From 475d18a6a9a89579d6d3c6b004b53b0004aed55c Mon Sep 17 00:00:00 2001 From: CI Date: Fri, 2 May 2025 18:02:28 +0000 Subject: [PATCH] Build branch update-readme with version update-readme (fb376b1) Build pipeline: viash-hub.htrnaseq.update-readme-wf7cg Source commit: https://github.com/viash-hub/htrnaseq/commit/fb376b17126d0ff90904cc426799d88782b8c68d Source message: Experiment wit size of figure --- README.md | 37 +++++++++++++----- README.qmd | 19 +++++++-- _viash.yaml | 2 +- assets/launch-parameters-5-small.png | Bin 41642 -> 20375 bytes .../eset/create_eset/.config.vsh.yaml | 4 +- .../executable/eset/create_eset/create_eset | 4 +- .../eset/create_fdata/.config.vsh.yaml | 4 +- .../executable/eset/create_fdata/create_fdata | 4 +- .../eset/create_pdata/.config.vsh.yaml | 4 +- .../executable/eset/create_pdata/create_pdata | 4 +- .../htrnaseq/check_eset/.config.vsh.yaml | 4 +- .../htrnaseq/check_eset/check_eset | 4 +- .../check_cutadapt_output/.config.vsh.yaml | 4 +- .../check_cutadapt_output | 4 +- .../io/publish_fastqs/.config.vsh.yaml | 4 +- .../io/publish_fastqs/publish_fastqs | 4 +- .../io/publish_results/.config.vsh.yaml | 4 +- .../io/publish_results/publish_results | 4 +- .../executable/parallel_map/.config.vsh.yaml | 4 +- target/executable/parallel_map/parallel_map | 4 +- .../report/create_report/.config.vsh.yaml | 4 +- .../report/create_report/create_report | 4 +- .../stats/combine_star_logs/.config.vsh.yaml | 4 +- .../stats/combine_star_logs/combine_star_logs | 4 +- .../generate_pool_statistics/.config.vsh.yaml | 4 +- .../generate_pool_statistics | 4 +- .../generate_well_statistics/.config.vsh.yaml | 4 +- .../generate_well_statistics | 4 +- .../eset/create_eset/.config.vsh.yaml | 4 +- target/nextflow/eset/create_eset/main.nf | 4 +- .../eset/create_fdata/.config.vsh.yaml | 4 +- target/nextflow/eset/create_fdata/main.nf | 4 +- .../eset/create_pdata/.config.vsh.yaml | 4 +- target/nextflow/eset/create_pdata/main.nf | 4 +- .../htrnaseq/check_eset/.config.vsh.yaml | 4 +- .../htrnaseq/check_eset/main.nf | 4 +- .../check_cutadapt_output/.config.vsh.yaml | 4 +- .../check_cutadapt_output/main.nf | 4 +- .../io/publish_fastqs/.config.vsh.yaml | 4 +- target/nextflow/io/publish_fastqs/main.nf | 4 +- .../io/publish_results/.config.vsh.yaml | 4 +- target/nextflow/io/publish_results/main.nf | 4 +- target/nextflow/parallel_map/.config.vsh.yaml | 4 +- target/nextflow/parallel_map/main.nf | 4 +- .../report/create_report/.config.vsh.yaml | 4 +- target/nextflow/report/create_report/main.nf | 4 +- .../stats/combine_star_logs/.config.vsh.yaml | 4 +- .../nextflow/stats/combine_star_logs/main.nf | 4 +- .../generate_pool_statistics/.config.vsh.yaml | 4 +- .../stats/generate_pool_statistics/main.nf | 4 +- .../generate_well_statistics/.config.vsh.yaml | 4 +- .../stats/generate_well_statistics/main.nf | 4 +- .../utils/concatRuns/.config.vsh.yaml | 4 +- target/nextflow/utils/concatRuns/main.nf | 4 +- .../utils/listInputDir/.config.vsh.yaml | 4 +- target/nextflow/utils/listInputDir/main.nf | 4 +- .../workflows/htrnaseq/.config.vsh.yaml | 4 +- target/nextflow/workflows/htrnaseq/main.nf | 4 +- .../workflows/runner/.config.vsh.yaml | 4 +- target/nextflow/workflows/runner/main.nf | 4 +- .../well_demultiplex/.config.vsh.yaml | 4 +- .../workflows/well_demultiplex/main.nf | 4 +- .../workflows/well_metadata/.config.vsh.yaml | 4 +- .../nextflow/workflows/well_metadata/main.nf | 4 +- 64 files changed, 163 insertions(+), 135 deletions(-) diff --git a/README.md b/README.md index 5e7d27dd..6a9a87cb 100644 --- a/README.md +++ b/README.md @@ -14,7 +14,7 @@ version](https://img.shields.io/badge/Viash-v0.9.2-blue)](https://viash.io) ## Introduction This workflow is designed to process high-throughput RNA-seq data, where -every well in a microarray plate is a sample. A fasta file provided as +every well of a microarray plate is a sample. A fasta file provided as input defines the mapping between sample barcodes and wells. The workflow is built in a modular fashion, where most of the base @@ -23,7 +23,8 @@ functionality is provided by components from supplemented by custom base components and workflow components in this package. -The full workflow can be split in two major subworkflows: +The full workflow is split in two major subworkflows that can be run +independently: - **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well. @@ -41,6 +42,10 @@ run in two ways: where a number of choices (input/output structure and location) have been made. +Input for the workflow has to be `fastq` files (zipped or not). For bcl +or other formats, please consider running +[demultiplex](https://www.viash-hub.com/packages/demultiplex) first. + ## Example usage ## Test and example data @@ -68,10 +73,10 @@ Press the ‘Launch’ button and follow the instructions. ![](assets/htrnaseq-launch-small.png) We will start an example run loading just one input and using a barcodes -fast file containing only 2 wells. +fasta file containing only 2 wells. In the first step, we add the `local` profile to the list of profiles in -order to the cpu and memory requirements of the workflow steps: +order to limit the cpu and memory requirements of the workflow steps: ![](assets/launch-parameters-1-small.png) In the next step, we provide the paramters as follows: @@ -87,7 +92,7 @@ the paramters as follows: - `annotation`: `gs://viash-hub-test-data/htrnaseq/v1/genomeDir/gencode.v41.annotation.gtf.gz` -Please not the following: Both `input_r1` and `input_r2` take multiple +Please note that both `input_r1` and `input_r2` can take multiple values. This means that one has to press ENTER after pasting the input path. @@ -98,10 +103,11 @@ run the workflow from the CLI. ## Run using NF-Tower / Seqera Cloud -It’s possible to run the workflow directly from Seqera Cloud. The -necessary schema file has been built and provided with the workflows in -order to use the form-based input. However, Seqera Cloud can not deal -with multiple-value parameters when using the form -based input. +It’s possible to run the workflow directly from [Seqera +Cloud](https://cloud.seqera.io). The necessary schema file has been +built and provided with the workflows in order to use the form-based +input. However, Seqera Cloud can not deal with multiple-value parameters +when using the form -based input. It’s better to use Viash Hub also here: @@ -121,7 +127,18 @@ In the next screen, pressing the ‘Launch’ button will actually start the workflow on Seqera Cloud. A message is shown when the submit was successful. -![](assets/launch-parameters-5-small.png) +![](assets/launch-parameters-5-small.png) \## Run from the CLI + +Running from the CLI directly without using Viash hub is possible. The +easiest is to just use the integrated help functionality, for instance +using the following: + +``` bash + nextflow run https://packages.viash-hub.com/vsh/htrnaseq.git \ + -revision v0.3.0 \ + -main-script target/nextflow/workflows/runner/main.nf \ + --help +``` # Contributions diff --git a/README.qmd b/README.qmd index be4ab77f..65a7730b 100644 --- a/README.qmd +++ b/README.qmd @@ -39,9 +39,9 @@ Open [Viash Hub](https://www.viash-hub.com) and browse to the [htrnaseq componen ![](assets/htrnaseq-launch-small.png) -We will start an example run loading just one input and using a barcodes fast file containing only 2 wells. +We will start an example run loading just one input and using a barcodes fasta file containing only 2 wells. -In the first step, we add the `local` profile to the list of profiles in order to the cpu and memory requirements of the workflow steps: +In the first step, we add the `local` profile to the list of profiles in order to limit the cpu and memory requirements of the workflow steps: ![](assets/launch-parameters-1-small.png) @@ -53,7 +53,7 @@ In the next step, we provide the paramters as follows: - `barcodesFasta`: `gs://viash-hub-test-data/htrnaseq/v1/2-wells-with-ids.fasta` - `annotation`: `gs://viash-hub-test-data/htrnaseq/v1/genomeDir/gencode.v41.annotation.gtf.gz` -Please not the following: Both `input_r1` and `input_r2` take multiple values. This means that one has to press ENTER after pasting the input path. +Please note that both `input_r1` and `input_r2` can take multiple values. This means that one has to press ENTER after pasting the input path. ![](assets/launch-parameters-2-small.png) @@ -62,7 +62,7 @@ Press the 'Launch' button at the end to get the instructions on how to run the w ## Run using NF-Tower / Seqera Cloud -It's possible to run the workflow directly from Seqera Cloud. The necessary schema file has been built and provided with the workflows in order to use the form-based input. However, Seqera Cloud can not deal with multiple-value parameters when using the form -based input. +It's possible to run the workflow directly from [Seqera Cloud](https://cloud.seqera.io). The necessary schema file has been built and provided with the workflows in order to use the form-based input. However, Seqera Cloud can not deal with multiple-value parameters when using the form -based input. It's better to use Viash Hub also here: @@ -77,6 +77,17 @@ Next, we need to fill in the paramters for the run. This is similar to before: In the next screen, pressing the 'Launch' button will actually start the workflow on Seqera Cloud. A message is shown when the submit was successful. ![](assets/launch-parameters-5-small.png) +## Run from the CLI + +Running from the CLI directly without using Viash hub is possible. The easiest is to just use the integrated help functionality, for instance using the following: + +```bash + nextflow run https://packages.viash-hub.com/vsh/htrnaseq.git \ + -revision v0.3.0 \ + -main-script target/nextflow/workflows/runner/main.nf \ + --help +``` + # Contributions diff --git a/_viash.yaml b/_viash.yaml index 59e641cd..e4d09436 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -3,7 +3,7 @@ summary: | A workflow for high-throughput RNA-seq data analyses. description: | This workflow is designed to process high-throughput RNA-seq data, where every - well in a microarray plate is a sample. A fasta file provided as input + well of a microarray plate is a sample. A fasta file provided as input defines the mapping between sample barcodes and wells. 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a/target/executable/eset/create_eset/.config.vsh.yaml b/target/executable/eset/create_eset/.config.vsh.yaml index 4ba3a778..9949e68c 100644 --- a/target/executable/eset/create_eset/.config.vsh.yaml +++ b/target/executable/eset/create_eset/.config.vsh.yaml @@ -203,14 +203,14 @@ build_info: output: "target/executable/eset/create_eset" executable: "target/executable/eset/create_eset/create_eset" viash_version: "0.9.2" - git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git a/target/executable/eset/create_eset/create_eset b/target/executable/eset/create_eset/create_eset index bf0e1a8d..bf1a8a10 100755 --- 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="2025-05-02T16:11:19Z" +LABEL org.opencontainers.image.created="2025-05-02T17:15:47Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="db4b3f68b2f5d18f357f4db6932d3186df28fd1c" +LABEL org.opencontainers.image.revision="fb376b17126d0ff90904cc426799d88782b8c68d" LABEL org.opencontainers.image.version="update-readme" VIASHDOCKER diff --git a/target/executable/eset/create_fdata/.config.vsh.yaml b/target/executable/eset/create_fdata/.config.vsh.yaml index 9744de80..a11c7529 100644 --- a/target/executable/eset/create_fdata/.config.vsh.yaml +++ b/target/executable/eset/create_fdata/.config.vsh.yaml @@ -180,14 +180,14 @@ build_info: output: "target/executable/eset/create_fdata" executable: "target/executable/eset/create_fdata/create_fdata" viash_version: "0.9.2" - git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git a/target/executable/eset/create_fdata/create_fdata b/target/executable/eset/create_fdata/create_fdata index 126b79cf..34a0f724 100755 --- 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="2025-05-02T16:11:19Z" +LABEL org.opencontainers.image.created="2025-05-02T17:15:47Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="db4b3f68b2f5d18f357f4db6932d3186df28fd1c" +LABEL org.opencontainers.image.revision="fb376b17126d0ff90904cc426799d88782b8c68d" LABEL org.opencontainers.image.version="update-readme" VIASHDOCKER diff --git a/target/executable/eset/create_pdata/.config.vsh.yaml b/target/executable/eset/create_pdata/.config.vsh.yaml index 2117a39c..b01c745b 100644 --- a/target/executable/eset/create_pdata/.config.vsh.yaml +++ b/target/executable/eset/create_pdata/.config.vsh.yaml @@ -194,14 +194,14 @@ build_info: output: "target/executable/eset/create_pdata" executable: "target/executable/eset/create_pdata/create_pdata" viash_version: "0.9.2" - git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git a/target/executable/eset/create_pdata/create_pdata b/target/executable/eset/create_pdata/create_pdata index 74674914..5cad61d9 100755 --- 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="2025-05-02T16:11:19Z" +LABEL org.opencontainers.image.created="2025-05-02T17:15:47Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="db4b3f68b2f5d18f357f4db6932d3186df28fd1c" +LABEL org.opencontainers.image.revision="fb376b17126d0ff90904cc426799d88782b8c68d" LABEL org.opencontainers.image.version="update-readme" VIASHDOCKER diff --git a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml index 37970f67..791c4d6d 100644 --- a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml +++ b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml @@ -152,14 +152,14 @@ 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: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset index eb3ceac5..102b25ed 100755 --- 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="2025-05-02T16:11:18Z" +LABEL org.opencontainers.image.created="2025-05-02T17:15:46Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="db4b3f68b2f5d18f357f4db6932d3186df28fd1c" +LABEL org.opencontainers.image.revision="fb376b17126d0ff90904cc426799d88782b8c68d" LABEL org.opencontainers.image.version="update-readme" VIASHDOCKER diff --git 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 index f352f590..7e586079 100644 --- 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 @@ -161,14 +161,14 @@ 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: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git 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 index 1d583325..98b94a6d 100755 --- 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="2025-05-02T16:11:20Z" +LABEL org.opencontainers.image.created="2025-05-02T17:15:48Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="db4b3f68b2f5d18f357f4db6932d3186df28fd1c" +LABEL org.opencontainers.image.revision="fb376b17126d0ff90904cc426799d88782b8c68d" LABEL org.opencontainers.image.version="update-readme" VIASHDOCKER diff --git a/target/executable/io/publish_fastqs/.config.vsh.yaml b/target/executable/io/publish_fastqs/.config.vsh.yaml index 6f69b3a5..825f9607 100644 --- a/target/executable/io/publish_fastqs/.config.vsh.yaml +++ b/target/executable/io/publish_fastqs/.config.vsh.yaml @@ -136,14 +136,14 @@ build_info: output: "target/executable/io/publish_fastqs" executable: "target/executable/io/publish_fastqs/publish_fastqs" viash_version: "0.9.2" - git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git a/target/executable/io/publish_fastqs/publish_fastqs b/target/executable/io/publish_fastqs/publish_fastqs index f9cd0b8c..24687e05 100755 --- 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="2025-05-02T16:11:18Z" +LABEL org.opencontainers.image.created="2025-05-02T17:15:46Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="db4b3f68b2f5d18f357f4db6932d3186df28fd1c" +LABEL org.opencontainers.image.revision="fb376b17126d0ff90904cc426799d88782b8c68d" LABEL org.opencontainers.image.version="update-readme" VIASHDOCKER diff --git a/target/executable/io/publish_results/.config.vsh.yaml b/target/executable/io/publish_results/.config.vsh.yaml index 82c0db13..38beae56 100644 --- a/target/executable/io/publish_results/.config.vsh.yaml +++ b/target/executable/io/publish_results/.config.vsh.yaml @@ -190,14 +190,14 @@ build_info: output: "target/executable/io/publish_results" executable: "target/executable/io/publish_results/publish_results" viash_version: "0.9.2" - git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git a/target/executable/io/publish_results/publish_results b/target/executable/io/publish_results/publish_results index 7f9999ef..5296a05e 100755 --- 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="2025-05-02T16:11:18Z" +LABEL org.opencontainers.image.created="2025-05-02T17:15:47Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="db4b3f68b2f5d18f357f4db6932d3186df28fd1c" +LABEL org.opencontainers.image.revision="fb376b17126d0ff90904cc426799d88782b8c68d" LABEL org.opencontainers.image.version="update-readme" VIASHDOCKER diff --git a/target/executable/parallel_map/.config.vsh.yaml b/target/executable/parallel_map/.config.vsh.yaml index 49af62c8..7d1d2791 100644 --- a/target/executable/parallel_map/.config.vsh.yaml +++ b/target/executable/parallel_map/.config.vsh.yaml @@ -282,14 +282,14 @@ build_info: output: "target/executable/parallel_map" executable: "target/executable/parallel_map/parallel_map" viash_version: "0.9.2" - git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git a/target/executable/parallel_map/parallel_map b/target/executable/parallel_map/parallel_map index 8c5385d1..ea63e3a0 100755 --- 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="2025-05-02T16:11:19Z" +LABEL org.opencontainers.image.created="2025-05-02T17:15:47Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="db4b3f68b2f5d18f357f4db6932d3186df28fd1c" +LABEL org.opencontainers.image.revision="fb376b17126d0ff90904cc426799d88782b8c68d" LABEL org.opencontainers.image.version="update-readme" VIASHDOCKER diff --git a/target/executable/report/create_report/.config.vsh.yaml b/target/executable/report/create_report/.config.vsh.yaml index 36a5e5bc..67811c4f 100644 --- a/target/executable/report/create_report/.config.vsh.yaml +++ b/target/executable/report/create_report/.config.vsh.yaml @@ -206,14 +206,14 @@ build_info: output: "target/executable/report/create_report" executable: "target/executable/report/create_report/create_report" viash_version: "0.9.2" - git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git a/target/executable/report/create_report/create_report b/target/executable/report/create_report/create_report index b921fa95..95a6862a 100755 --- 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="2025-05-02T16:11:19Z" +LABEL org.opencontainers.image.created="2025-05-02T17:15:47Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="db4b3f68b2f5d18f357f4db6932d3186df28fd1c" +LABEL org.opencontainers.image.revision="fb376b17126d0ff90904cc426799d88782b8c68d" LABEL org.opencontainers.image.version="update-readme" VIASHDOCKER diff --git a/target/executable/stats/combine_star_logs/.config.vsh.yaml b/target/executable/stats/combine_star_logs/.config.vsh.yaml index b878ae1d..0a369903 100644 --- a/target/executable/stats/combine_star_logs/.config.vsh.yaml +++ b/target/executable/stats/combine_star_logs/.config.vsh.yaml @@ -201,14 +201,14 @@ 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: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git a/target/executable/stats/combine_star_logs/combine_star_logs b/target/executable/stats/combine_star_logs/combine_star_logs index 23f46ec1..45309f2c 100755 --- 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="2025-05-02T16:11:18Z" +LABEL org.opencontainers.image.created="2025-05-02T17:15:46Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="db4b3f68b2f5d18f357f4db6932d3186df28fd1c" +LABEL org.opencontainers.image.revision="fb376b17126d0ff90904cc426799d88782b8c68d" LABEL org.opencontainers.image.version="update-readme" VIASHDOCKER diff --git a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml index 7d34f254..869bb257 100644 --- a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml +++ b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml @@ -185,14 +185,14 @@ 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: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git a/target/executable/stats/generate_pool_statistics/generate_pool_statistics b/target/executable/stats/generate_pool_statistics/generate_pool_statistics index f0da4bb0..4004763f 100755 --- 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="2025-05-02T16:11:18Z" +LABEL org.opencontainers.image.created="2025-05-02T17:15:46Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="db4b3f68b2f5d18f357f4db6932d3186df28fd1c" +LABEL org.opencontainers.image.revision="fb376b17126d0ff90904cc426799d88782b8c68d" LABEL org.opencontainers.image.version="update-readme" VIASHDOCKER diff --git a/target/executable/stats/generate_well_statistics/.config.vsh.yaml b/target/executable/stats/generate_well_statistics/.config.vsh.yaml index 0a167b47..1db91cc5 100644 --- a/target/executable/stats/generate_well_statistics/.config.vsh.yaml +++ b/target/executable/stats/generate_well_statistics/.config.vsh.yaml @@ -267,14 +267,14 @@ 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: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git a/target/executable/stats/generate_well_statistics/generate_well_statistics b/target/executable/stats/generate_well_statistics/generate_well_statistics index e1579f30..79bb0217 100755 --- 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="2025-05-02T16:11:18Z" +LABEL org.opencontainers.image.created="2025-05-02T17:15:46Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="db4b3f68b2f5d18f357f4db6932d3186df28fd1c" +LABEL org.opencontainers.image.revision="fb376b17126d0ff90904cc426799d88782b8c68d" LABEL org.opencontainers.image.version="update-readme" VIASHDOCKER diff --git a/target/nextflow/eset/create_eset/.config.vsh.yaml b/target/nextflow/eset/create_eset/.config.vsh.yaml index 13665407..6fda0590 100644 --- a/target/nextflow/eset/create_eset/.config.vsh.yaml +++ b/target/nextflow/eset/create_eset/.config.vsh.yaml @@ -203,14 +203,14 @@ build_info: output: "target/nextflow/eset/create_eset" executable: "target/nextflow/eset/create_eset/main.nf" viash_version: "0.9.2" - git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git a/target/nextflow/eset/create_eset/main.nf b/target/nextflow/eset/create_eset/main.nf index 47b7ebce..e87b5a31 100644 --- a/target/nextflow/eset/create_eset/main.nf +++ b/target/nextflow/eset/create_eset/main.nf @@ -3309,14 +3309,14 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_eset", "viash_version" : "0.9.2", - "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c", + "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", "version" : "update-readme", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", - "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", + "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", "info" : { "test_resources" : [ { diff --git a/target/nextflow/eset/create_fdata/.config.vsh.yaml b/target/nextflow/eset/create_fdata/.config.vsh.yaml index 9fe3e01b..8f684c89 100644 --- a/target/nextflow/eset/create_fdata/.config.vsh.yaml +++ b/target/nextflow/eset/create_fdata/.config.vsh.yaml @@ -180,14 +180,14 @@ build_info: output: "target/nextflow/eset/create_fdata" executable: "target/nextflow/eset/create_fdata/main.nf" viash_version: "0.9.2" - git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git a/target/nextflow/eset/create_fdata/main.nf b/target/nextflow/eset/create_fdata/main.nf index ab91818f..41b6d379 100644 --- a/target/nextflow/eset/create_fdata/main.nf +++ b/target/nextflow/eset/create_fdata/main.nf @@ -3279,14 +3279,14 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_fdata", "viash_version" : "0.9.2", - "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c", + "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", "version" : "update-readme", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", - "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", + "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", "info" : { "test_resources" : [ { diff --git a/target/nextflow/eset/create_pdata/.config.vsh.yaml b/target/nextflow/eset/create_pdata/.config.vsh.yaml index 24c41a2a..e1ecafe8 100644 --- a/target/nextflow/eset/create_pdata/.config.vsh.yaml +++ b/target/nextflow/eset/create_pdata/.config.vsh.yaml @@ -194,14 +194,14 @@ build_info: output: "target/nextflow/eset/create_pdata" executable: "target/nextflow/eset/create_pdata/main.nf" viash_version: "0.9.2" - git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git a/target/nextflow/eset/create_pdata/main.nf b/target/nextflow/eset/create_pdata/main.nf index 5202f4eb..549817ea 100644 --- a/target/nextflow/eset/create_pdata/main.nf +++ b/target/nextflow/eset/create_pdata/main.nf @@ -3293,14 +3293,14 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_pdata", "viash_version" : "0.9.2", - "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c", + "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", "version" : "update-readme", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", - "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", + "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", "info" : { "test_resources" : [ { diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml index dcd3ba13..ead8c047 100644 --- a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml +++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml @@ -152,14 +152,14 @@ 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: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf index 5fd9258e..3282de39 100644 --- a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf +++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf @@ -3233,14 +3233,14 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset", "viash_version" : "0.9.2", - "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c", + "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", "version" : "update-readme", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", - "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", + "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", "info" : { "test_resources" : [ { diff --git 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 index 2d040046..23a03202 100644 --- 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 @@ -161,14 +161,14 @@ 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: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git 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 index 75fe110b..236148b3 100644 --- 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 @@ -3244,14 +3244,14 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output", "viash_version" : "0.9.2", - "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c", + "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", "version" : "update-readme", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", - "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", + "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", "info" : { "test_resources" : [ { diff --git a/target/nextflow/io/publish_fastqs/.config.vsh.yaml b/target/nextflow/io/publish_fastqs/.config.vsh.yaml index 9a25d08d..21066fa8 100644 --- a/target/nextflow/io/publish_fastqs/.config.vsh.yaml +++ b/target/nextflow/io/publish_fastqs/.config.vsh.yaml @@ -136,14 +136,14 @@ build_info: output: "target/nextflow/io/publish_fastqs" executable: "target/nextflow/io/publish_fastqs/main.nf" viash_version: "0.9.2" - git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git a/target/nextflow/io/publish_fastqs/main.nf b/target/nextflow/io/publish_fastqs/main.nf index 53a17079..8f3b0e37 100644 --- a/target/nextflow/io/publish_fastqs/main.nf +++ b/target/nextflow/io/publish_fastqs/main.nf @@ -3207,14 +3207,14 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish_fastqs", "viash_version" : "0.9.2", - "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c", + "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", "version" : "update-readme", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", - "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", + "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", "info" : { "test_resources" : [ { diff --git a/target/nextflow/io/publish_results/.config.vsh.yaml b/target/nextflow/io/publish_results/.config.vsh.yaml index db60f97d..4593f3a4 100644 --- a/target/nextflow/io/publish_results/.config.vsh.yaml +++ b/target/nextflow/io/publish_results/.config.vsh.yaml @@ -190,14 +190,14 @@ build_info: output: "target/nextflow/io/publish_results" executable: "target/nextflow/io/publish_results/main.nf" viash_version: "0.9.2" - git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git a/target/nextflow/io/publish_results/main.nf b/target/nextflow/io/publish_results/main.nf index ac651387..bd8250ec 100644 --- a/target/nextflow/io/publish_results/main.nf +++ b/target/nextflow/io/publish_results/main.nf @@ -3267,14 +3267,14 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish_results", "viash_version" : "0.9.2", - "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c", + "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", "version" : "update-readme", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", - "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", + "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", "info" : { "test_resources" : [ { diff --git a/target/nextflow/parallel_map/.config.vsh.yaml b/target/nextflow/parallel_map/.config.vsh.yaml index a50d53af..357fd428 100644 --- a/target/nextflow/parallel_map/.config.vsh.yaml +++ b/target/nextflow/parallel_map/.config.vsh.yaml @@ -282,14 +282,14 @@ build_info: output: "target/nextflow/parallel_map" executable: "target/nextflow/parallel_map/main.nf" viash_version: "0.9.2" - git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git a/target/nextflow/parallel_map/main.nf b/target/nextflow/parallel_map/main.nf index 35e302e8..30e1b124 100644 --- a/target/nextflow/parallel_map/main.nf +++ b/target/nextflow/parallel_map/main.nf @@ -3379,14 +3379,14 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/parallel_map", "viash_version" : "0.9.2", - "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c", + "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", "version" : "update-readme", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", - "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", + "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", "info" : { "test_resources" : [ { diff --git a/target/nextflow/report/create_report/.config.vsh.yaml b/target/nextflow/report/create_report/.config.vsh.yaml index 954c6e16..e4c6f6fa 100644 --- a/target/nextflow/report/create_report/.config.vsh.yaml +++ b/target/nextflow/report/create_report/.config.vsh.yaml @@ -206,14 +206,14 @@ build_info: output: "target/nextflow/report/create_report" executable: "target/nextflow/report/create_report/main.nf" viash_version: "0.9.2" - git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git a/target/nextflow/report/create_report/main.nf b/target/nextflow/report/create_report/main.nf index e2f31721..640e68dd 100644 --- a/target/nextflow/report/create_report/main.nf +++ b/target/nextflow/report/create_report/main.nf @@ -3314,14 +3314,14 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/report/create_report", "viash_version" : "0.9.2", - "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c", + "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", "version" : "update-readme", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", - "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", + "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", "info" : { "test_resources" : [ { diff --git a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml index ffb1833e..d532e3c2 100644 --- a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml +++ b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml @@ -201,14 +201,14 @@ 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: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git a/target/nextflow/stats/combine_star_logs/main.nf b/target/nextflow/stats/combine_star_logs/main.nf index d8d486f1..0f331d51 100644 --- a/target/nextflow/stats/combine_star_logs/main.nf +++ b/target/nextflow/stats/combine_star_logs/main.nf @@ -3295,14 +3295,14 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/combine_star_logs", "viash_version" : "0.9.2", - "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c", + "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", "version" : "update-readme", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", - "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", + "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", "info" : { "test_resources" : [ { diff --git a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml index d8093861..5a868146 100644 --- a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml +++ b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml @@ -185,14 +185,14 @@ 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: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git a/target/nextflow/stats/generate_pool_statistics/main.nf b/target/nextflow/stats/generate_pool_statistics/main.nf index 703cabbf..efa1acc5 100644 --- a/target/nextflow/stats/generate_pool_statistics/main.nf +++ b/target/nextflow/stats/generate_pool_statistics/main.nf @@ -3279,14 +3279,14 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/generate_pool_statistics", "viash_version" : "0.9.2", - "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c", + "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", "version" : "update-readme", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", - "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", + "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", "info" : { "test_resources" : [ { diff --git a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml index c9c90e46..2a7d2067 100644 --- a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml +++ b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml @@ -267,14 +267,14 @@ 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: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git a/target/nextflow/stats/generate_well_statistics/main.nf b/target/nextflow/stats/generate_well_statistics/main.nf index ac6420c1..4c7c2f19 100644 --- a/target/nextflow/stats/generate_well_statistics/main.nf +++ b/target/nextflow/stats/generate_well_statistics/main.nf @@ -3374,14 +3374,14 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/generate_well_statistics", "viash_version" : "0.9.2", - "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c", + "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", "version" : "update-readme", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", - "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", + "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", "info" : { "test_resources" : [ { diff --git a/target/nextflow/utils/concatRuns/.config.vsh.yaml b/target/nextflow/utils/concatRuns/.config.vsh.yaml index 954742b6..599f01f9 100644 --- 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: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" dependencies: - "target/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/concat_text" @@ -166,7 +166,7 @@ package_config: version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git a/target/nextflow/utils/concatRuns/main.nf b/target/nextflow/utils/concatRuns/main.nf index 5f03b137..775002b6 100644 --- a/target/nextflow/utils/concatRuns/main.nf +++ b/target/nextflow/utils/concatRuns/main.nf @@ -3229,14 +3229,14 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/utils/concatRuns", "viash_version" : "0.9.2", - "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c", + "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", "version" : "update-readme", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", - "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", + "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", "info" : { "test_resources" : [ { diff --git a/target/nextflow/utils/listInputDir/.config.vsh.yaml b/target/nextflow/utils/listInputDir/.config.vsh.yaml index ca569c20..b9d72c5b 100644 --- a/target/nextflow/utils/listInputDir/.config.vsh.yaml +++ b/target/nextflow/utils/listInputDir/.config.vsh.yaml @@ -168,14 +168,14 @@ build_info: output: "target/nextflow/utils/listInputDir" executable: "target/nextflow/utils/listInputDir/main.nf" viash_version: "0.9.2" - git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git a/target/nextflow/utils/listInputDir/main.nf b/target/nextflow/utils/listInputDir/main.nf index 720d820b..248af017 100644 --- a/target/nextflow/utils/listInputDir/main.nf +++ b/target/nextflow/utils/listInputDir/main.nf @@ -3239,14 +3239,14 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/utils/listInputDir", "viash_version" : "0.9.2", - "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c", + "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", "version" : "update-readme", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", - "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", + "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", "info" : { "test_resources" : [ { diff --git a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml index 766f2107..9b4aa78f 100644 --- a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml +++ b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml @@ -328,7 +328,7 @@ build_info: output: "target/nextflow/workflows/htrnaseq" executable: "target/nextflow/workflows/htrnaseq/main.nf" viash_version: "0.9.2" - git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" dependencies: - "target/nextflow/stats/combine_star_logs" @@ -347,7 +347,7 @@ package_config: version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git a/target/nextflow/workflows/htrnaseq/main.nf b/target/nextflow/workflows/htrnaseq/main.nf index df26d422..4ad69fd8 100644 --- a/target/nextflow/workflows/htrnaseq/main.nf +++ b/target/nextflow/workflows/htrnaseq/main.nf @@ -3465,14 +3465,14 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/htrnaseq", "viash_version" : "0.9.2", - "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c", + "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", "version" : "update-readme", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", - "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", + "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", "info" : { "test_resources" : [ { diff --git a/target/nextflow/workflows/runner/.config.vsh.yaml b/target/nextflow/workflows/runner/.config.vsh.yaml index d9874fa4..09c3559d 100644 --- 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: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" dependencies: - "target/nextflow/utils/listInputDir" @@ -233,7 +233,7 @@ package_config: version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git a/target/nextflow/workflows/runner/main.nf b/target/nextflow/workflows/runner/main.nf index a06b1a04..61b98be1 100644 --- a/target/nextflow/workflows/runner/main.nf +++ b/target/nextflow/workflows/runner/main.nf @@ -3317,14 +3317,14 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/runner", "viash_version" : "0.9.2", - "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c", + "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", "version" : "update-readme", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", - "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", + "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", "info" : { "test_resources" : [ { diff --git a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml index b64f5788..a75c46f5 100644 --- 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: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/cutadapt" @@ -224,7 +224,7 @@ package_config: version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git a/target/nextflow/workflows/well_demultiplex/main.nf b/target/nextflow/workflows/well_demultiplex/main.nf index 02fbfafa..00f528be 100644 --- a/target/nextflow/workflows/well_demultiplex/main.nf +++ b/target/nextflow/workflows/well_demultiplex/main.nf @@ -3319,14 +3319,14 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/well_demultiplex", "viash_version" : "0.9.2", - "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c", + "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", "version" : "update-readme", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", - "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", + "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", "info" : { "test_resources" : [ { diff --git a/target/nextflow/workflows/well_metadata/.config.vsh.yaml b/target/nextflow/workflows/well_metadata/.config.vsh.yaml index e41b72a8..283b2259 100644 --- a/target/nextflow/workflows/well_metadata/.config.vsh.yaml +++ b/target/nextflow/workflows/well_metadata/.config.vsh.yaml @@ -212,14 +212,14 @@ build_info: output: "target/nextflow/workflows/well_metadata" executable: "target/nextflow/workflows/well_metadata/main.nf" viash_version: "0.9.2" - git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c" + git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" version: "update-readme" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ - \ where every\nwell in a microarray plate is a sample. A fasta file provided as\ + \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\ \ is built in a modular fashion, where most of the base functionality\nis provided\ \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\ diff --git a/target/nextflow/workflows/well_metadata/main.nf b/target/nextflow/workflows/well_metadata/main.nf index 506b9580..8d611971 100644 --- a/target/nextflow/workflows/well_metadata/main.nf +++ b/target/nextflow/workflows/well_metadata/main.nf @@ -3299,14 +3299,14 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/well_metadata", "viash_version" : "0.9.2", - "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c", + "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", "version" : "update-readme", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", - "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", + "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n", "info" : { "test_resources" : [ {