Build branch runner_multiple_input_directories with version runner_multiple_input_directories (fa4802b)

Build pipeline: viash-hub.htrnaseq.runner-multiple-input-directories-xxp5h Source commit: fa4802ba80 Source message: Fix trailing index there is no or only one lane
2025-02-13 15:08:14 +00:00
parent caa6cec4e2
commit c04b9cb0e1
60 changed files with 114 additions and 78 deletions
--- a/src/utils/listInputDir/main.nf
+++ b/src/utils/listInputDir/main.nf
@@ -18,18 +18,20 @@ 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}"

          def parsedFastq = f.name =~ regex
-
+          def lane = parsedFastq[0][3]
+          // Remove the trailing '_'
+          def lane_remove_trailing = lane == null ? "" : lane.replaceAll('_$', "")
          return [
            fastq: f,
            sample_id: parsedFastq[0][1],
            sample: parsedFastq[0][2],
-            lane: parsedFastq[0][3],
+            lane: lane_remove_trailing,
            read: parsedFastq[0][5],
          ]
        }
@@ -50,7 +52,8 @@ workflow run_wf {
              def new_state = fastq_state +
                r1_state.findAll{it.key in ["sample_id", "sample", "lane"]} + 
                ["_meta": ["join_id": id]]
-              return ["${sample_id}_${lane}".toString(), new_state]
+              def new_id = lane?.trim() ? sample_id : "${sample_id}_${lane}".toString()
+              return [new_id, new_state]
            }
            return result

--- a/src/workflows/well_demultiplex/main.nf
+++ b/src/workflows/well_demultiplex/main.nf
@@ -15,6 +15,21 @@ workflow run_wf {
      | flatMap {id, state ->
        assert state.input_r1.size() == state.input_r2.size(), \
          "Expected equal number of inputs for R1 and R2"
+        if (state.input_r1.size() == 1) {
+          // special case where we do not want to adjust the ID to add an index.
+          // If we do add an index, the file paths will contain "_0", which
+          // will not be removed. For the scenarios where we do have multiple lanes,
+          // the files will be concatenated later and a new file path without the index
+          // is created at that point.
+          def newState = state + [
+            "input_r1": state.input_r1[0],
+            "input_r2": state.input_r2[0],
+            "pool": id,
+            "n_lanes": 1,
+            "lane_sorting": 1,
+          ]
+          return [[id, newState]]
+        }
        // Store the number of lanes that were encountered here in order to
        // group them together in an asynchronous manner later by providing
        // the expected number of events to be grouped to groupTuple.
--- 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: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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="2025-02-13T11:46:10Z"
+LABEL org.opencontainers.image.created="2025-02-13T14:15:36Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59"
+LABEL org.opencontainers.image.revision="fa4802ba809fc4bf8534cdf4b18a30846225d19d"
 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: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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="2025-02-13T11:46:11Z"
+LABEL org.opencontainers.image.created="2025-02-13T14:15:36Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59"
+LABEL org.opencontainers.image.revision="fa4802ba809fc4bf8534cdf4b18a30846225d19d"
 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: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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="2025-02-13T11:46:10Z"
+LABEL org.opencontainers.image.created="2025-02-13T14:15:36Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59"
+LABEL org.opencontainers.image.revision="fa4802ba809fc4bf8534cdf4b18a30846225d19d"
 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: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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="2025-02-13T11:46:11Z"
+LABEL org.opencontainers.image.created="2025-02-13T14:15:36Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59"
+LABEL org.opencontainers.image.revision="fa4802ba809fc4bf8534cdf4b18a30846225d19d"
 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: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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="2025-02-13T11:46:10Z"
+LABEL org.opencontainers.image.created="2025-02-13T14:15:36Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59"
+LABEL org.opencontainers.image.revision="fa4802ba809fc4bf8534cdf4b18a30846225d19d"
 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: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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="2025-02-13T11:46:09Z"
+LABEL org.opencontainers.image.created="2025-02-13T14:15:34Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59"
+LABEL org.opencontainers.image.revision="fa4802ba809fc4bf8534cdf4b18a30846225d19d"
 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: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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="2025-02-13T11:46:09Z"
+LABEL org.opencontainers.image.created="2025-02-13T14:15:35Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59"
+LABEL org.opencontainers.image.revision="fa4802ba809fc4bf8534cdf4b18a30846225d19d"
 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: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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="2025-02-13T11:46:11Z"
+LABEL org.opencontainers.image.created="2025-02-13T14:15:37Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59"
+LABEL org.opencontainers.image.revision="fa4802ba809fc4bf8534cdf4b18a30846225d19d"
 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: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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="2025-02-13T11:46:11Z"
+LABEL org.opencontainers.image.created="2025-02-13T14:15:37Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59"
+LABEL org.opencontainers.image.revision="fa4802ba809fc4bf8534cdf4b18a30846225d19d"
 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: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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="2025-02-13T11:46:09Z"
+LABEL org.opencontainers.image.created="2025-02-13T14:15:34Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59"
+LABEL org.opencontainers.image.revision="fa4802ba809fc4bf8534cdf4b18a30846225d19d"
 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: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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="2025-02-13T11:46:09Z"
+LABEL org.opencontainers.image.created="2025-02-13T14:15:35Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59"
+LABEL org.opencontainers.image.revision="fa4802ba809fc4bf8534cdf4b18a30846225d19d"
 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: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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="2025-02-13T11:46:10Z"
+LABEL org.opencontainers.image.created="2025-02-13T14:15:36Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59"
+LABEL org.opencontainers.image.revision="fa4802ba809fc4bf8534cdf4b18a30846225d19d"
 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: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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" : "ed9480768e77078704939482fe909186c92b0b59",
+    "git_commit" : "fa4802ba809fc4bf8534cdf4b18a30846225d19d",
    "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: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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" : "ed9480768e77078704939482fe909186c92b0b59",
+    "git_commit" : "fa4802ba809fc4bf8534cdf4b18a30846225d19d",
    "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: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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" : "ed9480768e77078704939482fe909186c92b0b59",
+    "git_commit" : "fa4802ba809fc4bf8534cdf4b18a30846225d19d",
    "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: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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" : "ed9480768e77078704939482fe909186c92b0b59",
+    "git_commit" : "fa4802ba809fc4bf8534cdf4b18a30846225d19d",
    "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: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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" : "ed9480768e77078704939482fe909186c92b0b59",
+    "git_commit" : "fa4802ba809fc4bf8534cdf4b18a30846225d19d",
    "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: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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" : "ed9480768e77078704939482fe909186c92b0b59",
+    "git_commit" : "fa4802ba809fc4bf8534cdf4b18a30846225d19d",
    "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: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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" : "ed9480768e77078704939482fe909186c92b0b59",
+    "git_commit" : "fa4802ba809fc4bf8534cdf4b18a30846225d19d",
    "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: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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" : "ed9480768e77078704939482fe909186c92b0b59",
+    "git_commit" : "fa4802ba809fc4bf8534cdf4b18a30846225d19d",
    "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: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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" : "ed9480768e77078704939482fe909186c92b0b59",
+    "git_commit" : "fa4802ba809fc4bf8534cdf4b18a30846225d19d",
    "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: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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" : "ed9480768e77078704939482fe909186c92b0b59",
+    "git_commit" : "fa4802ba809fc4bf8534cdf4b18a30846225d19d",
    "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: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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" : "ed9480768e77078704939482fe909186c92b0b59",
+    "git_commit" : "fa4802ba809fc4bf8534cdf4b18a30846225d19d",
    "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: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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" : "ed9480768e77078704939482fe909186c92b0b59",
+    "git_commit" : "fa4802ba809fc4bf8534cdf4b18a30846225d19d",
    "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
@@ -155,7 +155,7 @@ build_info:
  output: "target/nextflow/utils/listInputDir"
  executable: "target/nextflow/utils/listInputDir/main.nf"
  viash_version: "0.9.0"
-  git_commit: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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
@@ -2992,7 +2992,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/utils/listInputDir",
    "viash_version" : "0.9.0",
-    "git_commit" : "ed9480768e77078704939482fe909186c92b0b59",
+    "git_commit" : "fa4802ba809fc4bf8534cdf4b18a30846225d19d",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
@@ -3059,18 +3059,20 @@ 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}"

          def parsedFastq = f.name =~ regex
-
+          def lane = parsedFastq[0][3]
+          // Remove the trailing '_'
+          def lane_remove_trailing = lane == null ? "" : lane.replaceAll('_$', "")
          return [
            fastq: f,
            sample_id: parsedFastq[0][1],
            sample: parsedFastq[0][2],
-            lane: parsedFastq[0][3],
+            lane: lane_remove_trailing,
            read: parsedFastq[0][5],
          ]
        }
@@ -3091,7 +3093,8 @@ workflow run_wf {
              def new_state = fastq_state +
                r1_state.findAll{it.key in ["sample_id", "sample", "lane"]} + 
                ["_meta": ["join_id": id]]
-              return ["${sample_id}_${lane}".toString(), new_state]
+              def new_id = lane?.trim() ? sample_id : "${sample_id}_${lane}".toString()
+              return [new_id, new_state]
            }
            return result

--- 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: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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" : "ed9480768e77078704939482fe909186c92b0b59",
+    "git_commit" : "fa4802ba809fc4bf8534cdf4b18a30846225d19d",
    "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: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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" : "ed9480768e77078704939482fe909186c92b0b59",
+    "git_commit" : "fa4802ba809fc4bf8534cdf4b18a30846225d19d",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- 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: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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" : "ed9480768e77078704939482fe909186c92b0b59",
+    "git_commit" : "fa4802ba809fc4bf8534cdf4b18a30846225d19d",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
@@ -3150,6 +3150,21 @@ workflow run_wf {
      | flatMap {id, state ->
        assert state.input_r1.size() == state.input_r2.size(), \
          "Expected equal number of inputs for R1 and R2"
+        if (state.input_r1.size() == 1) {
+          // special case where we do not want to adjust the ID to add an index.
+          // If we do add an index, the file paths will contain "_0", which
+          // will not be removed. For the scenarios where we do have multiple lanes,
+          // the files will be concatenated later and a new file path without the index
+          // is created at that point.
+          def newState = state + [
+            "input_r1": state.input_r1[0],
+            "input_r2": state.input_r2[0],
+            "pool": id,
+            "n_lanes": 1,
+            "lane_sorting": 1,
+          ]
+          return [[id, newState]]
+        }
        // Store the number of lanes that were encountered here in order to
        // group them together in an asynchronous manner later by providing
        // the expected number of events to be grouped to groupTuple.
--- 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: "ed9480768e77078704939482fe909186c92b0b59"
+  git_commit: "fa4802ba809fc4bf8534cdf4b18a30846225d19d"
  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" : "ed9480768e77078704939482fe909186c92b0b59",
+    "git_commit" : "fa4802ba809fc4bf8534cdf4b18a30846225d19d",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {