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Build branch htrnaseq/v0.12 with version v0.12.2 to htrnaseq on branch v0.12 (f0f85f5)

Browse Source 
Build pipeline: viash-hub.htrnaseq.v0.12-j94lf

Source commit: f0f85f5774

Source message: Bump version to v0.12.2
This commit is contained in:
CI
2025-09-23 13:05:57 +00:00
parent e6c08d3edf
commit 050b56eea2
118 changed files with 426 additions and 420 deletions
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10
target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "check_eset"
namespace: "integration_test_components/htrnaseq"
version: "v0.12.1"
version: "v0.12.2"
authors:
- name: "Dries Schaumont"
roles:
@@ -134,7 +134,7 @@ engines:
id: "docker"
image: "bioconductor/bioconductor_docker:3.19"
target_registry: "images.viash-hub.com"
target_tag: "v0.12.1"
target_tag: "v0.12.2"
namespace_separator: "/"
setup:
- type: "r"
@@ -155,11 +155,11 @@ build_info:
output: "target/executable/integration_test_components/htrnaseq/check_eset"
executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset"
viash_version: "0.9.4"
git_commit: "32476d30426827c70014658cf0746ffcf55be62c"
git_commit: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "v0.12.1"
version: "v0.12.2"
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 of a microarray plate is a sample. A fasta file provided as\
@@ -191,7 +191,7 @@ package_config:
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.1'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.2'"
keywords:
- "bioinformatics"
- "sequencing"

2
target/executable/integration_test_components/htrnaseq/check_eset/_viash.yaml
View File

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.1
version: v0.12.2
summary: |
A workflow for high-throughput RNA-seq data analyses.
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 is split in two major subworkflows that can be run independently:\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 [(opinionated) `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\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"

14
target/executable/integration_test_components/htrnaseq/check_eset/check_eset
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# check_eset v0.12.1
# check_eset v0.12.2
#
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -455,10 +455,10 @@ 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="2025-09-19T07:50:15Z"
LABEL org.opencontainers.image.created="2025-09-23T12:11:21Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="32476d30426827c70014658cf0746ffcf55be62c"
LABEL org.opencontainers.image.version="v0.12.1"
LABEL org.opencontainers.image.revision="f0f85f57744b71e17ee3c0afe1a221cd20903aef"
LABEL org.opencontainers.image.version="v0.12.2"
VIASHDOCKER
fi
@@ -575,7 +575,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "check_eset v0.12.1"
echo "check_eset v0.12.2"
echo ""
echo "This component test the ExpressionSet object as output by the main pipeline."
echo ""
@@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "check_eset v0.12.1"
echo "check_eset v0.12.2"
exit
;;
--eset)
@@ -754,7 +754,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/htrnaseq/check_eset:v0.12.1'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/htrnaseq/check_eset:v0.12.2'
fi
# print dockerfile

10
target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "check_cutadapt_output"
namespace: "integration_test_components/well_demultiplexing"
version: "v0.12.1"
version: "v0.12.2"
authors:
- name: "Dries Schaumont"
roles:
@@ -141,7 +141,7 @@ engines:
id: "docker"
image: "python:3.12-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.12.1"
target_tag: "v0.12.2"
namespace_separator: "/"
setup:
- type: "apt"
@@ -164,11 +164,11 @@ 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: "0.9.4"
git_commit: "32476d30426827c70014658cf0746ffcf55be62c"
git_commit: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "v0.12.1"
version: "v0.12.2"
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 of a microarray plate is a sample. A fasta file provided as\
@@ -200,7 +200,7 @@ package_config:
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.1'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.2'"
keywords:
- "bioinformatics"
- "sequencing"

2
target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml
View File

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.1
version: v0.12.2
summary: |
A workflow for high-throughput RNA-seq data analyses.
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 is split in two major subworkflows that can be run independently:\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 [(opinionated) `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\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"

14
target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# check_cutadapt_output v0.12.1
# check_cutadapt_output v0.12.2
#
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -457,10 +457,10 @@ 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="2025-09-19T07:50:14Z"
LABEL org.opencontainers.image.created="2025-09-23T12:11:21Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="32476d30426827c70014658cf0746ffcf55be62c"
LABEL org.opencontainers.image.version="v0.12.1"
LABEL org.opencontainers.image.revision="f0f85f57744b71e17ee3c0afe1a221cd20903aef"
LABEL org.opencontainers.image.version="v0.12.2"
VIASHDOCKER
fi
@@ -577,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "check_cutadapt_output v0.12.1"
echo "check_cutadapt_output v0.12.2"
echo ""
echo "This component test the cutadapt output from the well_demultiplex subworkflow."
echo ""
@@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "check_cutadapt_output v0.12.1"
echo "check_cutadapt_output v0.12.2"
exit
;;
--fastq_r1)
@@ -783,7 +783,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output:v0.12.1'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output:v0.12.2'
fi
# print dockerfile