Build branch save-params with version save-params (afdc3f4)

Build pipeline: viash-hub.htrnaseq.save-params-h7kx4 Source commit: afdc3f4ed8 Source message: keep id in component
2025-05-06 09:04:20 +00:00
parent 0668575b40
commit d67e37efb9
65 changed files with 77 additions and 104 deletions
--- a/src/utils/save_params/script.py
+++ b/src/utils/save_params/script.py
@@ -21,18 +21,9 @@ def decode_params_yaml(encoded_yaml):
    
    return yaml_data

-# def replace_id(value, sample_id):
-#     if isinstance(value, str):
-#         return value.replace('$id', sample_id)
-#     elif isinstance(value, list):
-#         return [replace_id(item, sample_id) for item in value]
-#     return value
-
 print(par['params_yaml'])

 params = decode_params_yaml(par['params_yaml'])
-# for key, value in params.items():
-#     params[key] = replace_id(value, par["id"])

 with open(par["output"], 'w') as f:
    yaml.dump(params, f, default_flow_style=False, Dumper=Dumper)
--- a/target/executable/eset/create_eset/.config.vsh.yaml
+++ b/target/executable/eset/create_eset/.config.vsh.yaml
@@ -203,7 +203,7 @@ build_info:
  output: "target/executable/eset/create_eset"
  executable: "target/executable/eset/create_eset/create_eset"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -456,9 +456,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR

 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="2025-05-02T07:23:37Z"
+LABEL org.opencontainers.image.created="2025-05-06T08:16:05Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="b9a380acae42705fc901f8d9e73e698ef55f4b65"
+LABEL org.opencontainers.image.revision="afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
 LABEL org.opencontainers.image.version="save-params"

 VIASHDOCKER
--- a/target/executable/eset/create_fdata/.config.vsh.yaml
+++ b/target/executable/eset/create_fdata/.config.vsh.yaml
@@ -180,7 +180,7 @@ build_info:
  output: "target/executable/eset/create_fdata"
  executable: "target/executable/eset/create_fdata/create_fdata"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -458,9 +458,9 @@ 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="2025-05-02T07:23:36Z"
+LABEL org.opencontainers.image.created="2025-05-06T08:16:05Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="b9a380acae42705fc901f8d9e73e698ef55f4b65"
+LABEL org.opencontainers.image.revision="afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
 LABEL org.opencontainers.image.version="save-params"

 VIASHDOCKER
--- a/target/executable/eset/create_pdata/.config.vsh.yaml
+++ b/target/executable/eset/create_pdata/.config.vsh.yaml
@@ -194,7 +194,7 @@ build_info:
  output: "target/executable/eset/create_pdata"
  executable: "target/executable/eset/create_pdata/create_pdata"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -458,9 +458,9 @@ 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="2025-05-02T07:23:37Z"
+LABEL org.opencontainers.image.created="2025-05-06T08:16:06Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="b9a380acae42705fc901f8d9e73e698ef55f4b65"
+LABEL org.opencontainers.image.revision="afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
 LABEL org.opencontainers.image.version="save-params"

 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
@@ -152,7 +152,7 @@ build_info:
  output: "target/executable/integration_test_components/htrnaseq/check_eset"
  executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -455,9 +455,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR

 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="2025-05-02T07:23:35Z"
+LABEL org.opencontainers.image.created="2025-05-06T08:16:04Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="b9a380acae42705fc901f8d9e73e698ef55f4b65"
+LABEL org.opencontainers.image.revision="afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
 LABEL org.opencontainers.image.version="save-params"

 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
@@ -161,7 +161,7 @@ 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: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -457,9 +457,9 @@ 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="2025-05-02T07:23:37Z"
+LABEL org.opencontainers.image.created="2025-05-06T08:16:06Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="b9a380acae42705fc901f8d9e73e698ef55f4b65"
+LABEL org.opencontainers.image.revision="afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
 LABEL org.opencontainers.image.version="save-params"

 VIASHDOCKER
--- a/target/executable/io/publish_fastqs/.config.vsh.yaml
+++ b/target/executable/io/publish_fastqs/.config.vsh.yaml
@@ -136,7 +136,7 @@ build_info:
  output: "target/executable/io/publish_fastqs"
  executable: "target/executable/io/publish_fastqs/publish_fastqs"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -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_fastqs"
-LABEL org.opencontainers.image.created="2025-05-02T07:23:36Z"
+LABEL org.opencontainers.image.created="2025-05-06T08:16:05Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="b9a380acae42705fc901f8d9e73e698ef55f4b65"
+LABEL org.opencontainers.image.revision="afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
 LABEL org.opencontainers.image.version="save-params"

 VIASHDOCKER
--- a/target/executable/io/publish_results/.config.vsh.yaml
+++ b/target/executable/io/publish_results/.config.vsh.yaml
@@ -190,7 +190,7 @@ build_info:
  output: "target/executable/io/publish_results"
  executable: "target/executable/io/publish_results/publish_results"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -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_results"
-LABEL org.opencontainers.image.created="2025-05-02T07:23:36Z"
+LABEL org.opencontainers.image.created="2025-05-06T08:16:05Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="b9a380acae42705fc901f8d9e73e698ef55f4b65"
+LABEL org.opencontainers.image.revision="afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
 LABEL org.opencontainers.image.version="save-params"

 VIASHDOCKER
--- a/target/executable/parallel_map/.config.vsh.yaml
+++ b/target/executable/parallel_map/.config.vsh.yaml
@@ -282,7 +282,7 @@ build_info:
  output: "target/executable/parallel_map"
  executable: "target/executable/parallel_map/parallel_map"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -461,9 +461,9 @@ 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="2025-05-02T07:23:37Z"
+LABEL org.opencontainers.image.created="2025-05-06T08:16:06Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="b9a380acae42705fc901f8d9e73e698ef55f4b65"
+LABEL org.opencontainers.image.revision="afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
 LABEL org.opencontainers.image.version="save-params"

 VIASHDOCKER
--- a/target/executable/report/create_report/.config.vsh.yaml
+++ b/target/executable/report/create_report/.config.vsh.yaml
@@ -206,7 +206,7 @@ build_info:
  output: "target/executable/report/create_report"
  executable: "target/executable/report/create_report/create_report"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -462,9 +462,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR

 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="2025-05-02T07:23:37Z"
+LABEL org.opencontainers.image.created="2025-05-06T08:16:06Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="b9a380acae42705fc901f8d9e73e698ef55f4b65"
+LABEL org.opencontainers.image.revision="afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
 LABEL org.opencontainers.image.version="save-params"

 VIASHDOCKER
--- a/target/executable/stats/combine_star_logs/.config.vsh.yaml
+++ b/target/executable/stats/combine_star_logs/.config.vsh.yaml
@@ -201,7 +201,7 @@ build_info:
  output: "target/executable/stats/combine_star_logs"
  executable: "target/executable/stats/combine_star_logs/combine_star_logs"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -457,9 +457,9 @@ 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="2025-05-02T07:23:35Z"
+LABEL org.opencontainers.image.created="2025-05-06T08:16:04Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="b9a380acae42705fc901f8d9e73e698ef55f4b65"
+LABEL org.opencontainers.image.revision="afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
 LABEL org.opencontainers.image.version="save-params"

 VIASHDOCKER
--- a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
+++ b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
@@ -185,7 +185,7 @@ build_info:
  output: "target/executable/stats/generate_pool_statistics"
  executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -458,9 +458,9 @@ 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="2025-05-02T07:23:36Z"
+LABEL org.opencontainers.image.created="2025-05-06T08:16:05Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="b9a380acae42705fc901f8d9e73e698ef55f4b65"
+LABEL org.opencontainers.image.revision="afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
 LABEL org.opencontainers.image.version="save-params"

 VIASHDOCKER
--- a/target/executable/stats/generate_well_statistics/.config.vsh.yaml
+++ b/target/executable/stats/generate_well_statistics/.config.vsh.yaml
@@ -267,7 +267,7 @@ build_info:
  output: "target/executable/stats/generate_well_statistics"
  executable: "target/executable/stats/generate_well_statistics/generate_well_statistics"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -461,9 +461,9 @@ 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="2025-05-02T07:23:36Z"
+LABEL org.opencontainers.image.created="2025-05-06T08:16:05Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="b9a380acae42705fc901f8d9e73e698ef55f4b65"
+LABEL org.opencontainers.image.revision="afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
 LABEL org.opencontainers.image.version="save-params"

 VIASHDOCKER
--- a/target/executable/utils/save_params/.config.vsh.yaml
+++ b/target/executable/utils/save_params/.config.vsh.yaml
@@ -146,7 +146,7 @@ build_info:
  output: "target/executable/utils/save_params"
  executable: "target/executable/utils/save_params/save_params"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/utils/save_params/save_params
+++ b/target/executable/utils/save_params/save_params
@@ -453,9 +453,9 @@ RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "pyyaml"

 LABEL org.opencontainers.image.description="Companion container for running component utils save_params"
-LABEL org.opencontainers.image.created="2025-05-02T07:23:38Z"
+LABEL org.opencontainers.image.created="2025-05-06T08:16:06Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="b9a380acae42705fc901f8d9e73e698ef55f4b65"
+LABEL org.opencontainers.image.revision="afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
 LABEL org.opencontainers.image.version="save-params"

 VIASHDOCKER
@@ -1085,18 +1085,9 @@ def decode_params_yaml(encoded_yaml):
    
    return yaml_data

-# def replace_id(value, sample_id):
-#     if isinstance(value, str):
-#         return value.replace('\$id', sample_id)
-#     elif isinstance(value, list):
-#         return [replace_id(item, sample_id) for item in value]
-#     return value
-
 print(par['params_yaml'])

 params = decode_params_yaml(par['params_yaml'])
-# for key, value in params.items():
-#     params[key] = replace_id(value, par["id"])

 with open(par["output"], 'w') as f:
    yaml.dump(params, f, default_flow_style=False, Dumper=Dumper)
--- a/target/nextflow/eset/create_eset/.config.vsh.yaml
+++ b/target/nextflow/eset/create_eset/.config.vsh.yaml
@@ -203,7 +203,7 @@ build_info:
  output: "target/nextflow/eset/create_eset"
  executable: "target/nextflow/eset/create_eset/main.nf"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -3309,7 +3309,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_eset",
    "viash_version" : "0.9.2",
-    "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65",
+    "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6",
    "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
@@ -180,7 +180,7 @@ build_info:
  output: "target/nextflow/eset/create_fdata"
  executable: "target/nextflow/eset/create_fdata/main.nf"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -3279,7 +3279,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_fdata",
    "viash_version" : "0.9.2",
-    "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65",
+    "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6",
    "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
@@ -194,7 +194,7 @@ build_info:
  output: "target/nextflow/eset/create_pdata"
  executable: "target/nextflow/eset/create_pdata/main.nf"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -3293,7 +3293,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_pdata",
    "viash_version" : "0.9.2",
-    "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65",
+    "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6",
    "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
@@ -152,7 +152,7 @@ build_info:
  output: "target/nextflow/integration_test_components/htrnaseq/check_eset"
  executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -3233,7 +3233,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
    "viash_version" : "0.9.2",
-    "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65",
+    "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6",
    "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
@@ -161,7 +161,7 @@ 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: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -3244,7 +3244,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
    "viash_version" : "0.9.2",
-    "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65",
+    "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6",
    "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
@@ -136,7 +136,7 @@ build_info:
  output: "target/nextflow/io/publish_fastqs"
  executable: "target/nextflow/io/publish_fastqs/main.nf"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -3207,7 +3207,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish_fastqs",
    "viash_version" : "0.9.2",
-    "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65",
+    "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6",
    "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
@@ -190,7 +190,7 @@ build_info:
  output: "target/nextflow/io/publish_results"
  executable: "target/nextflow/io/publish_results/main.nf"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -3267,7 +3267,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish_results",
    "viash_version" : "0.9.2",
-    "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65",
+    "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6",
    "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
@@ -282,7 +282,7 @@ build_info:
  output: "target/nextflow/parallel_map"
  executable: "target/nextflow/parallel_map/main.nf"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -3379,7 +3379,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/parallel_map",
    "viash_version" : "0.9.2",
-    "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65",
+    "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6",
    "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
@@ -206,7 +206,7 @@ build_info:
  output: "target/nextflow/report/create_report"
  executable: "target/nextflow/report/create_report/main.nf"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -3314,7 +3314,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/report/create_report",
    "viash_version" : "0.9.2",
-    "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65",
+    "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6",
    "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
@@ -201,7 +201,7 @@ build_info:
  output: "target/nextflow/stats/combine_star_logs"
  executable: "target/nextflow/stats/combine_star_logs/main.nf"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -3295,7 +3295,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/combine_star_logs",
    "viash_version" : "0.9.2",
-    "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65",
+    "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6",
    "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
@@ -185,7 +185,7 @@ build_info:
  output: "target/nextflow/stats/generate_pool_statistics"
  executable: "target/nextflow/stats/generate_pool_statistics/main.nf"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -3279,7 +3279,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/generate_pool_statistics",
    "viash_version" : "0.9.2",
-    "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65",
+    "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6",
    "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
@@ -267,7 +267,7 @@ build_info:
  output: "target/nextflow/stats/generate_well_statistics"
  executable: "target/nextflow/stats/generate_well_statistics/main.nf"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -3374,7 +3374,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/generate_well_statistics",
    "viash_version" : "0.9.2",
-    "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65",
+    "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/utils/concatRuns/.config.vsh.yaml
+++ b/target/nextflow/utils/concatRuns/.config.vsh.yaml
@@ -157,7 +157,7 @@ build_info:
  output: "target/nextflow/utils/concatRuns"
  executable: "target/nextflow/utils/concatRuns/main.nf"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  git_remote: "https://github.com/viash-hub/htrnaseq"
  dependencies:
  - "target/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/concat_text"
--- a/target/nextflow/utils/concatRuns/main.nf
+++ b/target/nextflow/utils/concatRuns/main.nf
@@ -3229,7 +3229,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/utils/concatRuns",
    "viash_version" : "0.9.2",
-    "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65",
+    "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6",
    "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
@@ -168,7 +168,7 @@ build_info:
  output: "target/nextflow/utils/listInputDir"
  executable: "target/nextflow/utils/listInputDir/main.nf"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -3239,7 +3239,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/utils/listInputDir",
    "viash_version" : "0.9.2",
-    "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65",
+    "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/utils/save_params/.config.vsh.yaml
+++ b/target/nextflow/utils/save_params/.config.vsh.yaml
@@ -146,7 +146,7 @@ build_info:
  output: "target/nextflow/utils/save_params"
  executable: "target/nextflow/utils/save_params/main.nf"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/utils/save_params/main.nf
+++ b/target/nextflow/utils/save_params/main.nf
@@ -3221,7 +3221,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/utils/save_params",
    "viash_version" : "0.9.2",
-    "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65",
+    "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
@@ -3320,18 +3320,9 @@ def decode_params_yaml(encoded_yaml):
    
    return yaml_data

-# def replace_id(value, sample_id):
-#     if isinstance(value, str):
-#         return value.replace('\\$id', sample_id)
-#     elif isinstance(value, list):
-#         return [replace_id(item, sample_id) for item in value]
-#     return value
-
 print(par['params_yaml'])

 params = decode_params_yaml(par['params_yaml'])
-# for key, value in params.items():
-#     params[key] = replace_id(value, par["id"])

 with open(par["output"], 'w') as f:
    yaml.dump(params, f, default_flow_style=False, Dumper=Dumper)
--- a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
+++ b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
@@ -342,7 +342,7 @@ build_info:
  output: "target/nextflow/workflows/htrnaseq"
  executable: "target/nextflow/workflows/htrnaseq/main.nf"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -3484,7 +3484,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/htrnaseq",
    "viash_version" : "0.9.2",
-    "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65",
+    "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6",
    "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
@@ -221,7 +221,7 @@ build_info:
  output: "target/nextflow/workflows/runner"
  executable: "target/nextflow/workflows/runner/main.nf"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -3317,7 +3317,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/runner",
    "viash_version" : "0.9.2",
-    "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65",
+    "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6",
    "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
@@ -214,7 +214,7 @@ build_info:
  output: "target/nextflow/workflows/well_demultiplex"
  executable: "target/nextflow/workflows/well_demultiplex/main.nf"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -3319,7 +3319,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/well_demultiplex",
    "viash_version" : "0.9.2",
-    "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65",
+    "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6",
    "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
@@ -212,7 +212,7 @@ build_info:
  output: "target/nextflow/workflows/well_metadata"
  executable: "target/nextflow/workflows/well_metadata/main.nf"
  viash_version: "0.9.2"
-  git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65"
+  git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6"
  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
@@ -3299,7 +3299,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/well_metadata",
    "viash_version" : "0.9.2",
-    "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65",
+    "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {