish_fastqs"
  executable: "target/executable/io/publish_fastqs/publish_fastqs"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/io/publish_fastqs/publish_fastqs
+++ b/target/executable/io/publish_fastqs/publish_fastqs
@@ -470,9 +470,9 @@ RUN apt-get update && \
  rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.description="Companion container for running component io publish_fastqs"
-LABEL org.opencontainers.image.created="2025-02-13T08:19:01Z"
+LABEL org.opencontainers.image.created="2025-02-13T11:46:09Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59"
 LABEL org.opencontainers.image.version="runner_multiple_input_directories"

 VIASHDOCKER
--- a/target/executable/io/publish_results/.config.vsh.yaml
+++ b/target/executable/io/publish_results/.config.vsh.yaml
@@ -187,7 +187,7 @@ build_info:
  output: "target/executable/io/publish_results"
  executable: "target/executable/io/publish_results/publish_results"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/io/publish_results/publish_results
+++ b/target/executable/io/publish_results/publish_results
@@ -484,9 +484,9 @@ RUN apt-get update && \
  rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.description="Companion container for running component io publish_results"
-LABEL org.opencontainers.image.created="2025-02-13T08:19:02Z"
+LABEL org.opencontainers.image.created="2025-02-13T11:46:09Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59"
 LABEL org.opencontainers.image.version="runner_multiple_input_directories"

 VIASHDOCKER
--- a/target/executable/parallel_map/.config.vsh.yaml
+++ b/target/executable/parallel_map/.config.vsh.yaml
@@ -279,7 +279,7 @@ build_info:
  output: "target/executable/parallel_map"
  executable: "target/executable/parallel_map/parallel_map"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/parallel_map/parallel_map
+++ b/target/executable/parallel_map/parallel_map
@@ -540,9 +540,9 @@ ENV STAR_BINARY=STAR
 COPY STAR /usr/local/bin/$STAR_BINARY
 LABEL org.opencontainers.image.authors="Dries Schaumont, Toni Verbeiren"
 LABEL org.opencontainers.image.description="Companion container for running component parallel_map"
-LABEL org.opencontainers.image.created="2025-02-13T08:19:04Z"
+LABEL org.opencontainers.image.created="2025-02-13T11:46:11Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59"
 LABEL org.opencontainers.image.version="runner_multiple_input_directories"

 VIASHDOCKER
--- a/target/executable/report/create_report/.config.vsh.yaml
+++ b/target/executable/report/create_report/.config.vsh.yaml
@@ -201,7 +201,7 @@ build_info:
  output: "target/executable/report/create_report"
  executable: "target/executable/report/create_report/create_report"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/report/create_report/create_report
+++ b/target/executable/report/create_report/create_report
@@ -476,9 +476,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag

 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component report create_report"
-LABEL org.opencontainers.image.created="2025-02-13T08:19:04Z"
+LABEL org.opencontainers.image.created="2025-02-13T11:46:11Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59"
 LABEL org.opencontainers.image.version="runner_multiple_input_directories"

 VIASHDOCKER
--- a/target/executable/stats/combine_star_logs/.config.vsh.yaml
+++ b/target/executable/stats/combine_star_logs/.config.vsh.yaml
@@ -198,7 +198,7 @@ build_info:
  output: "target/executable/stats/combine_star_logs"
  executable: "target/executable/stats/combine_star_logs/combine_star_logs"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/stats/combine_star_logs/combine_star_logs
+++ b/target/executable/stats/combine_star_logs/combine_star_logs
@@ -490,9 +490,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component stats combine_star_logs"
-LABEL org.opencontainers.image.created="2025-02-13T08:19:01Z"
+LABEL org.opencontainers.image.created="2025-02-13T11:46:09Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59"
 LABEL org.opencontainers.image.version="runner_multiple_input_directories"

 VIASHDOCKER
--- a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
+++ b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
@@ -182,7 +182,7 @@ build_info:
  output: "target/executable/stats/generate_pool_statistics"
  executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/stats/generate_pool_statistics/generate_pool_statistics
+++ b/target/executable/stats/generate_pool_statistics/generate_pool_statistics
@@ -483,9 +483,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component stats generate_pool_statistics"
-LABEL org.opencontainers.image.created="2025-02-13T08:19:02Z"
+LABEL org.opencontainers.image.created="2025-02-13T11:46:09Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59"
 LABEL org.opencontainers.image.version="runner_multiple_input_directories"

 VIASHDOCKER
--- a/target/executable/stats/generate_well_statistics/.config.vsh.yaml
+++ b/target/executable/stats/generate_well_statistics/.config.vsh.yaml
@@ -262,7 +262,7 @@ build_info:
  output: "target/executable/stats/generate_well_statistics"
  executable: "target/executable/stats/generate_well_statistics/generate_well_statistics"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/stats/generate_well_statistics/generate_well_statistics
+++ b/target/executable/stats/generate_well_statistics/generate_well_statistics
@@ -520,9 +520,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component stats generate_well_statistics"
-LABEL org.opencontainers.image.created="2025-02-13T08:19:02Z"
+LABEL org.opencontainers.image.created="2025-02-13T11:46:10Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59"
 LABEL org.opencontainers.image.version="runner_multiple_input_directories"

 VIASHDOCKER
--- a/target/nextflow/eset/create_eset/.config.vsh.yaml
+++ b/target/nextflow/eset/create_eset/.config.vsh.yaml
@@ -198,7 +198,7 @@ build_info:
  output: "target/nextflow/eset/create_eset"
  executable: "target/nextflow/eset/create_eset/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/eset/create_eset/main.nf
+++ b/target/nextflow/eset/create_eset/main.nf
@@ -3072,7 +3072,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_eset",
    "viash_version" : "0.9.0",
-    "git_commit" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad",
+    "git_commit" : "ed9480768e77078704939482fe909186c92b0b59",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/eset/create_fdata/.config.vsh.yaml
+++ b/target/nextflow/eset/create_fdata/.config.vsh.yaml
@@ -177,7 +177,7 @@ build_info:
  output: "target/nextflow/eset/create_fdata"
  executable: "target/nextflow/eset/create_fdata/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/eset/create_fdata/main.nf
+++ b/target/nextflow/eset/create_fdata/main.nf
@@ -3044,7 +3044,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_fdata",
    "viash_version" : "0.9.0",
-    "git_commit" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad",
+    "git_commit" : "ed9480768e77078704939482fe909186c92b0b59",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/eset/create_pdata/.config.vsh.yaml
+++ b/target/nextflow/eset/create_pdata/.config.vsh.yaml
@@ -191,7 +191,7 @@ build_info:
  output: "target/nextflow/eset/create_pdata"
  executable: "target/nextflow/eset/create_pdata/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/eset/create_pdata/main.nf
+++ b/target/nextflow/eset/create_pdata/main.nf
@@ -3058,7 +3058,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_pdata",
    "viash_version" : "0.9.0",
-    "git_commit" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad",
+    "git_commit" : "ed9480768e77078704939482fe909186c92b0b59",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
@@ -148,7 +148,7 @@ build_info:
  output: "target/nextflow/integration_test_components/htrnaseq/check_eset"
  executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
@@ -2997,7 +2997,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
    "viash_version" : "0.9.0",
-    "git_commit" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad",
+    "git_commit" : "ed9480768e77078704939482fe909186c92b0b59",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
+++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
@@ -158,7 +158,7 @@ build_info:
  output: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output"
  executable: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf
+++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf
@@ -3009,7 +3009,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
    "viash_version" : "0.9.0",
-    "git_commit" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad",
+    "git_commit" : "ed9480768e77078704939482fe909186c92b0b59",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/io/publish_fastqs/.config.vsh.yaml
+++ b/target/nextflow/io/publish_fastqs/.config.vsh.yaml
@@ -143,7 +143,7 @@ build_info:
  output: "target/nextflow/io/publish_fastqs"
  executable: "target/nextflow/io/publish_fastqs/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/io/publish_fastqs/main.nf
+++ b/target/nextflow/io/publish_fastqs/main.nf
@@ -2983,7 +2983,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish_fastqs",
    "viash_version" : "0.9.0",
-    "git_commit" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad",
+    "git_commit" : "ed9480768e77078704939482fe909186c92b0b59",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/io/publish_results/.config.vsh.yaml
+++ b/target/nextflow/io/publish_results/.config.vsh.yaml
@@ -187,7 +187,7 @@ build_info:
  output: "target/nextflow/io/publish_results"
  executable: "target/nextflow/io/publish_results/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/io/publish_results/main.nf
+++ b/target/nextflow/io/publish_results/main.nf
@@ -3032,7 +3032,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish_results",
    "viash_version" : "0.9.0",
-    "git_commit" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad",
+    "git_commit" : "ed9480768e77078704939482fe909186c92b0b59",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/parallel_map/.config.vsh.yaml
+++ b/target/nextflow/parallel_map/.config.vsh.yaml
@@ -279,7 +279,7 @@ build_info:
  output: "target/nextflow/parallel_map"
  executable: "target/nextflow/parallel_map/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/parallel_map/main.nf
+++ b/target/nextflow/parallel_map/main.nf
@@ -3144,7 +3144,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/parallel_map",
    "viash_version" : "0.9.0",
-    "git_commit" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad",
+    "git_commit" : "ed9480768e77078704939482fe909186c92b0b59",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/report/create_report/.config.vsh.yaml
+++ b/target/nextflow/report/create_report/.config.vsh.yaml
@@ -201,7 +201,7 @@ build_info:
  output: "target/nextflow/report/create_report"
  executable: "target/nextflow/report/create_report/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/report/create_report/main.nf
+++ b/target/nextflow/report/create_report/main.nf
@@ -3077,7 +3077,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/report/create_report",
    "viash_version" : "0.9.0",
-    "git_commit" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad",
+    "git_commit" : "ed9480768e77078704939482fe909186c92b0b59",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
+++ b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
@@ -198,7 +198,7 @@ build_info:
  output: "target/nextflow/stats/combine_star_logs"
  executable: "target/nextflow/stats/combine_star_logs/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/stats/combine_star_logs/main.nf
+++ b/target/nextflow/stats/combine_star_logs/main.nf
@@ -3060,7 +3060,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/combine_star_logs",
    "viash_version" : "0.9.0",
-    "git_commit" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad",
+    "git_commit" : "ed9480768e77078704939482fe909186c92b0b59",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
+++ b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
@@ -182,7 +182,7 @@ build_info:
  output: "target/nextflow/stats/generate_pool_statistics"
  executable: "target/nextflow/stats/generate_pool_statistics/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/stats/generate_pool_statistics/main.nf
+++ b/target/nextflow/stats/generate_pool_statistics/main.nf
@@ -3044,7 +3044,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/generate_pool_statistics",
    "viash_version" : "0.9.0",
-    "git_commit" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad",
+    "git_commit" : "ed9480768e77078704939482fe909186c92b0b59",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
+++ b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
@@ -262,7 +262,7 @@ build_info:
  output: "target/nextflow/stats/generate_well_statistics"
  executable: "target/nextflow/stats/generate_well_statistics/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/stats/generate_well_statistics/main.nf
+++ b/target/nextflow/stats/generate_well_statistics/main.nf
@@ -3135,7 +3135,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/generate_well_statistics",
    "viash_version" : "0.9.0",
-    "git_commit" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad",
+    "git_commit" : "ed9480768e77078704939482fe909186c92b0b59",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/utils/listInputDir/.config.vsh.yaml
+++ b/target/nextflow/utils/listInputDir/.config.vsh.yaml
@@ -54,6 +54,14 @@ argument_groups:
    direction: "output"
    multiple: false
    multiple_sep: ";"
+  - type: "string"
+    name: "--sample_id"
+    description: "Sample name"
+    info: null
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
 resources:
 - type: "nextflow_script"
  path: "main.nf"
@@ -147,7 +155,7 @@ build_info:
  output: "target/nextflow/utils/listInputDir"
  executable: "target/nextflow/utils/listInputDir/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/utils/listInputDir/main.nf
+++ b/target/nextflow/utils/listInputDir/main.nf
@@ -2867,6 +2867,15 @@ meta = [
          "direction" : "output",
          "multiple" : false,
          "multiple_sep" : ";"
+        },
+        {
+          "type" : "string",
+          "name" : "--sample_id",
+          "description" : "Sample name",
+          "required" : false,
+          "direction" : "output",
+          "multiple" : false,
+          "multiple_sep" : ";"
        }
      ]
    }
@@ -2983,7 +2992,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/utils/listInputDir",
    "viash_version" : "0.9.0",
-    "git_commit" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad",
+    "git_commit" : "ed9480768e77078704939482fe909186c92b0b59",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
@@ -3050,7 +3059,7 @@ workflow run_wf {

        println("Extracting information from fastq/fasta filenames")
        def processed_fastqs = allFastqs.collect { f ->
-          def regex = ~/^(\w+)_S(\d+)_(L(\d+)_)?R(\d)_(\d+)\.fast[qa](\.gz)?$/
+          def regex = ~/^(\w+)_S(\d+)_(L(\d+))_?R(\d)_(\d+)\.fast[qa](\.gz)?$/
          def validFastq = f.name ==~ regex

          assert validFastq: "${f} does not match the regex ${regex}"
@@ -3068,20 +3077,27 @@ workflow run_wf {

        println("Group paired fastq/fasta files")
        def grouped = processed_fastqs
-          .groupBy({it.sample_id})
-          .collect{ k, vs ->
-            def r1 = vs.find{it.read == "1"}
-            def r2 = vs.find{it.read == "2"}
-            def newState = [
-              r1_output: r1.fastq,
-              r2_output: r2.fastq
-            ]
-            def updtState = newState + vs[0].findAll{ it.key in ["sample", "lane"] }
-            return [k, updtState]
-          }
+          .groupBy({it.sample_id}, {it.lane})
+          .collectMany{ sample_id, states_per_lane ->
+            def result = states_per_lane.collect{lane, lane_states ->
+              assert lane_states.size() == 2, "Expected to find two fastq files per lane! " +
+                "Found ${lane_states.size()}. State: ${states_per_lane}"
+              def r1_state = lane_states.find({it.read == "1"})
+              def r2_state = lane_states.find({it.read == "2"})
+              def fastq_state = [
+                "r1_output": r1_state.fastq,
+                "r2_output": r2_state.fastq
+              ]
+              def new_state = fastq_state +
+                r1_state.findAll{it.key in ["sample_id", "sample", "lane"]} + 
+                ["_meta": ["join_id": id]]
+              return ["${sample_id}_${lane}".toString(), new_state]
+            }
+            return result
+
+          }
+          return grouped

-        grouped
-          .collect{ [ it[0], it[1] + [ _meta: [ join_id: id ] ] ] }
      }

  emit: out_
--- a/target/nextflow/utils/listInputDir/nextflow_schema.json
+++ b/target/nextflow/utils/listInputDir/nextflow_schema.json
@@ -65,6 +65,16 @@
            }
    

+        ,
+                "sample_id": {
+                "type":
+                "string",
+                "description": "Type: `string`. Sample name",
+                "help_text": "Type: `string`. Sample name"
+            
+            }
+    
+
 }
 },
    
--- a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
+++ b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
@@ -319,7 +319,7 @@ build_info:
  output: "target/nextflow/workflows/htrnaseq"
  executable: "target/nextflow/workflows/htrnaseq/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
  dependencies:
  - "target/nextflow/stats/combine_star_logs"
--- a/target/nextflow/workflows/htrnaseq/main.nf
+++ b/target/nextflow/workflows/htrnaseq/main.nf
@@ -3223,7 +3223,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/htrnaseq",
    "viash_version" : "0.9.0",
-    "git_commit" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad",
+    "git_commit" : "ed9480768e77078704939482fe909186c92b0b59",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/workflows/runner/.config.vsh.yaml
+++ b/target/nextflow/workflows/runner/.config.vsh.yaml
@@ -197,7 +197,7 @@ build_info:
  output: "target/nextflow/workflows/runner"
  executable: "target/nextflow/workflows/runner/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
  dependencies:
  - "target/nextflow/utils/listInputDir"
--- a/target/nextflow/workflows/runner/main.nf
+++ b/target/nextflow/workflows/runner/main.nf
@@ -3057,7 +3057,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/runner",
    "viash_version" : "0.9.0",
-    "git_commit" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad",
+    "git_commit" : "ed9480768e77078704939482fe909186c92b0b59",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
@@ -3145,6 +3145,7 @@ workflow run_wf {
      // there might be multiple FASTQs for a single sample that correspond to the
      // lanes. So the fastq files must be gathered across lanes and input folders
      // in order to create an input lists for R1 and R2.
+      | map {id, state -> [state.sample_id, state]}
      | groupTuple(by: 0, sort: { state1, state2 ->
        if (state1.index == state2.index) {
          return state1.lane <=> state2.lane
--- a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
+++ b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
@@ -211,7 +211,7 @@ build_info:
  output: "target/nextflow/workflows/well_demultiplex"
  executable: "target/nextflow/workflows/well_demultiplex/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
  dependencies:
  - "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/cutadapt"
--- a/target/nextflow/workflows/well_demultiplex/main.nf
+++ b/target/nextflow/workflows/well_demultiplex/main.nf
@@ -3084,7 +3084,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/well_demultiplex",
    "viash_version" : "0.9.0",
-    "git_commit" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad",
+    "git_commit" : "ed9480768e77078704939482fe909186c92b0b59",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/workflows/well_metadata/.config.vsh.yaml
+++ b/target/nextflow/workflows/well_metadata/.config.vsh.yaml
@@ -209,7 +209,7 @@ build_info:
  output: "target/nextflow/workflows/well_metadata"
  executable: "target/nextflow/workflows/well_metadata/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad"
+  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/workflows/well_metadata/main.nf
+++ b/target/nextflow/workflows/well_metadata/main.nf
@@ -3064,7 +3064,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/well_metadata",
    "viash_version" : "0.9.0",
-    "git_commit" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad",
+    "git_commit" : "ed9480768e77078704939482fe909186c92b0b59",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {