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Build branch htrnaseq/v0.12 with version v0.12.3 to htrnaseq on branch v0.12 (7c7b7fe)

Browse Source 
Build pipeline: viash-hub.htrnaseq.v0.12-77xk8

Source commit: 7c7b7fec25

Source message: Prep v0.12.3 release - update _viash.yaml
This commit is contained in:
CI
2025-10-09 13:08:37 +00:00
parent 050b56eea2
commit f0b6b4a45c
120 changed files with 436 additions and 430 deletions
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12
CHANGELOG.md
View File

@@ -1,3 +1,9 @@
# htrnaseq v0.12.3
## Bug fixes
* Allow for annotation of more than 20 pools (PR #78).
# htrnaseq v0.12.2
## Bug fixes
@@ -6,17 +12,17 @@
# htrnaseq v0.12.1
# Minor changes
## Minor changes
* Update `parallel_map` cpu label from `lowcpu` to `highcpu` (PR 75).
# htrnaseq v0.12.0
# Minor changes
## Minor changes
* Improve publishing speed by keeping symbolic links (PR #74).
# Bug fixes
## Bug fixes
* Avoid double slashes in the publish directory path in order to not create empty objects on S3 (PR #72).

2
_viash.yaml
View File

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.2
version: v0.12.3
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"

6
src/report/template.Rmd
View File

@@ -170,10 +170,10 @@ if (length(Design_levels) == 1) {
} else {
colours <- c("#d6e0ff")
names(colours) <- c("nonEmpty")
colourList[[annotVar]] <- list(
colourList[[annotationVar]] <- list(
"colours" = colours,
"annotVar" = annotVar,
"text" = annotVar
"annotVar" = annotationVar,
"text" = annotationVar
)
}
```

10
target/executable/eset/create_eset/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "create_eset"
namespace: "eset"
version: "v0.12.2"
version: "v0.12.3"
authors:
- name: "Dries Schaumont"
roles:
@@ -178,7 +178,7 @@ engines:
id: "docker"
image: "rocker/r2u:24.04"
target_registry: "images.viash-hub.com"
target_tag: "v0.12.2"
target_tag: "v0.12.3"
namespace_separator: "/"
setup:
- type: "r"
@@ -206,11 +206,11 @@ build_info:
output: "target/executable/eset/create_eset"
executable: "target/executable/eset/create_eset/create_eset"
viash_version: "0.9.4"
git_commit: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_commit: "7c7b7fec254ba6b77d985706fc955449445d83f5"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "v0.12.2"
version: "v0.12.3"
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\
@@ -242,7 +242,7 @@ package_config:
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.2'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.3'"
keywords:
- "bioinformatics"
- "sequencing"

2
target/executable/eset/create_eset/_viash.yaml
View File

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.2
version: v0.12.3
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/eset/create_eset/create_eset
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# create_eset v0.12.2
# create_eset v0.12.3
#
# 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
@@ -456,10 +456,10 @@ 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="2025-09-23T12:11:21Z"
LABEL org.opencontainers.image.created="2025-10-09T12:16:24Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="f0f85f57744b71e17ee3c0afe1a221cd20903aef"
LABEL org.opencontainers.image.version="v0.12.2"
LABEL org.opencontainers.image.revision="7c7b7fec254ba6b77d985706fc955449445d83f5"
LABEL org.opencontainers.image.version="v0.12.3"
VIASHDOCKER
fi
@@ -576,7 +576,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "create_eset v0.12.2"
echo "create_eset v0.12.3"
echo ""
echo "Arguments:"
echo " --pDataFile"
@@ -642,7 +642,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "create_eset v0.12.2"
echo "create_eset v0.12.3"
exit
;;
--pDataFile)
@@ -794,7 +794,7 @@ if [[ "$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/eset/create_eset:v0.12.2'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_eset:v0.12.3'
fi
# print dockerfile

10
target/executable/eset/create_fdata/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "create_fdata"
namespace: "eset"
version: "v0.12.2"
version: "v0.12.3"
authors:
- name: "Dries Schaumont"
roles:
@@ -154,7 +154,7 @@ engines:
id: "docker"
image: "python:3.12-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.12.2"
target_tag: "v0.12.3"
namespace_separator: "/"
setup:
- type: "apt"
@@ -183,11 +183,11 @@ build_info:
output: "target/executable/eset/create_fdata"
executable: "target/executable/eset/create_fdata/create_fdata"
viash_version: "0.9.4"
git_commit: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_commit: "7c7b7fec254ba6b77d985706fc955449445d83f5"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "v0.12.2"
version: "v0.12.3"
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\
@@ -219,7 +219,7 @@ package_config:
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.2'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.3'"
keywords:
- "bioinformatics"
- "sequencing"

2
target/executable/eset/create_fdata/_viash.yaml
View File

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.2
version: v0.12.3
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/eset/create_fdata/create_fdata
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# create_fdata v0.12.2
# create_fdata v0.12.3
#
# 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
@@ -458,10 +458,10 @@ 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="2025-09-23T12:11:20Z"
LABEL org.opencontainers.image.created="2025-10-09T12:16:23Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="f0f85f57744b71e17ee3c0afe1a221cd20903aef"
LABEL org.opencontainers.image.version="v0.12.2"
LABEL org.opencontainers.image.revision="7c7b7fec254ba6b77d985706fc955449445d83f5"
LABEL org.opencontainers.image.version="v0.12.3"
VIASHDOCKER
fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "create_fdata v0.12.2"
echo "create_fdata v0.12.3"
echo ""
echo "Create a fdata file"
echo ""
@@ -643,7 +643,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "create_fdata v0.12.2"
echo "create_fdata v0.12.3"
exit
;;
--gtf)
@@ -756,7 +756,7 @@ if [[ "$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/eset/create_fdata:v0.12.2'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_fdata:v0.12.3'
fi
# print dockerfile

10
target/executable/eset/create_pdata/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "create_pdata"
namespace: "eset"
version: "v0.12.2"
version: "v0.12.3"
authors:
- name: "Dries Schaumont"
roles:
@@ -168,7 +168,7 @@ engines:
id: "docker"
image: "python:3.12-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.12.2"
target_tag: "v0.12.3"
namespace_separator: "/"
setup:
- type: "apt"
@@ -197,11 +197,11 @@ build_info:
output: "target/executable/eset/create_pdata"
executable: "target/executable/eset/create_pdata/create_pdata"
viash_version: "0.9.4"
git_commit: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_commit: "7c7b7fec254ba6b77d985706fc955449445d83f5"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "v0.12.2"
version: "v0.12.3"
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\
@@ -233,7 +233,7 @@ package_config:
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.2'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.3'"
keywords:
- "bioinformatics"
- "sequencing"

2
target/executable/eset/create_pdata/_viash.yaml
View File

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.2
version: v0.12.3
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/eset/create_pdata/create_pdata
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# create_pdata v0.12.2
# create_pdata v0.12.3
#
# 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
@@ -458,10 +458,10 @@ 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="2025-09-23T12:11:19Z"
LABEL org.opencontainers.image.created="2025-10-09T12:16:22Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="f0f85f57744b71e17ee3c0afe1a221cd20903aef"
LABEL org.opencontainers.image.version="v0.12.2"
LABEL org.opencontainers.image.revision="7c7b7fec254ba6b77d985706fc955449445d83f5"
LABEL org.opencontainers.image.version="v0.12.3"
VIASHDOCKER
fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "create_pdata v0.12.2"
echo "create_pdata v0.12.3"
echo ""
echo "Create a pdata file by combining the mapping statistics"
echo ""
@@ -653,7 +653,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "create_pdata v0.12.2"
echo "create_pdata v0.12.3"
exit
;;
--star_stats_file)
@@ -777,7 +777,7 @@ if [[ "$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/eset/create_pdata:v0.12.2'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_pdata:v0.12.3'
fi
# print dockerfile

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: "v0.12.2"
version: "v0.12.3"
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: "v0.12.2"
target_tag: "v0.12.3"
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: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_commit: "7c7b7fec254ba6b77d985706fc955449445d83f5"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "v0.12.2"
version: "v0.12.3"
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 := 'v0.12.2'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.3'"
keywords:
- "bioinformatics"
- "sequencing"

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

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.2
version: v0.12.3
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 v0.12.2
# check_eset v0.12.3
#
# 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="2025-09-23T12:11:21Z"
LABEL org.opencontainers.image.created="2025-10-09T12:16:24Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="f0f85f57744b71e17ee3c0afe1a221cd20903aef"
LABEL org.opencontainers.image.version="v0.12.2"
LABEL org.opencontainers.image.revision="7c7b7fec254ba6b77d985706fc955449445d83f5"
LABEL org.opencontainers.image.version="v0.12.3"
VIASHDOCKER
fi
@@ -575,7 +575,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "check_eset v0.12.2"
echo "check_eset v0.12.3"
echo ""
echo "This component test the ExpressionSet object as output by the main pipeline."
echo ""
@@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "check_eset v0.12.2"
echo "check_eset v0.12.3"
exit
;;
--eset)
@@ -754,7 +754,7 @@ if [[ "$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:v0.12.2'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/htrnaseq/check_eset:v0.12.3'
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: "v0.12.2"
version: "v0.12.3"
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: "v0.12.2"
target_tag: "v0.12.3"
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: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_commit: "7c7b7fec254ba6b77d985706fc955449445d83f5"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "v0.12.2"
version: "v0.12.3"
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 := 'v0.12.2'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.3'"
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: v0.12.2
version: v0.12.3
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 v0.12.2
# check_cutadapt_output v0.12.3
#
# 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="2025-09-23T12:11:21Z"
LABEL org.opencontainers.image.created="2025-10-09T12:16:24Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="f0f85f57744b71e17ee3c0afe1a221cd20903aef"
LABEL org.opencontainers.image.version="v0.12.2"
LABEL org.opencontainers.image.revision="7c7b7fec254ba6b77d985706fc955449445d83f5"
LABEL org.opencontainers.image.version="v0.12.3"
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 v0.12.2"
echo "check_cutadapt_output v0.12.3"
echo ""
echo "This component test the cutadapt output from the well_demultiplex subworkflow."
echo ""
@@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "check_cutadapt_output v0.12.2"
echo "check_cutadapt_output v0.12.3"
exit
;;
--fastq_r1)
@@ -783,7 +783,7 @@ if [[ "$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:v0.12.2'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output:v0.12.3'
fi
# print dockerfile

10
target/executable/io/publish_fastqs/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "publish_fastqs"
namespace: "io"
version: "v0.12.2"
version: "v0.12.3"
argument_groups:
- name: "Input arguments"
arguments:
@@ -121,7 +121,7 @@ engines:
id: "docker"
image: "debian:stable-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.12.2"
target_tag: "v0.12.3"
namespace_separator: "/"
setup:
- type: "apt"
@@ -139,11 +139,11 @@ build_info:
output: "target/executable/io/publish_fastqs"
executable: "target/executable/io/publish_fastqs/publish_fastqs"
viash_version: "0.9.4"
git_commit: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_commit: "7c7b7fec254ba6b77d985706fc955449445d83f5"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "v0.12.2"
version: "v0.12.3"
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\
@@ -175,7 +175,7 @@ package_config:
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.2'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.3'"
keywords:
- "bioinformatics"
- "sequencing"

2
target/executable/io/publish_fastqs/_viash.yaml
View File

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.2
version: v0.12.3
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/io/publish_fastqs/publish_fastqs
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# publish_fastqs v0.12.2
# publish_fastqs v0.12.3
#
# 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
@@ -450,10 +450,10 @@ 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="2025-09-23T12:11:21Z"
LABEL org.opencontainers.image.created="2025-10-09T12:16:24Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="f0f85f57744b71e17ee3c0afe1a221cd20903aef"
LABEL org.opencontainers.image.version="v0.12.2"
LABEL org.opencontainers.image.revision="7c7b7fec254ba6b77d985706fc955449445d83f5"
LABEL org.opencontainers.image.version="v0.12.3"
VIASHDOCKER
fi
@@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "publish_fastqs v0.12.2"
echo "publish_fastqs v0.12.3"
echo ""
echo "Publish the fastq files per well"
echo ""
@@ -631,7 +631,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "publish_fastqs v0.12.2"
echo "publish_fastqs v0.12.3"
exit
;;
--input)
@@ -750,7 +750,7 @@ if [[ "$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/io/publish_fastqs:v0.12.2'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_fastqs:v0.12.3'
fi
# print dockerfile

10
target/executable/io/publish_results/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "publish_results"
namespace: "io"
version: "v0.12.2"
version: "v0.12.3"
argument_groups:
- name: "Input arguments"
arguments:
@@ -261,7 +261,7 @@ engines:
id: "docker"
image: "debian:stable-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.12.2"
target_tag: "v0.12.3"
namespace_separator: "/"
setup:
- type: "apt"
@@ -279,11 +279,11 @@ build_info:
output: "target/executable/io/publish_results"
executable: "target/executable/io/publish_results/publish_results"
viash_version: "0.9.4"
git_commit: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_commit: "7c7b7fec254ba6b77d985706fc955449445d83f5"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "v0.12.2"
version: "v0.12.3"
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\
@@ -315,7 +315,7 @@ package_config:
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.2'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.3'"
keywords:
- "bioinformatics"
- "sequencing"

2
target/executable/io/publish_results/_viash.yaml
View File

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.2
version: v0.12.3
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/io/publish_results/publish_results
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# publish_results v0.12.2
# publish_results v0.12.3
#
# 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
@@ -450,10 +450,10 @@ 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="2025-09-23T12:11:21Z"
LABEL org.opencontainers.image.created="2025-10-09T12:16:24Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="f0f85f57744b71e17ee3c0afe1a221cd20903aef"
LABEL org.opencontainers.image.version="v0.12.2"
LABEL org.opencontainers.image.revision="7c7b7fec254ba6b77d985706fc955449445d83f5"
LABEL org.opencontainers.image.version="v0.12.3"
VIASHDOCKER
fi
@@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "publish_results v0.12.2"
echo "publish_results v0.12.3"
echo ""
echo "Publish the results"
echo ""
@@ -683,7 +683,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "publish_results v0.12.2"
echo "publish_results v0.12.3"
exit
;;
--star_output)
@@ -986,7 +986,7 @@ if [[ "$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/io/publish_results:v0.12.2'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_results:v0.12.3'
fi
# print dockerfile

10
target/executable/parallel_map/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "parallel_map"
version: "v0.12.2"
version: "v0.12.3"
authors:
- name: "Dries Schaumont"
roles:
@@ -248,7 +248,7 @@ engines:
id: "docker"
image: "debian:stable-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.12.2"
target_tag: "v0.12.3"
namespace_separator: "/"
setup:
- type: "apt"
@@ -285,11 +285,11 @@ build_info:
output: "target/executable/parallel_map"
executable: "target/executable/parallel_map/parallel_map"
viash_version: "0.9.4"
git_commit: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_commit: "7c7b7fec254ba6b77d985706fc955449445d83f5"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "v0.12.2"
version: "v0.12.3"
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\
@@ -321,7 +321,7 @@ package_config:
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.2'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.3'"
keywords:
- "bioinformatics"
- "sequencing"

2
target/executable/parallel_map/_viash.yaml
View File

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.2
version: v0.12.3
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/parallel_map/parallel_map
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# parallel_map v0.12.2
# parallel_map v0.12.3
#
# 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
@@ -461,10 +461,10 @@ 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="2025-09-23T12:11:20Z"
LABEL org.opencontainers.image.created="2025-10-09T12:16:24Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="f0f85f57744b71e17ee3c0afe1a221cd20903aef"
LABEL org.opencontainers.image.version="v0.12.2"
LABEL org.opencontainers.image.revision="7c7b7fec254ba6b77d985706fc955449445d83f5"
LABEL org.opencontainers.image.version="v0.12.3"
VIASHDOCKER
fi
@@ -581,7 +581,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "parallel_map v0.12.2"
echo "parallel_map v0.12.3"
echo ""
echo "Map wells in batch, using STAR"
echo "Spliced Transcripts Alignment to a Reference (C) Alexander Dobin"
@@ -705,7 +705,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "parallel_map v0.12.2"
echo "parallel_map v0.12.3"
exit
;;
--input_r1)
@@ -907,7 +907,7 @@ if [[ "$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/parallel_map:v0.12.2'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/parallel_map:v0.12.3'
fi
# print dockerfile

10
target/executable/report/create_report/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "create_report"
namespace: "report"
version: "v0.12.2"
version: "v0.12.3"
authors:
- name: "Dries Schaumont"
roles:
@@ -159,7 +159,7 @@ engines:
id: "docker"
image: "rocker/r2u:24.04"
target_registry: "images.viash-hub.com"
target_tag: "v0.12.2"
target_tag: "v0.12.3"
namespace_separator: "/"
setup:
- type: "apt"
@@ -215,11 +215,11 @@ build_info:
output: "target/executable/report/create_report"
executable: "target/executable/report/create_report/create_report"
viash_version: "0.9.4"
git_commit: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_commit: "7c7b7fec254ba6b77d985706fc955449445d83f5"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "v0.12.2"
version: "v0.12.3"
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\
@@ -251,7 +251,7 @@ package_config:
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.2'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.3'"
keywords:
- "bioinformatics"
- "sequencing"

2
target/executable/report/create_report/_viash.yaml
View File

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.2
version: v0.12.3
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/report/create_report/create_report
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# create_report v0.12.2
# create_report v0.12.3
#
# 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
@@ -465,10 +465,10 @@ 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="2025-09-23T12:11:21Z"
LABEL org.opencontainers.image.created="2025-10-09T12:16:24Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="f0f85f57744b71e17ee3c0afe1a221cd20903aef"
LABEL org.opencontainers.image.version="v0.12.2"
LABEL org.opencontainers.image.revision="7c7b7fec254ba6b77d985706fc955449445d83f5"
LABEL org.opencontainers.image.version="v0.12.3"
VIASHDOCKER
fi
@@ -585,7 +585,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "create_report v0.12.2"
echo "create_report v0.12.3"
echo ""
echo "Create a basic QC report in HTML format based on a number of esets."
echo ""
@@ -644,7 +644,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "create_report v0.12.2"
echo "create_report v0.12.3"
exit
;;
--eset)
@@ -763,7 +763,7 @@ if [[ "$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/report/create_report:v0.12.2'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/report/create_report:v0.12.3'
fi
# print dockerfile

6
target/executable/report/create_report/template.Rmd
View File

@@ -170,10 +170,10 @@ if (length(Design_levels) == 1) {
} else {
colours <- c("#d6e0ff")
names(colours) <- c("nonEmpty")
colourList[[annotVar]] <- list(
colourList[[annotationVar]] <- list(
"colours" = colours,
"annotVar" = annotVar,
"text" = annotVar
"annotVar" = annotationVar,
"text" = annotationVar
)
}
```

10
target/executable/stats/combine_star_logs/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "combine_star_logs"
namespace: "stats"
version: "v0.12.2"
version: "v0.12.3"
authors:
- name: "Dries Schaumont"
roles:
@@ -175,7 +175,7 @@ engines:
id: "docker"
image: "python:3.12-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.12.2"
target_tag: "v0.12.3"
namespace_separator: "/"
setup:
- type: "apt"
@@ -204,11 +204,11 @@ build_info:
output: "target/executable/stats/combine_star_logs"
executable: "target/executable/stats/combine_star_logs/combine_star_logs"
viash_version: "0.9.4"
git_commit: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_commit: "7c7b7fec254ba6b77d985706fc955449445d83f5"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "v0.12.2"
version: "v0.12.3"
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\
@@ -240,7 +240,7 @@ package_config:
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.2'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.3'"
keywords:
- "bioinformatics"
- "sequencing"

2
target/executable/stats/combine_star_logs/_viash.yaml
View File

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.2
version: v0.12.3
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/stats/combine_star_logs/combine_star_logs
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# combine_star_logs v0.12.2
# combine_star_logs v0.12.3
#
# 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 stats combine_star_logs"
LABEL org.opencontainers.image.created="2025-09-23T12:11:20Z"
LABEL org.opencontainers.image.created="2025-10-09T12:16:23Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="f0f85f57744b71e17ee3c0afe1a221cd20903aef"
LABEL org.opencontainers.image.version="v0.12.2"
LABEL org.opencontainers.image.revision="7c7b7fec254ba6b77d985706fc955449445d83f5"
LABEL org.opencontainers.image.version="v0.12.3"
VIASHDOCKER
fi
@@ -577,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "combine_star_logs v0.12.2"
echo "combine_star_logs v0.12.3"
echo ""
echo "Arguments:"
echo " --barcodes"
@@ -655,7 +655,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "combine_star_logs v0.12.2"
echo "combine_star_logs v0.12.3"
exit
;;
--barcodes)
@@ -825,7 +825,7 @@ if [[ "$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/stats/combine_star_logs:v0.12.2'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/combine_star_logs:v0.12.3'
fi
# print dockerfile

10
target/executable/stats/generate_pool_statistics/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "generate_pool_statistics"
namespace: "stats"
version: "v0.12.2"
version: "v0.12.3"
authors:
- name: "Dries Schaumont"
roles:
@@ -159,7 +159,7 @@ engines:
id: "docker"
image: "python:3.12-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.12.2"
target_tag: "v0.12.3"
namespace_separator: "/"
setup:
- type: "apt"
@@ -188,11 +188,11 @@ build_info:
output: "target/executable/stats/generate_pool_statistics"
executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics"
viash_version: "0.9.4"
git_commit: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_commit: "7c7b7fec254ba6b77d985706fc955449445d83f5"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "v0.12.2"
version: "v0.12.3"
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\
@@ -224,7 +224,7 @@ package_config:
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.2'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.3'"
keywords:
- "bioinformatics"
- "sequencing"

2
target/executable/stats/generate_pool_statistics/_viash.yaml
View File

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.2
version: v0.12.3
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/stats/generate_pool_statistics/generate_pool_statistics
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# generate_pool_statistics v0.12.2
# generate_pool_statistics v0.12.3
#
# 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
@@ -458,10 +458,10 @@ 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="2025-09-23T12:11:20Z"
LABEL org.opencontainers.image.created="2025-10-09T12:16:23Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="f0f85f57744b71e17ee3c0afe1a221cd20903aef"
LABEL org.opencontainers.image.version="v0.12.2"
LABEL org.opencontainers.image.revision="7c7b7fec254ba6b77d985706fc955449445d83f5"
LABEL org.opencontainers.image.version="v0.12.3"
VIASHDOCKER
fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "generate_pool_statistics v0.12.2"
echo "generate_pool_statistics v0.12.3"
echo ""
echo "Arguments:"
echo " --nrReadsNrGenesPerChrom"
@@ -648,7 +648,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "generate_pool_statistics v0.12.2"
echo "generate_pool_statistics v0.12.3"
exit
;;
--nrReadsNrGenesPerChrom)
@@ -767,7 +767,7 @@ if [[ "$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/stats/generate_pool_statistics:v0.12.2'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_pool_statistics:v0.12.3'
fi
# print dockerfile

10
target/executable/stats/generate_well_statistics/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "generate_well_statistics"
namespace: "stats"
version: "v0.12.2"
version: "v0.12.3"
authors:
- name: "Dries Schaumont"
roles:
@@ -230,7 +230,7 @@ engines:
id: "docker"
image: "python:3.13-trixie"
target_registry: "images.viash-hub.com"
target_tag: "v0.12.2"
target_tag: "v0.12.3"
namespace_separator: "/"
setup:
- type: "apt"
@@ -260,11 +260,11 @@ build_info:
output: "target/executable/stats/generate_well_statistics"
executable: "target/executable/stats/generate_well_statistics/generate_well_statistics"
viash_version: "0.9.4"
git_commit: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_commit: "7c7b7fec254ba6b77d985706fc955449445d83f5"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "v0.12.2"
version: "v0.12.3"
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\
@@ -296,7 +296,7 @@ package_config:
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.2'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.3'"
keywords:
- "bioinformatics"
- "sequencing"

2
target/executable/stats/generate_well_statistics/_viash.yaml
View File

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.2
version: v0.12.3
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/stats/generate_well_statistics/generate_well_statistics
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# generate_well_statistics v0.12.2
# generate_well_statistics v0.12.3
#
# 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
@@ -458,10 +458,10 @@ 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="2025-09-23T12:11:20Z"
LABEL org.opencontainers.image.created="2025-10-09T12:16:23Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="f0f85f57744b71e17ee3c0afe1a221cd20903aef"
LABEL org.opencontainers.image.version="v0.12.2"
LABEL org.opencontainers.image.revision="7c7b7fec254ba6b77d985706fc955449445d83f5"
LABEL org.opencontainers.image.version="v0.12.3"
VIASHDOCKER
fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "generate_well_statistics v0.12.2"
echo "generate_well_statistics v0.12.3"
echo ""
echo "Generate summary statistics from BAM files generated by STAR solo."
echo ""
@@ -682,7 +682,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "generate_well_statistics v0.12.2"
echo "generate_well_statistics v0.12.3"
exit
;;
--input)
@@ -861,7 +861,7 @@ if [[ "$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/stats/generate_well_statistics:v0.12.2'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_well_statistics:v0.12.3'
fi
# print dockerfile

10
target/executable/utils/save_params/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "save_params"
namespace: "utils"
version: "v0.12.2"
version: "v0.12.3"
argument_groups:
- name: "Inputs"
arguments:
@@ -128,7 +128,7 @@ engines:
id: "docker"
image: "python:3.12-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.12.2"
target_tag: "v0.12.3"
namespace_separator: "/"
setup:
- type: "apt"
@@ -151,11 +151,11 @@ build_info:
output: "target/executable/utils/save_params"
executable: "target/executable/utils/save_params/save_params"
viash_version: "0.9.4"
git_commit: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_commit: "7c7b7fec254ba6b77d985706fc955449445d83f5"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "v0.12.2"
version: "v0.12.3"
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\
@@ -187,7 +187,7 @@ package_config:
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.2'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.3'"
keywords:
- "bioinformatics"
- "sequencing"

2
target/executable/utils/save_params/_viash.yaml
View File

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.2
version: v0.12.3
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/utils/save_params/save_params
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# save_params v0.12.2
# save_params v0.12.3
#
# 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
@@ -453,10 +453,10 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "pyyaml"
LABEL org.opencontainers.image.description="Companion container for running component utils save_params"
LABEL org.opencontainers.image.created="2025-09-23T12:11:20Z"
LABEL org.opencontainers.image.created="2025-10-09T12:16:23Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="f0f85f57744b71e17ee3c0afe1a221cd20903aef"
LABEL org.opencontainers.image.version="v0.12.2"
LABEL org.opencontainers.image.revision="7c7b7fec254ba6b77d985706fc955449445d83f5"
LABEL org.opencontainers.image.version="v0.12.3"
VIASHDOCKER
fi
@@ -573,7 +573,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "save_params v0.12.2"
echo "save_params v0.12.3"
echo ""
echo "Save parameters to a YAML file"
echo ""
@@ -639,7 +639,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "save_params v0.12.2"
echo "save_params v0.12.3"
exit
;;
--id)
@@ -763,7 +763,7 @@ if [[ "$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/utils/save_params:v0.12.2'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/utils/save_params:v0.12.3'
fi
# print dockerfile

10
target/nextflow/eset/create_eset/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "create_eset"
namespace: "eset"
version: "v0.12.2"
version: "v0.12.3"
authors:
- name: "Dries Schaumont"
roles:
@@ -178,7 +178,7 @@ engines:
id: "docker"
image: "rocker/r2u:24.04"
target_registry: "images.viash-hub.com"
target_tag: "v0.12.2"
target_tag: "v0.12.3"
namespace_separator: "/"
setup:
- type: "r"
@@ -206,11 +206,11 @@ build_info:
output: "target/nextflow/eset/create_eset"
executable: "target/nextflow/eset/create_eset/main.nf"
viash_version: "0.9.4"
git_commit: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_commit: "7c7b7fec254ba6b77d985706fc955449445d83f5"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "v0.12.2"
version: "v0.12.3"
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\
@@ -242,7 +242,7 @@ package_config:
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.2'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.3'"
keywords:
- "bioinformatics"
- "sequencing"

2
target/nextflow/eset/create_eset/_viash.yaml
View File

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.2
version: v0.12.3
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/nextflow/eset/create_eset/main.nf
View File

@@ -1,4 +1,4 @@
// create_eset v0.12.2
// create_eset v0.12.3
//
// 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
@@ -3036,7 +3036,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "create_eset",
"namespace" : "eset",
"version" : "v0.12.2",
"version" : "v0.12.3",
"authors" : [
{
"name" : "Dries Schaumont",
@@ -3271,7 +3271,7 @@ meta = [
"id" : "docker",
"image" : "rocker/r2u:24.04",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.12.2",
"target_tag" : "v0.12.3",
"namespace_separator" : "/",
"setup" : [
{
@@ -3309,12 +3309,12 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_eset",
"viash_version" : "0.9.4",
"git_commit" : "f0f85f57744b71e17ee3c0afe1a221cd20903aef",
"git_commit" : "7c7b7fec254ba6b77d985706fc955449445d83f5",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "v0.12.2",
"version" : "v0.12.3",
"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 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",
"info" : {
@@ -3332,7 +3332,7 @@ meta = [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.12.2'"
".engines[.type == 'docker'].target_tag := 'v0.12.3'"
],
"keywords" : [
"bioinformatics",
@@ -4207,7 +4207,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/htrnaseq/eset/create_eset",
"tag" : "v0.12.2"
"tag" : "v0.12.3"
},
"tag" : "$id"
}'''),

2
target/nextflow/eset/create_eset/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'eset/create_eset'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.12.2'
version = 'v0.12.3'
author = 'Dries Schaumont, Marijke Van Moerbeke'
}

10
target/nextflow/eset/create_fdata/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "create_fdata"
namespace: "eset"
version: "v0.12.2"
version: "v0.12.3"
authors:
- name: "Dries Schaumont"
roles:
@@ -154,7 +154,7 @@ engines:
id: "docker"
image: "python:3.12-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.12.2"
target_tag: "v0.12.3"
namespace_separator: "/"
setup:
- type: "apt"
@@ -183,11 +183,11 @@ build_info:
output: "target/nextflow/eset/create_fdata"
executable: "target/nextflow/eset/create_fdata/main.nf"
viash_version: "0.9.4"
git_commit: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_commit: "7c7b7fec254ba6b77d985706fc955449445d83f5"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "v0.12.2"
version: "v0.12.3"
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\
@@ -219,7 +219,7 @@ package_config:
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.2'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.3'"
keywords:
- "bioinformatics"
- "sequencing"

2
target/nextflow/eset/create_fdata/_viash.yaml
View File

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.2
version: v0.12.3
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/nextflow/eset/create_fdata/main.nf
View File

@@ -1,4 +1,4 @@
// create_fdata v0.12.2
// create_fdata v0.12.3
//
// 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
@@ -3036,7 +3036,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "create_fdata",
"namespace" : "eset",
"version" : "v0.12.2",
"version" : "v0.12.3",
"authors" : [
{
"name" : "Dries Schaumont",
@@ -3238,7 +3238,7 @@ meta = [
"id" : "docker",
"image" : "python:3.12-slim",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.12.2",
"target_tag" : "v0.12.3",
"namespace_separator" : "/",
"setup" : [
{
@@ -3279,12 +3279,12 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_fdata",
"viash_version" : "0.9.4",
"git_commit" : "f0f85f57744b71e17ee3c0afe1a221cd20903aef",
"git_commit" : "7c7b7fec254ba6b77d985706fc955449445d83f5",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "v0.12.2",
"version" : "v0.12.3",
"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 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",
"info" : {
@@ -3302,7 +3302,7 @@ meta = [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.12.2'"
".engines[.type == 'docker'].target_tag := 'v0.12.3'"
],
"keywords" : [
"bioinformatics",
@@ -3872,7 +3872,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/htrnaseq/eset/create_fdata",
"tag" : "v0.12.2"
"tag" : "v0.12.3"
},
"tag" : "$id"
}'''),

2
target/nextflow/eset/create_fdata/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'eset/create_fdata'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.12.2'
version = 'v0.12.3'
description = 'Create a fdata file\n'
author = 'Dries Schaumont, Marijke Van Moerbeke'
}

10
target/nextflow/eset/create_pdata/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "create_pdata"
namespace: "eset"
version: "v0.12.2"
version: "v0.12.3"
authors:
- name: "Dries Schaumont"
roles:
@@ -168,7 +168,7 @@ engines:
id: "docker"
image: "python:3.12-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.12.2"
target_tag: "v0.12.3"
namespace_separator: "/"
setup:
- type: "apt"
@@ -197,11 +197,11 @@ build_info:
output: "target/nextflow/eset/create_pdata"
executable: "target/nextflow/eset/create_pdata/main.nf"
viash_version: "0.9.4"
git_commit: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_commit: "7c7b7fec254ba6b77d985706fc955449445d83f5"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "v0.12.2"
version: "v0.12.3"
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\
@@ -233,7 +233,7 @@ package_config:
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.2'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.3'"
keywords:
- "bioinformatics"
- "sequencing"

2
target/nextflow/eset/create_pdata/_viash.yaml
View File

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.2
version: v0.12.3
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/nextflow/eset/create_pdata/main.nf
View File

@@ -1,4 +1,4 @@
// create_pdata v0.12.2
// create_pdata v0.12.3
//
// 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
@@ -3036,7 +3036,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "create_pdata",
"namespace" : "eset",
"version" : "v0.12.2",
"version" : "v0.12.3",
"authors" : [
{
"name" : "Dries Schaumont",
@@ -3252,7 +3252,7 @@ meta = [
"id" : "docker",
"image" : "python:3.12-slim",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.12.2",
"target_tag" : "v0.12.3",
"namespace_separator" : "/",
"setup" : [
{
@@ -3293,12 +3293,12 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_pdata",
"viash_version" : "0.9.4",
"git_commit" : "f0f85f57744b71e17ee3c0afe1a221cd20903aef",
"git_commit" : "7c7b7fec254ba6b77d985706fc955449445d83f5",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "v0.12.2",
"version" : "v0.12.3",
"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 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",
"info" : {
@@ -3316,7 +3316,7 @@ meta = [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.12.2'"
".engines[.type == 'docker'].target_tag := 'v0.12.3'"
],
"keywords" : [
"bioinformatics",
@@ -3812,7 +3812,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/htrnaseq/eset/create_pdata",
"tag" : "v0.12.2"
"tag" : "v0.12.3"
},
"tag" : "$id"
}'''),

2
target/nextflow/eset/create_pdata/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'eset/create_pdata'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.12.2'
version = 'v0.12.3'
description = 'Create a pdata file by combining the mapping statistics \n'
author = 'Dries Schaumont, Marijke Van Moerbeke'
}

10
target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "check_eset"
namespace: "integration_test_components/htrnaseq"
version: "v0.12.2"
version: "v0.12.3"
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: "v0.12.2"
target_tag: "v0.12.3"
namespace_separator: "/"
setup:
- type: "r"
@@ -155,11 +155,11 @@ build_info:
output: "target/nextflow/integration_test_components/htrnaseq/check_eset"
executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf"
viash_version: "0.9.4"
git_commit: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_commit: "7c7b7fec254ba6b77d985706fc955449445d83f5"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "v0.12.2"
version: "v0.12.3"
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 := 'v0.12.2'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.3'"
keywords:
- "bioinformatics"
- "sequencing"

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

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.2
version: v0.12.3
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/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
View File

@@ -1,4 +1,4 @@
// check_eset v0.12.2
// check_eset v0.12.3
//
// 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
@@ -3035,7 +3035,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "check_eset",
"namespace" : "integration_test_components/htrnaseq",
"version" : "v0.12.2",
"version" : "v0.12.3",
"authors" : [
{
"name" : "Dries Schaumont",
@@ -3206,7 +3206,7 @@ meta = [
"id" : "docker",
"image" : "bioconductor/bioconductor_docker:3.19",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.12.2",
"target_tag" : "v0.12.3",
"namespace_separator" : "/",
"setup" : [
{
@@ -3233,12 +3233,12 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
"viash_version" : "0.9.4",
"git_commit" : "f0f85f57744b71e17ee3c0afe1a221cd20903aef",
"git_commit" : "7c7b7fec254ba6b77d985706fc955449445d83f5",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "v0.12.2",
"version" : "v0.12.3",
"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 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",
"info" : {
@@ -3256,7 +3256,7 @@ meta = [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.12.2'"
".engines[.type == 'docker'].target_tag := 'v0.12.3'"
],
"keywords" : [
"bioinformatics",
@@ -3906,7 +3906,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/htrnaseq/integration_test_components/htrnaseq/check_eset",
"tag" : "v0.12.2"
"tag" : "v0.12.3"
},
"tag" : "$id"
}'''),

2
target/nextflow/integration_test_components/htrnaseq/check_eset/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'integration_test_components/htrnaseq/check_eset'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.12.2'
version = 'v0.12.3'
description = 'This component test the ExpressionSet object as output by the main pipeline.'
author = 'Dries Schaumont'
}

10
target/nextflow/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: "v0.12.2"
version: "v0.12.3"
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: "v0.12.2"
target_tag: "v0.12.3"
namespace_separator: "/"
setup:
- type: "apt"
@@ -164,11 +164,11 @@ 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: "0.9.4"
git_commit: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_commit: "7c7b7fec254ba6b77d985706fc955449445d83f5"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "v0.12.2"
version: "v0.12.3"
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 := 'v0.12.2'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.3'"
keywords:
- "bioinformatics"
- "sequencing"

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

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.2
version: v0.12.3
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/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf
View File

@@ -1,4 +1,4 @@
// check_cutadapt_output v0.12.2
// check_cutadapt_output v0.12.3
//
// 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
@@ -3035,7 +3035,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "check_cutadapt_output",
"namespace" : "integration_test_components/well_demultiplexing",
"version" : "v0.12.2",
"version" : "v0.12.3",
"authors" : [
{
"name" : "Dries Schaumont",
@@ -3213,7 +3213,7 @@ meta = [
"id" : "docker",
"image" : "python:3.12-slim",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.12.2",
"target_tag" : "v0.12.3",
"namespace_separator" : "/",
"setup" : [
{
@@ -3244,12 +3244,12 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
"viash_version" : "0.9.4",
"git_commit" : "f0f85f57744b71e17ee3c0afe1a221cd20903aef",
"git_commit" : "7c7b7fec254ba6b77d985706fc955449445d83f5",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "v0.12.2",
"version" : "v0.12.3",
"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 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",
"info" : {
@@ -3267,7 +3267,7 @@ meta = [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.12.2'"
".engines[.type == 'docker'].target_tag := 'v0.12.3'"
],
"keywords" : [
"bioinformatics",
@@ -3786,7 +3786,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output",
"tag" : "v0.12.2"
"tag" : "v0.12.3"
},
"tag" : "$id"
}'''),

2
target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'integration_test_components/well_demultiplexing/check_cutadapt_output'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.12.2'
version = 'v0.12.3'
description = 'This component test the cutadapt output from the well_demultiplex subworkflow.'
author = 'Dries Schaumont'
}

10
target/nextflow/io/publish_fastqs/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "publish_fastqs"
namespace: "io"
version: "v0.12.2"
version: "v0.12.3"
argument_groups:
- name: "Input arguments"
arguments:
@@ -121,7 +121,7 @@ engines:
id: "docker"
image: "debian:stable-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.12.2"
target_tag: "v0.12.3"
namespace_separator: "/"
setup:
- type: "apt"
@@ -139,11 +139,11 @@ build_info:
output: "target/nextflow/io/publish_fastqs"
executable: "target/nextflow/io/publish_fastqs/main.nf"
viash_version: "0.9.4"
git_commit: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_commit: "7c7b7fec254ba6b77d985706fc955449445d83f5"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "v0.12.2"
version: "v0.12.3"
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\
@@ -175,7 +175,7 @@ package_config:
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.2'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.3'"
keywords:
- "bioinformatics"
- "sequencing"

2
target/nextflow/io/publish_fastqs/_viash.yaml
View File

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.2
version: v0.12.3
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/nextflow/io/publish_fastqs/main.nf
View File

@@ -1,4 +1,4 @@
// publish_fastqs v0.12.2
// publish_fastqs v0.12.3
//
// 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
@@ -3032,7 +3032,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "publish_fastqs",
"namespace" : "io",
"version" : "v0.12.2",
"version" : "v0.12.3",
"argument_groups" : [
{
"name" : "Input arguments",
@@ -3184,7 +3184,7 @@ meta = [
"id" : "docker",
"image" : "debian:stable-slim",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.12.2",
"target_tag" : "v0.12.3",
"namespace_separator" : "/",
"setup" : [
{
@@ -3207,12 +3207,12 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/publish_fastqs",
"viash_version" : "0.9.4",
"git_commit" : "f0f85f57744b71e17ee3c0afe1a221cd20903aef",
"git_commit" : "7c7b7fec254ba6b77d985706fc955449445d83f5",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "v0.12.2",
"version" : "v0.12.3",
"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 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",
"info" : {
@@ -3230,7 +3230,7 @@ meta = [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.12.2'"
".engines[.type == 'docker'].target_tag := 'v0.12.3'"
],
"keywords" : [
"bioinformatics",
@@ -3682,7 +3682,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/htrnaseq/io/publish_fastqs",
"tag" : "v0.12.2"
"tag" : "v0.12.3"
},
"tag" : "$id"
}'''),

2
target/nextflow/io/publish_fastqs/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'io/publish_fastqs'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.12.2'
version = 'v0.12.3'
description = 'Publish the fastq files per well'
}

10
target/nextflow/io/publish_results/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "publish_results"
namespace: "io"
version: "v0.12.2"
version: "v0.12.3"
argument_groups:
- name: "Input arguments"
arguments:
@@ -261,7 +261,7 @@ engines:
id: "docker"
image: "debian:stable-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.12.2"
target_tag: "v0.12.3"
namespace_separator: "/"
setup:
- type: "apt"
@@ -279,11 +279,11 @@ build_info:
output: "target/nextflow/io/publish_results"
executable: "target/nextflow/io/publish_results/main.nf"
viash_version: "0.9.4"
git_commit: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_commit: "7c7b7fec254ba6b77d985706fc955449445d83f5"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "v0.12.2"
version: "v0.12.3"
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\
@@ -315,7 +315,7 @@ package_config:
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.2'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.3'"
keywords:
- "bioinformatics"
- "sequencing"

2
target/nextflow/io/publish_results/_viash.yaml
View File

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.2
version: v0.12.3
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/nextflow/io/publish_results/main.nf
View File

@@ -1,4 +1,4 @@
// publish_results v0.12.2
// publish_results v0.12.3
//
// 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
@@ -3032,7 +3032,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "publish_results",
"namespace" : "io",
"version" : "v0.12.2",
"version" : "v0.12.3",
"argument_groups" : [
{
"name" : "Input arguments",
@@ -3346,7 +3346,7 @@ meta = [
"id" : "docker",
"image" : "debian:stable-slim",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.12.2",
"target_tag" : "v0.12.3",
"namespace_separator" : "/",
"setup" : [
{
@@ -3369,12 +3369,12 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/publish_results",
"viash_version" : "0.9.4",
"git_commit" : "f0f85f57744b71e17ee3c0afe1a221cd20903aef",
"git_commit" : "7c7b7fec254ba6b77d985706fc955449445d83f5",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "v0.12.2",
"version" : "v0.12.3",
"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 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",
"info" : {
@@ -3392,7 +3392,7 @@ meta = [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.12.2'"
".engines[.type == 'docker'].target_tag := 'v0.12.3'"
],
"keywords" : [
"bioinformatics",
@@ -3909,7 +3909,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/htrnaseq/io/publish_results",
"tag" : "v0.12.2"
"tag" : "v0.12.3"
},
"tag" : "$id"
}'''),

2
target/nextflow/io/publish_results/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'io/publish_results'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.12.2'
version = 'v0.12.3'
description = 'Publish the results'
}

10
target/nextflow/parallel_map/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "parallel_map"
version: "v0.12.2"
version: "v0.12.3"
authors:
- name: "Dries Schaumont"
roles:
@@ -248,7 +248,7 @@ engines:
id: "docker"
image: "debian:stable-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.12.2"
target_tag: "v0.12.3"
namespace_separator: "/"
setup:
- type: "apt"
@@ -285,11 +285,11 @@ build_info:
output: "target/nextflow/parallel_map"
executable: "target/nextflow/parallel_map/main.nf"
viash_version: "0.9.4"
git_commit: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_commit: "7c7b7fec254ba6b77d985706fc955449445d83f5"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "v0.12.2"
version: "v0.12.3"
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\
@@ -321,7 +321,7 @@ package_config:
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.2'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.3'"
keywords:
- "bioinformatics"
- "sequencing"

2
target/nextflow/parallel_map/_viash.yaml
View File

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.2
version: v0.12.3
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/nextflow/parallel_map/main.nf
View File

@@ -1,4 +1,4 @@
// parallel_map v0.12.2
// parallel_map v0.12.3
//
// 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
@@ -3035,7 +3035,7 @@ meta = [
"resources_dir": moduleDir.toRealPath().normalize(),
"config": processConfig(readJsonBlob('''{
"name" : "parallel_map",
"version" : "v0.12.2",
"version" : "v0.12.3",
"authors" : [
{
"name" : "Dries Schaumont",
@@ -3332,7 +3332,7 @@ meta = [
"id" : "docker",
"image" : "debian:stable-slim",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.12.2",
"target_tag" : "v0.12.3",
"namespace_separator" : "/",
"setup" : [
{
@@ -3379,12 +3379,12 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/parallel_map",
"viash_version" : "0.9.4",
"git_commit" : "f0f85f57744b71e17ee3c0afe1a221cd20903aef",
"git_commit" : "7c7b7fec254ba6b77d985706fc955449445d83f5",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "v0.12.2",
"version" : "v0.12.3",
"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 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",
"info" : {
@@ -3402,7 +3402,7 @@ meta = [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.12.2'"
".engines[.type == 'docker'].target_tag := 'v0.12.3'"
],
"keywords" : [
"bioinformatics",
@@ -4171,7 +4171,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/htrnaseq/parallel_map",
"tag" : "v0.12.2"
"tag" : "v0.12.3"
},
"tag" : "$id"
}'''),

2
target/nextflow/parallel_map/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'parallel_map'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.12.2'
version = 'v0.12.3'
description = 'Map wells in batch, using STAR\nSpliced Transcripts Alignment to a Reference (C) Alexander Dobin\nhttps://github.com/alexdobin/STAR\n'
author = 'Dries Schaumont, Toni Verbeiren'
}

10
target/nextflow/report/create_report/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "create_report"
namespace: "report"
version: "v0.12.2"
version: "v0.12.3"
authors:
- name: "Dries Schaumont"
roles:
@@ -159,7 +159,7 @@ engines:
id: "docker"
image: "rocker/r2u:24.04"
target_registry: "images.viash-hub.com"
target_tag: "v0.12.2"
target_tag: "v0.12.3"
namespace_separator: "/"
setup:
- type: "apt"
@@ -215,11 +215,11 @@ build_info:
output: "target/nextflow/report/create_report"
executable: "target/nextflow/report/create_report/main.nf"
viash_version: "0.9.4"
git_commit: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_commit: "7c7b7fec254ba6b77d985706fc955449445d83f5"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "v0.12.2"
version: "v0.12.3"
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\
@@ -251,7 +251,7 @@ package_config:
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.2'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.3'"
keywords:
- "bioinformatics"
- "sequencing"

2
target/nextflow/report/create_report/_viash.yaml
View File

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.2
version: v0.12.3
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/nextflow/report/create_report/main.nf
View File

@@ -1,4 +1,4 @@
// create_report v0.12.2
// create_report v0.12.3
//
// 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
@@ -3036,7 +3036,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "create_report",
"namespace" : "report",
"version" : "v0.12.2",
"version" : "v0.12.3",
"authors" : [
{
"name" : "Dries Schaumont",
@@ -3251,7 +3251,7 @@ meta = [
"id" : "docker",
"image" : "rocker/r2u:24.04",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.12.2",
"target_tag" : "v0.12.3",
"namespace_separator" : "/",
"setup" : [
{
@@ -3323,12 +3323,12 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/report/create_report",
"viash_version" : "0.9.4",
"git_commit" : "f0f85f57744b71e17ee3c0afe1a221cd20903aef",
"git_commit" : "7c7b7fec254ba6b77d985706fc955449445d83f5",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "v0.12.2",
"version" : "v0.12.3",
"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 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",
"info" : {
@@ -3346,7 +3346,7 @@ meta = [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.12.2'"
".engines[.type == 'docker'].target_tag := 'v0.12.3'"
],
"keywords" : [
"bioinformatics",
@@ -3831,7 +3831,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/htrnaseq/report/create_report",
"tag" : "v0.12.2"
"tag" : "v0.12.3"
},
"tag" : "$id"
}'''),

2
target/nextflow/report/create_report/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'report/create_report'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.12.2'
version = 'v0.12.3'
description = 'Create a basic QC report in HTML format based on a number of esets.\n'
author = 'Dries Schaumont, Marijke Van Moerbeke'
}

6
target/nextflow/report/create_report/template.Rmd
View File

@@ -170,10 +170,10 @@ if (length(Design_levels) == 1) {
} else {
colours <- c("#d6e0ff")
names(colours) <- c("nonEmpty")
colourList[[annotVar]] <- list(
colourList[[annotationVar]] <- list(
"colours" = colours,
"annotVar" = annotVar,
"text" = annotVar
"annotVar" = annotationVar,
"text" = annotationVar
)
}
```

10
target/nextflow/stats/combine_star_logs/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "combine_star_logs"
namespace: "stats"
version: "v0.12.2"
version: "v0.12.3"
authors:
- name: "Dries Schaumont"
roles:
@@ -175,7 +175,7 @@ engines:
id: "docker"
image: "python:3.12-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.12.2"
target_tag: "v0.12.3"
namespace_separator: "/"
setup:
- type: "apt"
@@ -204,11 +204,11 @@ build_info:
output: "target/nextflow/stats/combine_star_logs"
executable: "target/nextflow/stats/combine_star_logs/main.nf"
viash_version: "0.9.4"
git_commit: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_commit: "7c7b7fec254ba6b77d985706fc955449445d83f5"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "v0.12.2"
version: "v0.12.3"
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\
@@ -240,7 +240,7 @@ package_config:
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.2'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.3'"
keywords:
- "bioinformatics"
- "sequencing"

2
target/nextflow/stats/combine_star_logs/_viash.yaml
View File

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.2
version: v0.12.3
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/nextflow/stats/combine_star_logs/main.nf
View File

@@ -1,4 +1,4 @@
// combine_star_logs v0.12.2
// combine_star_logs v0.12.3
//
// 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
@@ -3035,7 +3035,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "combine_star_logs",
"namespace" : "stats",
"version" : "v0.12.2",
"version" : "v0.12.3",
"authors" : [
{
"name" : "Dries Schaumont",
@@ -3254,7 +3254,7 @@ meta = [
"id" : "docker",
"image" : "python:3.12-slim",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.12.2",
"target_tag" : "v0.12.3",
"namespace_separator" : "/",
"setup" : [
{
@@ -3295,12 +3295,12 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/combine_star_logs",
"viash_version" : "0.9.4",
"git_commit" : "f0f85f57744b71e17ee3c0afe1a221cd20903aef",
"git_commit" : "7c7b7fec254ba6b77d985706fc955449445d83f5",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "v0.12.2",
"version" : "v0.12.3",
"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 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",
"info" : {
@@ -3318,7 +3318,7 @@ meta = [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.12.2'"
".engines[.type == 'docker'].target_tag := 'v0.12.3'"
],
"keywords" : [
"bioinformatics",
@@ -3977,7 +3977,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/htrnaseq/stats/combine_star_logs",
"tag" : "v0.12.2"
"tag" : "v0.12.3"
},
"tag" : "$id"
}'''),

2
target/nextflow/stats/combine_star_logs/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'stats/combine_star_logs'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.12.2'
version = 'v0.12.3'
author = 'Dries Schaumont'
}

10
target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "generate_pool_statistics"
namespace: "stats"
version: "v0.12.2"
version: "v0.12.3"
authors:
- name: "Dries Schaumont"
roles:
@@ -159,7 +159,7 @@ engines:
id: "docker"
image: "python:3.12-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.12.2"
target_tag: "v0.12.3"
namespace_separator: "/"
setup:
- type: "apt"
@@ -188,11 +188,11 @@ build_info:
output: "target/nextflow/stats/generate_pool_statistics"
executable: "target/nextflow/stats/generate_pool_statistics/main.nf"
viash_version: "0.9.4"
git_commit: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_commit: "7c7b7fec254ba6b77d985706fc955449445d83f5"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "v0.12.2"
version: "v0.12.3"
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\
@@ -224,7 +224,7 @@ package_config:
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.2'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.3'"
keywords:
- "bioinformatics"
- "sequencing"

2
target/nextflow/stats/generate_pool_statistics/_viash.yaml
View File

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.2
version: v0.12.3
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/nextflow/stats/generate_pool_statistics/main.nf
View File

@@ -1,4 +1,4 @@
// generate_pool_statistics v0.12.2
// generate_pool_statistics v0.12.3
//
// 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
@@ -3036,7 +3036,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "generate_pool_statistics",
"namespace" : "stats",
"version" : "v0.12.2",
"version" : "v0.12.3",
"authors" : [
{
"name" : "Dries Schaumont",
@@ -3238,7 +3238,7 @@ meta = [
"id" : "docker",
"image" : "python:3.12-slim",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.12.2",
"target_tag" : "v0.12.3",
"namespace_separator" : "/",
"setup" : [
{
@@ -3279,12 +3279,12 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/generate_pool_statistics",
"viash_version" : "0.9.4",
"git_commit" : "f0f85f57744b71e17ee3c0afe1a221cd20903aef",
"git_commit" : "7c7b7fec254ba6b77d985706fc955449445d83f5",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "v0.12.2",
"version" : "v0.12.3",
"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 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",
"info" : {
@@ -3302,7 +3302,7 @@ meta = [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.12.2'"
".engines[.type == 'docker'].target_tag := 'v0.12.3'"
],
"keywords" : [
"bioinformatics",
@@ -3832,7 +3832,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/htrnaseq/stats/generate_pool_statistics",
"tag" : "v0.12.2"
"tag" : "v0.12.3"
},
"tag" : "$id"
}'''),

2
target/nextflow/stats/generate_pool_statistics/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'stats/generate_pool_statistics'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.12.2'
version = 'v0.12.3'
author = 'Dries Schaumont, Marijke Van Moerbeke'
}

10
target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "generate_well_statistics"
namespace: "stats"
version: "v0.12.2"
version: "v0.12.3"
authors:
- name: "Dries Schaumont"
roles:
@@ -230,7 +230,7 @@ engines:
id: "docker"
image: "python:3.13-trixie"
target_registry: "images.viash-hub.com"
target_tag: "v0.12.2"
target_tag: "v0.12.3"
namespace_separator: "/"
setup:
- type: "apt"
@@ -260,11 +260,11 @@ build_info:
output: "target/nextflow/stats/generate_well_statistics"
executable: "target/nextflow/stats/generate_well_statistics/main.nf"
viash_version: "0.9.4"
git_commit: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_commit: "7c7b7fec254ba6b77d985706fc955449445d83f5"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "v0.12.2"
version: "v0.12.3"
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\
@@ -296,7 +296,7 @@ package_config:
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.2'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.3'"
keywords:
- "bioinformatics"
- "sequencing"

2
target/nextflow/stats/generate_well_statistics/_viash.yaml
View File

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.2
version: v0.12.3
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/nextflow/stats/generate_well_statistics/main.nf
View File

@@ -1,4 +1,4 @@
// generate_well_statistics v0.12.2
// generate_well_statistics v0.12.3
//
// 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
@@ -3036,7 +3036,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "generate_well_statistics",
"namespace" : "stats",
"version" : "v0.12.2",
"version" : "v0.12.3",
"authors" : [
{
"name" : "Dries Schaumont",
@@ -3319,7 +3319,7 @@ meta = [
"id" : "docker",
"image" : "python:3.13-trixie",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.12.2",
"target_tag" : "v0.12.3",
"namespace_separator" : "/",
"setup" : [
{
@@ -3361,12 +3361,12 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/generate_well_statistics",
"viash_version" : "0.9.4",
"git_commit" : "f0f85f57744b71e17ee3c0afe1a221cd20903aef",
"git_commit" : "7c7b7fec254ba6b77d985706fc955449445d83f5",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "v0.12.2",
"version" : "v0.12.3",
"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 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",
"info" : {
@@ -3384,7 +3384,7 @@ meta = [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.12.2'"
".engines[.type == 'docker'].target_tag := 'v0.12.3'"
],
"keywords" : [
"bioinformatics",
@@ -3905,7 +3905,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/htrnaseq/stats/generate_well_statistics",
"tag" : "v0.12.2"
"tag" : "v0.12.3"
},
"tag" : "$id"
}'''),

2
target/nextflow/stats/generate_well_statistics/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'stats/generate_well_statistics'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.12.2'
version = 'v0.12.3'
description = 'Generate summary statistics from BAM files generated by STAR solo.'
author = 'Dries Schaumont, Marijke Van Moerbeke'
}

8
target/nextflow/utils/concatRuns/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "concatRuns"
namespace: "utils"
version: "v0.12.2"
version: "v0.12.3"
argument_groups:
- name: "Arguments"
arguments:
@@ -160,13 +160,13 @@ build_info:
output: "target/nextflow/utils/concatRuns"
executable: "target/nextflow/utils/concatRuns/main.nf"
viash_version: "0.9.4"
git_commit: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_commit: "7c7b7fec254ba6b77d985706fc955449445d83f5"
git_remote: "https://github.com/viash-hub/htrnaseq"
dependencies:
- "target/dependencies/vsh/vsh/craftbox/v0.3.0/nextflow/concat_text"
package_config:
name: "htrnaseq"
version: "v0.12.2"
version: "v0.12.3"
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\
@@ -198,7 +198,7 @@ package_config:
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.2'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.3'"
keywords:
- "bioinformatics"
- "sequencing"

2
target/nextflow/utils/concatRuns/_viash.yaml
View File

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.2
version: v0.12.3
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"

10
target/nextflow/utils/concatRuns/main.nf
View File

@@ -1,4 +1,4 @@
// concatRuns v0.12.2
// concatRuns v0.12.3
//
// 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
@@ -3032,7 +3032,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "concatRuns",
"namespace" : "utils",
"version" : "v0.12.2",
"version" : "v0.12.3",
"argument_groups" : [
{
"name" : "Arguments",
@@ -3229,12 +3229,12 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/utils/concatRuns",
"viash_version" : "0.9.4",
"git_commit" : "f0f85f57744b71e17ee3c0afe1a221cd20903aef",
"git_commit" : "7c7b7fec254ba6b77d985706fc955449445d83f5",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "v0.12.2",
"version" : "v0.12.3",
"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 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",
"info" : {
@@ -3252,7 +3252,7 @@ meta = [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.12.2'"
".engines[.type == 'docker'].target_tag := 'v0.12.3'"
],
"keywords" : [
"bioinformatics",

2
target/nextflow/utils/concatRuns/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'utils/concatRuns'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.12.2'
version = 'v0.12.3'
description = 'Concatenate well FASTQ files from different runs in order to increase sequencing depth.\n'
}

8
target/nextflow/utils/listInputDir/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "listInputDir"
namespace: "utils"
version: "v0.12.2"
version: "v0.12.3"
argument_groups:
- name: "Arguments"
arguments:
@@ -169,11 +169,11 @@ build_info:
output: "target/nextflow/utils/listInputDir"
executable: "target/nextflow/utils/listInputDir/main.nf"
viash_version: "0.9.4"
git_commit: "f0f85f57744b71e17ee3c0afe1a221cd20903aef"
git_commit: "7c7b7fec254ba6b77d985706fc955449445d83f5"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "v0.12.2"
version: "v0.12.3"
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\
@@ -205,7 +205,7 @@ package_config:
\ '_viash.yaml'}\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.2'"
- ".engines[.type == 'docker'].target_tag := 'v0.12.3'"
keywords:
- "bioinformatics"
- "sequencing"

2
target/nextflow/utils/listInputDir/_viash.yaml
View File

@@ -1,5 +1,5 @@
name: htrnaseq
version: v0.12.2
version: v0.12.3
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"

10
target/nextflow/utils/listInputDir/main.nf
View File

@@ -1,4 +1,4 @@
// listInputDir v0.12.2
// listInputDir v0.12.3
//
// 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
@@ -3032,7 +3032,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "listInputDir",
"namespace" : "utils",
"version" : "v0.12.2",
"version" : "v0.12.3",
"argument_groups" : [
{
"name" : "Arguments",
@@ -3236,12 +3236,12 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/utils/listInputDir",
"viash_version" : "0.9.4",
"git_commit" : "f0f85f57744b71e17ee3c0afe1a221cd20903aef",
"git_commit" : "7c7b7fec254ba6b77d985706fc955449445d83f5",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "v0.12.2",
"version" : "v0.12.3",
"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 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",
"info" : {
@@ -3259,7 +3259,7 @@ meta = [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.12.2'"
".engines[.type == 'docker'].target_tag := 'v0.12.3'"
],
"keywords" : [
"bioinformatics",

2
target/nextflow/utils/listInputDir/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'utils/listInputDir'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.12.2'
version = 'v0.12.3'
description = 'List the contents of a directory and parse contained fastq files'
}

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