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MIT License
Copyright (c) 2021 OpenPipelines
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

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# HT-RNAseq - A pipeline for processing high-throughput RNA-seq data
# HT-RNAseq
[![ViashHub](https://img.shields.io/badge/ViashHub-htrnaseq-7a4baa.svg)](https://www.viash-hub.com/packages/htrnaseq)
[![GitHub](https://img.shields.io/badge/GitHub-viash--hub%2Fhtrnaseq-blue.svg)](https://github.com/viash-hub/htrnaseq)
[![GitHub
License](https://img.shields.io/github/license/viash-hub/htrnaseq.svg)](https://github.com/viash-hub/htrnaseq/blob/main/LICENSE)
[![GitHub
Issues](https://img.shields.io/github/issues/viash-hub/htrnaseq.svg)](https://github.com/viash-hub/htrnaseq/issues)
[![Viash
version](https://img.shields.io/badge/Viash-v0.9.2-blue.svg)](https://viash.io)
## Introduction
__TODO__: Add a description of the pipeline here.
## Test data
This workflow is designed to process high-throughput RNA-seq data, where
every well of a microarray plate is a sample. A fasta file provided as
input defines the mapping between sample barcodes and wells.
As test data, we use [a DRUGseq dataset](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE176150) from the [NCBI Sequence Read Archive](https://www.ncbi.nlm.nih.gov/sra).
The workflow is built in a modular fashion, where most of the base
functionality is provided by components from
[`biobox`](https://www.viash-hub.com/packages/biobox/latest)
supplemented by custom base components and workflow components in this
package.
The original data has been (partly) subsampled to reduce the test runtime. We used [seqtk](https://github.com/lh3/seqtk) for this with a seed of 1, e.g.:
The full workflow is split in two major subworkflows that can be run
independently:
```bash
- **Well-demultiplexing:** Split the input (plate/pool level) fastq
files per well.
- **Mapping, counting and QC:** Run per-well mapping, counting and
generate QC reports.
Each of those can be started individually, or the full workflow can be
run in two ways:
1. Run the [main
workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq)
containing the main functionality.
2. Run the [(opinionated)
`runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner)
where a number of choices (input/output structure and location) have
been made.
Input for the workflow has to be `fastq` files (zipped or not). For bcl
or other formats, please consider running
[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.
``` mermaid lang="mermaid"
flowchart TB
subgraph runner [runner]
direction TB
subgraph htrnaseq [HT-RNAseq]
direction LR
demultiplex[Well demultiplexing]
map
report
eset
end
end
demultiplex --> map --> report --> eset
class runner container
class htrnaseq container
class demultiplex container-inner
class map container-inner
class report container-inner
class eset container-inner
class demultiplex node
class map node
class report node
class eset node
```
## Example usage
### Test and example data
If you want to explore this workflow, it’s possible to the use data we
use as test data: [a DRUGseq
dataset](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE176150)
from the [NCBI Sequence Read Archive](https://www.ncbi.nlm.nih.gov/sra).
For the unit and integration tests, this data has been (partly)
subsampled to reduce the test runtime. We used
[seqtk](https://github.com/lh3/seqtk) for this with a seed of 1, e.g.:
``` bash
seqtk sample -s1 orig/SRR14730302/VH02001614_S8_R1_001.fastq.gz 10000 > 10k/SRR14730302/VH02001614_S8_R1_001.fastq.gz
```
The data is available at: `gs://viash-hub-test-data/htrnaseq/v1/`:
This data is available at: `gs://viash-hub-resources/htrnaseq/v1/`.
```
❯ gcstree -f viash-hub-test-data/htrnaseq/v1/
viash-hub-test-data
└── htrnaseq
└── v1
├── [ 48] 2-wells.fasta
├── [465.3K] GSE176150_metadata.csv
├── 100k
│ ├── SRR14730301
│ │ ├── [8.5M] VH02001612_S9_R1_001.fastq
│ │ └── [14.9M] VH02001612_S9_R2_001.fastq
│ └── SRR14730302
│ ├── [8.5M] VH02001614_S8_R1_001.fastq.gz
│ └── [14.9M] VH02001614_S8_R2_001.fastq.gz
├── 10k
│ ├── SRR14730301
│ │ ├── [845.4K] VH02001612_S9_R1_001.fastq
│ │ └── [1.5M] VH02001612_S9_R2_001.fastq
│ └── SRR14730302
│ ├── [845.3K] VH02001614_S8_R1_001.fastq.gz
│ └── [1.5M] VH02001614_S8_R2_001.fastq.gz
└── orig
├── [20.4G] SRR14730301
│ └── [20.4G] SRR14730301
├── SRR14730301
│ ├── [9.1G] VH02001612_S9_R1_001.fastq.gz
│ └── [22.0G] VH02001612_S9_R2_001.fastq.gz
├── [16.9G] SRR14730302
│ └── [16.9G] SRR14730302
├── SRR14730302
│ ├── [7.6G] VH02001614_S8_R1_001.fastq.gz
│ └── [18.0G] VH02001614_S8_R2_001.fastq.gz
├── [18.0G] SRR14730303
│ └── [18.0G] SRR14730303
├── SRR14730303
│ ├── [8.1G] VH02001618_S7_R1_001.fastq.gz
│ └── [19.2G] VH02001618_S7_R2_001.fastq.gz
├── [16.5G] SRR14730304
│ └── [16.5G] SRR14730304
├── SRR14730304
│ ├── [7.5G] VH02001700_S6_R1_001.fastq.gz
│ └── [17.8G] VH02001700_S6_R2_001.fastq.gz
├── [19.0G] SRR14730305
│ └── [19.0G] SRR14730305
├── SRR14730305
│ ├── [8.4G] VH02001702_S5_R1_001.fastq.gz
│ └── [20.6G] VH02001702_S5_R2_001.fastq.gz
├── [14.6G] SRR14730306
│ └── [14.6G] SRR14730306
├── SRR14730306
│ ├── [6.6G] VH02001704_S4_R1_001.fastq.gz
│ └── [16.0G] VH02001704_S4_R2_001.fastq.gz
├── [21.5G] SRR14730307
│ └── [21.5G] SRR14730307
├── SRR14730307
│ ├── [9.6G] VH02001708_S3_R1_001.fastq.gz
│ └── [23.2G] VH02001708_S3_R2_001.fastq.gz
├── [20.7G] SRR14730308
│ └── [20.7G] SRR14730308
├── SRR14730308
│ ├── [9.3G] VH02001710_S2_R1_001.fastq.gz
│ └── [22.1G] VH02001710_S2_R2_001.fastq.gz
├── [15.8G] SRR14730309
│ └── [15.8G] SRR14730309
└── SRR14730309
├── [7.2G] VH02001712_S1_R1_001.fastq.gz
└── [16.9G] VH02001712_S1_R2_001.fastq.gz
### Run from Viash Hub
18 directories, 37 files
Open [Viash Hub](https://www.viash-hub.com) and browse to the [htrnaseq
component](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq).
Press the ‘Launch’ button and follow the instructions.
![](assets/htrnaseq-launch-small.png)
We will start an example run loading just one input and using a barcodes
fasta file containing only 2 wells.
In the first step, we add the `local` profile to the list of profiles in
order to limit the cpu and memory requirements of the workflow steps:
![](assets/launch-parameters-1-small.png)
In the next step, we provide the paramters as follows:
- `input_r1`:
`gs://viash-hub-test-data/htrnaseq/v1/100k/SRR14730301/VH02001612_S9_R1_001.fastq`
- `input_r2`:
`gs://viash-hub-test-data/htrnaseq/v1/100k/SRR14730301/VH02001612_S9_R2_001.fastq`
- `genomeDir`:
`gs://viash-hub-test-data/htrnaseq/v1/genomeDir/subset/Homo_sapiens/v0.0.3/`
- `barcodesFasta`:
`gs://viash-hub-test-data/htrnaseq/v1/2-wells-with-ids.fasta`
- `annotation`:
`gs://viash-hub-test-data/htrnaseq/v1/genomeDir/gencode.v41.annotation.gtf.gz`
Please note that both `input_r1` and `input_r2` can take multiple
values. This means that one has to press ENTER after pasting the input
path.
![](assets/launch-parameters-2-small.png)
Press the ‘Launch’ button at the end to get the instructions on how to
run the workflow from the CLI.
### Run using NF-Tower / Seqera Cloud
It’s possible to run the workflow directly from [Seqera
Cloud](https://cloud.seqera.io). The necessary [Nextflow schema
file](https://nextflow-io.github.io/nf-schema/latest/nextflow_schema/nextflow_schema_specification/)
has been built and provided with the workflows in order to use the
form-based input. However, Seqera Cloud can not deal with multiple-value
parameters when using the form-based input. Therefore, it’s better to
use Viash Hub also here:
First, select the option to run the workflow using Seqera Cloud. You
will need to create an API token for your account. Once this token is
filled in in the corresponding field, you will get the option to select
a ‘Workspace’ and a ‘Compute environment’.
![](assets/launch-parameters-3-small.png)
Next, we need to fill in the parameters for the run. This is similar to
before:
![](assets/launch-parameters-4-small.png)
In the next screen, pressing the ‘Launch’ button will actually start the
workflow on Seqera Cloud. A message is shown when the submit was
successful.
![](assets/launch-parameters-5-small.png)
### Run from the CLI
Running from the CLI directly without using Viash hub is possible. The
easiest is to just use the integrated help functionality, for instance
using the following:
``` bash
nextflow run https://packages.viash-hub.com/vsh/htrnaseq.git \
-revision v0.3.0 \
-main-script target/nextflow/workflows/runner/main.nf \
--help
```
### (Optional) Resource usage tuning
The `orig` directory contains the original fastq files. The fastq files are available for 10k and 100k subsamples in the `10k` and `100k` directories, respectively.
Nextflow’s labels can be used to specify the amount of resources a
process can use. This workflow uses the following labels for CPU and
memory:
The `2-wells.fasta` file contains the barcodes for 2 wells.
- `verylowmem`, `lowmem`, `midmem`, `highmem`
- `verylowcpu`, `lowcpu`, `midcpu`, `highcpu`
## Test run
The defaults for these labels can be found at
`src/config/labels.config`. Nextflow checks that the specified resources
for a process do not exceed what is available on the machine and will
not start if it does. Create your own config file to tune the labels to
your needs, for example:
The pipeline can be run by creating a `params.yaml` file like this:
// Resource labels
withLabel: verylowcpu { cpus = 2 }
withLabel: lowcpu { cpus = 8 }
withLabel: midcpu { cpus = 16 }
withLabel: highcpu { cpus = 32 }
```yaml
param_list:
- input_r1: "gs://viash-hub-test-data/htrnaseq/v1/100k/SRR14730301/VH02001612_S9_R1_001.fastq"
input_r2: "gs://viash-hub-test-data/htrnaseq/v1/100k/SRR14730301/VH02001612_S9_R2_001.fastq"
genomeDir: "gs://viash-hub-test-data/htrnaseq/v1/genomeDir/gencode.v41.star.sparse"
barcodesFasta: "gs://viash-hub-test-data/htrnaseq/v1/2-wells.fasta"
id: sample_one
- input_r1: "gs://viash-hub-test-data/htrnaseq/v1/100k/SRR14730302/VH02001614_S8_R1_001.fastq"
input_r2: "gs://viash-hub-test-data/htrnaseq/v1/100k/SRR14730302/VH02001614_S8_R2_001.fastq"
genomeDir: "gs://viash-hub-test-data/htrnaseq/v1/genomeDir/gencode.v41.star.sparse"
barcodesFasta: "gs://viash-hub-test-data/htrnaseq/v1/2-wells.fasta"
id: sample_two
```
withLabel: verylowmem { memory = { get_memory( 4.GB * task.attempt ) } }
withLabel: lowmem { memory = { get_memory( 8.GB * task.attempt ) } }
withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
withLabel: highmem { memory = { get_memory( 64.GB * task.attempt ) } }
and then:
When starting nextflow using the CLI, you can use `-c` to provide the
file to nextflow and overwrite the defaults.
```bash
viash ns build --setup cb
nextflow run . -main-script target/nextflow/workflows/htrnaseq/main.nf \
-profile docker \
-c target/nextflow/workflows/htrnaseq/nextflow.config \
-params-file params.yaml \
-resume \
--publish_dir output
```
## Contributions
Or, by running `src/workflows/htrnaseq/integration_test.sh`.
Developed in collaboration with Data Intuitive and Open Analytics.
# Special Thanks
Developed in collaboration with Data Intuitive and Open Analytics.
Other contributions are welcome.

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---
format: gfm
---
```{r setup, include=FALSE}
project <- yaml::read_yaml("_viash.yaml")
license <- paste0(project$links$repository, "/blob/main/LICENSE")
contributing <- paste0(project$links$repository, "/blob/main/CONTRIBUTING.md")
```
# HT-RNAseq
[![ViashHub](https://img.shields.io/badge/ViashHub-`r project$name`-7a4baa.svg)](https://www.viash-hub.com/packages/`r project$name`)
[![GitHub](https://img.shields.io/badge/GitHub-viash--hub%2F`r project$name`-blue.svg)](`r project$links$repository`)
[![GitHub License](https://img.shields.io/github/license/viash-hub/`r project$name`.svg)](`r license`)
[![GitHub Issues](https://img.shields.io/github/issues/viash-hub/`r project$name`.svg)](`r project$links$issue_tracker`)
[![Viash version](https://img.shields.io/badge/Viash-v`r gsub("-", "--", project$viash_version)`-blue.svg)](https://viash.io)
## Introduction
`r project$description`
```{mermaid lang='mermaid'}
flowchart TB
subgraph runner [runner]
direction TB
subgraph htrnaseq [HT-RNAseq]
direction LR
demultiplex[Well demultiplexing]
map
report
eset
end
end
demultiplex --> map --> report --> eset
class runner container
class htrnaseq container
class demultiplex container-inner
class map container-inner
class report container-inner
class eset container-inner
class demultiplex node
class map node
class report node
class eset node
```
## Example usage
### Test and example data
If you want to explore this workflow, it's possible to the use data we use as test data: [a DRUGseq dataset](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE176150) from the [NCBI Sequence Read Archive](https://www.ncbi.nlm.nih.gov/sra). For the unit and integration tests, this data has been (partly) subsampled to reduce the test runtime. We used [seqtk](https://github.com/lh3/seqtk) for this with a seed of 1, e.g.:
```bash
seqtk sample -s1 orig/SRR14730302/VH02001614_S8_R1_001.fastq.gz 10000 > 10k/SRR14730302/VH02001614_S8_R1_001.fastq.gz
```
This data is available at: `gs://viash-hub-test-data/htrnaseq/v1/`.
### Run from Viash Hub
Open [Viash Hub](https://www.viash-hub.com) and browse to the [htrnaseq component](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq). Press the 'Launch' button and follow the instructions.
![](assets/htrnaseq-launch-small.png)
We will start an example run loading just one input and using a barcodes fasta file containing only 2 wells.
In the first step, we add the `local` profile to the list of profiles in order to limit the cpu and memory requirements of the workflow steps:
![](assets/launch-parameters-1-small.png)
In the next step, we provide the paramters as follows:
- `input_r1`: `gs://viash-hub-test-data/htrnaseq/v1/100k/SRR14730301/VH02001612_S9_R1_001.fastq`
- `input_r2`: `gs://viash-hub-test-data/htrnaseq/v1/100k/SRR14730301/VH02001612_S9_R2_001.fastq`
- `genomeDir`: `gs://viash-hub-test-data/htrnaseq/v1/genomeDir/subset/Homo_sapiens/v0.0.3/`
- `barcodesFasta`: `gs://viash-hub-test-data/htrnaseq/v1/2-wells-with-ids.fasta`
- `annotation`: `gs://viash-hub-test-data/htrnaseq/v1/genomeDir/gencode.v41.annotation.gtf.gz`
Please note that both `input_r1` and `input_r2` can take multiple values. This means that one has to press ENTER after pasting the input path.
![](assets/launch-parameters-2-small.png)
Press the 'Launch' button at the end to get the instructions on how to run the workflow from the CLI.
### Run using NF-Tower / Seqera Cloud
It's possible to run the workflow directly from [Seqera Cloud](https://cloud.seqera.io). The necessary [Nextflow schema file](https://nextflow-io.github.io/nf-schema/latest/nextflow_schema/nextflow_schema_specification/) has been built and provided with the workflows in order to use the form-based input. However, Seqera Cloud can not deal with multiple-value parameters when using the form-based input. Therefore, it's better to use Viash Hub also here:
First, select the option to run the workflow using Seqera Cloud. You will need to create an API token for your account. Once this token is filled in in the corresponding field, you will get the option to select a 'Workspace' and a 'Compute environment'.
![](assets/launch-parameters-3-small.png)
Next, we need to fill in the parameters for the run. This is similar to before:
![](assets/launch-parameters-4-small.png)
In the next screen, pressing the 'Launch' button will actually start the workflow on Seqera Cloud. A message is shown when the submit was successful.
![](assets/launch-parameters-5-small.png)
### Run from the CLI
Running from the CLI directly without using Viash hub is possible. The easiest is to just use the integrated help functionality, for instance using the following:
```bash
nextflow run https://packages.viash-hub.com/vsh/htrnaseq.git \
-revision v0.3.0 \
-main-script target/nextflow/workflows/runner/main.nf \
--help
```
### (Optional) Resource usage tuning
Nextflow's labels can be used to specify the amount of resources a process can use. This workflow uses the following labels for CPU and memory:
* `verylowmem`, `lowmem`, `midmem`, `highmem`
* `verylowcpu`, `lowcpu`, `midcpu`, `highcpu`
The defaults for these labels can be found at `src/config/labels.config`. Nextflow checks that the specified resources for a process do not exceed what is available on the machine and will not start if it does. Create your own config file to tune the labels to your needs, for example:
```
// Resource labels
withLabel: verylowcpu { cpus = 2 }
withLabel: lowcpu { cpus = 8 }
withLabel: midcpu { cpus = 16 }
withLabel: highcpu { cpus = 32 }
withLabel: verylowmem { memory = { get_memory( 4.GB * task.attempt ) } }
withLabel: lowmem { memory = { get_memory( 8.GB * task.attempt ) } }
withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
withLabel: highmem { memory = { get_memory( 64.GB * task.attempt ) } }
```
When starting nextflow using the CLI, you can use `-c` to provide the file to nextflow and overwrite the defaults.
## Contributions
Developed in collaboration with Data Intuitive and Open Analytics.
Other contributions are welcome.

38
_viash.yaml
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@@ -1,8 +1,42 @@
name: htrnaseq
summary: |
A workflow for high-throughput RNA-seq data analyses.
description: |
High-throughput pipeline [WIP]
This workflow is designed to process high-throughput RNA-seq data, where every
well of a microarray plate is a sample. A fasta file provided as input
defines the mapping between sample barcodes and wells.
The workflow is built in a modular fashion, where most of the base functionality
is provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)
supplemented by custom base components and workflow components in this package.
The full workflow is split in two major subworkflows that can be run independently:
* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.
* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.
Each of those can be started individually, or the full workflow can be run in two ways:
1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq)
containing the main functionality.
2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a
number of choices (input/output structure and location) have been made.
Input for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running
[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.
license: MIT
keywords: [bioinformatics, sequence, high-throughput, mapping, counting, pipeline]
keywords:
[
bioinformatics,
sequencing,
high-throughput,
RNAseq,
mapping,
counting,
pipeline,
workflow,
]
links:
issue_tracker: https://github.com/viash-hub/htrnaseq/issues
repository: https://github.com/viash-hub/htrnaseq

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24
target/executable/eset/create_eset/.config.vsh.yaml
View File

@@ -203,12 +203,28 @@ build_info:
output: "target/executable/eset/create_eset"
executable: "target/executable/eset/create_eset/create_eset"
viash_version: "0.9.4"
git_commit: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -225,11 +241,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

4
target/executable/eset/create_eset/create_eset
View File

@@ -456,9 +456,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component eset create_eset"
LABEL org.opencontainers.image.created="2025-04-30T10:35:22Z"
LABEL org.opencontainers.image.created="2025-05-07T09:35:10Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="a62a15edd24e20595ec87bc641f1d829bd1e60d0"
LABEL org.opencontainers.image.revision="28e59b1fb79832767993f62358551f8aafafc3cf"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

24
target/executable/eset/create_fdata/.config.vsh.yaml
View File

@@ -180,12 +180,28 @@ build_info:
output: "target/executable/eset/create_fdata"
executable: "target/executable/eset/create_fdata/create_fdata"
viash_version: "0.9.4"
git_commit: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -202,11 +218,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

4
target/executable/eset/create_fdata/create_fdata
View File

@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component eset create_fdata"
LABEL org.opencontainers.image.created="2025-04-30T10:35:21Z"
LABEL org.opencontainers.image.created="2025-05-07T09:35:10Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="a62a15edd24e20595ec87bc641f1d829bd1e60d0"
LABEL org.opencontainers.image.revision="28e59b1fb79832767993f62358551f8aafafc3cf"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

24
target/executable/eset/create_pdata/.config.vsh.yaml
View File

@@ -194,12 +194,28 @@ build_info:
output: "target/executable/eset/create_pdata"
executable: "target/executable/eset/create_pdata/create_pdata"
viash_version: "0.9.4"
git_commit: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -216,11 +232,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

4
target/executable/eset/create_pdata/create_pdata
View File

@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component eset create_pdata"
LABEL org.opencontainers.image.created="2025-04-30T10:35:22Z"
LABEL org.opencontainers.image.created="2025-05-07T09:35:10Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="a62a15edd24e20595ec87bc641f1d829bd1e60d0"
LABEL org.opencontainers.image.revision="28e59b1fb79832767993f62358551f8aafafc3cf"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

24
target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
View File

@@ -152,12 +152,28 @@ 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: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -174,11 +190,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

4
target/executable/integration_test_components/htrnaseq/check_eset/check_eset
View File

@@ -455,9 +455,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
LABEL org.opencontainers.image.authors="Dries Schaumont"
LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/htrnaseq check_eset"
LABEL org.opencontainers.image.created="2025-04-30T10:35:21Z"
LABEL org.opencontainers.image.created="2025-05-07T09:35:09Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="a62a15edd24e20595ec87bc641f1d829bd1e60d0"
LABEL org.opencontainers.image.revision="28e59b1fb79832767993f62358551f8aafafc3cf"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

24
target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
View File

@@ -161,12 +161,28 @@ 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: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -183,11 +199,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

4
target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output
View File

@@ -457,9 +457,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont"
LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/well_demultiplexing check_cutadapt_output"
LABEL org.opencontainers.image.created="2025-04-30T10:35:23Z"
LABEL org.opencontainers.image.created="2025-05-07T09:35:11Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="a62a15edd24e20595ec87bc641f1d829bd1e60d0"
LABEL org.opencontainers.image.revision="28e59b1fb79832767993f62358551f8aafafc3cf"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

24
target/executable/io/publish_fastqs/.config.vsh.yaml
View File

@@ -136,12 +136,28 @@ build_info:
output: "target/executable/io/publish_fastqs"
executable: "target/executable/io/publish_fastqs/publish_fastqs"
viash_version: "0.9.4"
git_commit: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -158,11 +174,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

4
target/executable/io/publish_fastqs/publish_fastqs
View File

@@ -450,9 +450,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component io publish_fastqs"
LABEL org.opencontainers.image.created="2025-04-30T10:35:21Z"
LABEL org.opencontainers.image.created="2025-05-07T09:35:09Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="a62a15edd24e20595ec87bc641f1d829bd1e60d0"
LABEL org.opencontainers.image.revision="28e59b1fb79832767993f62358551f8aafafc3cf"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

24
target/executable/io/publish_results/.config.vsh.yaml
View File

@@ -190,12 +190,28 @@ build_info:
output: "target/executable/io/publish_results"
executable: "target/executable/io/publish_results/publish_results"
viash_version: "0.9.4"
git_commit: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -212,11 +228,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

4
target/executable/io/publish_results/publish_results
View File

@@ -450,9 +450,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component io publish_results"
LABEL org.opencontainers.image.created="2025-04-30T10:35:21Z"
LABEL org.opencontainers.image.created="2025-05-07T09:35:10Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="a62a15edd24e20595ec87bc641f1d829bd1e60d0"
LABEL org.opencontainers.image.revision="28e59b1fb79832767993f62358551f8aafafc3cf"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

24
target/executable/parallel_map/.config.vsh.yaml
View File

@@ -282,12 +282,28 @@ build_info:
output: "target/executable/parallel_map"
executable: "target/executable/parallel_map/parallel_map"
viash_version: "0.9.4"
git_commit: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -304,11 +320,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

4
target/executable/parallel_map/parallel_map
View File

@@ -461,9 +461,9 @@ ENV STAR_BINARY=STAR
COPY STAR /usr/local/bin/$STAR_BINARY
LABEL org.opencontainers.image.authors="Dries Schaumont, Toni Verbeiren"
LABEL org.opencontainers.image.description="Companion container for running component parallel_map"
LABEL org.opencontainers.image.created="2025-04-30T10:35:22Z"
LABEL org.opencontainers.image.created="2025-05-07T09:35:11Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="a62a15edd24e20595ec87bc641f1d829bd1e60d0"
LABEL org.opencontainers.image.revision="28e59b1fb79832767993f62358551f8aafafc3cf"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

24
target/executable/report/create_report/.config.vsh.yaml
View File

@@ -212,12 +212,28 @@ build_info:
output: "target/executable/report/create_report"
executable: "target/executable/report/create_report/create_report"
viash_version: "0.9.4"
git_commit: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -234,11 +250,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

4
target/executable/report/create_report/create_report
View File

@@ -465,9 +465,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component report create_report"
LABEL org.opencontainers.image.created="2025-04-30T10:35:22Z"
LABEL org.opencontainers.image.created="2025-05-07T09:35:11Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="a62a15edd24e20595ec87bc641f1d829bd1e60d0"
LABEL org.opencontainers.image.revision="28e59b1fb79832767993f62358551f8aafafc3cf"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

24
target/executable/stats/combine_star_logs/.config.vsh.yaml
View File

@@ -201,12 +201,28 @@ 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: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -223,11 +239,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

4
target/executable/stats/combine_star_logs/combine_star_logs
View File

@@ -457,9 +457,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont"
LABEL org.opencontainers.image.description="Companion container for running component stats combine_star_logs"
LABEL org.opencontainers.image.created="2025-04-30T10:35:21Z"
LABEL org.opencontainers.image.created="2025-05-07T09:35:09Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="a62a15edd24e20595ec87bc641f1d829bd1e60d0"
LABEL org.opencontainers.image.revision="28e59b1fb79832767993f62358551f8aafafc3cf"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

24
target/executable/stats/generate_pool_statistics/.config.vsh.yaml
View File

@@ -185,12 +185,28 @@ 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: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -207,11 +223,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

4
target/executable/stats/generate_pool_statistics/generate_pool_statistics
View File

@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component stats generate_pool_statistics"
LABEL org.opencontainers.image.created="2025-04-30T10:35:21Z"
LABEL org.opencontainers.image.created="2025-05-07T09:35:09Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="a62a15edd24e20595ec87bc641f1d829bd1e60d0"
LABEL org.opencontainers.image.revision="28e59b1fb79832767993f62358551f8aafafc3cf"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

24
target/executable/stats/generate_well_statistics/.config.vsh.yaml
View File

@@ -267,12 +267,28 @@ 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: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -289,11 +305,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

4
target/executable/stats/generate_well_statistics/generate_well_statistics
View File

@@ -461,9 +461,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component stats generate_well_statistics"
LABEL org.opencontainers.image.created="2025-04-30T10:35:21Z"
LABEL org.opencontainers.image.created="2025-05-07T09:35:09Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="a62a15edd24e20595ec87bc641f1d829bd1e60d0"
LABEL org.opencontainers.image.revision="28e59b1fb79832767993f62358551f8aafafc3cf"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

24
target/nextflow/eset/create_eset/.config.vsh.yaml
View File

@@ -203,12 +203,28 @@ build_info:
output: "target/nextflow/eset/create_eset"
executable: "target/nextflow/eset/create_eset/main.nf"
viash_version: "0.9.4"
git_commit: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -225,11 +241,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

11
target/nextflow/eset/create_eset/main.nf
View File

@@ -3304,13 +3304,14 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_eset",
"viash_version" : "0.9.4",
"git_commit" : "a62a15edd24e20595ec87bc641f1d829bd1e60d0",
"git_commit" : "28e59b1fb79832767993f62358551f8aafafc3cf",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "main",
"description" : "High-throughput pipeline [WIP]\n",
"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" : {
"test_resources" : [
{
@@ -3330,11 +3331,13 @@ meta = [
],
"keywords" : [
"bioinformatics",
"sequence",
"sequencing",
"high-throughput",
"RNAseq",
"mapping",
"counting",
"pipeline"
"pipeline",
"workflow"
],
"license" : "MIT",
"organization" : "vsh",

24
target/nextflow/eset/create_fdata/.config.vsh.yaml
View File

@@ -180,12 +180,28 @@ build_info:
output: "target/nextflow/eset/create_fdata"
executable: "target/nextflow/eset/create_fdata/main.nf"
viash_version: "0.9.4"
git_commit: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -202,11 +218,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

11
target/nextflow/eset/create_fdata/main.nf
View File

@@ -3274,13 +3274,14 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_fdata",
"viash_version" : "0.9.4",
"git_commit" : "a62a15edd24e20595ec87bc641f1d829bd1e60d0",
"git_commit" : "28e59b1fb79832767993f62358551f8aafafc3cf",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "main",
"description" : "High-throughput pipeline [WIP]\n",
"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" : {
"test_resources" : [
{
@@ -3300,11 +3301,13 @@ meta = [
],
"keywords" : [
"bioinformatics",
"sequence",
"sequencing",
"high-throughput",
"RNAseq",
"mapping",
"counting",
"pipeline"
"pipeline",
"workflow"
],
"license" : "MIT",
"organization" : "vsh",

24
target/nextflow/eset/create_pdata/.config.vsh.yaml
View File

@@ -194,12 +194,28 @@ build_info:
output: "target/nextflow/eset/create_pdata"
executable: "target/nextflow/eset/create_pdata/main.nf"
viash_version: "0.9.4"
git_commit: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -216,11 +232,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

11
target/nextflow/eset/create_pdata/main.nf
View File

@@ -3288,13 +3288,14 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_pdata",
"viash_version" : "0.9.4",
"git_commit" : "a62a15edd24e20595ec87bc641f1d829bd1e60d0",
"git_commit" : "28e59b1fb79832767993f62358551f8aafafc3cf",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "main",
"description" : "High-throughput pipeline [WIP]\n",
"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" : {
"test_resources" : [
{
@@ -3314,11 +3315,13 @@ meta = [
],
"keywords" : [
"bioinformatics",
"sequence",
"sequencing",
"high-throughput",
"RNAseq",
"mapping",
"counting",
"pipeline"
"pipeline",
"workflow"
],
"license" : "MIT",
"organization" : "vsh",

24
target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
View File

@@ -152,12 +152,28 @@ 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: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -174,11 +190,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

11
target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
View File

@@ -3228,13 +3228,14 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
"viash_version" : "0.9.4",
"git_commit" : "a62a15edd24e20595ec87bc641f1d829bd1e60d0",
"git_commit" : "28e59b1fb79832767993f62358551f8aafafc3cf",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "main",
"description" : "High-throughput pipeline [WIP]\n",
"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" : {
"test_resources" : [
{
@@ -3254,11 +3255,13 @@ meta = [
],
"keywords" : [
"bioinformatics",
"sequence",
"sequencing",
"high-throughput",
"RNAseq",
"mapping",
"counting",
"pipeline"
"pipeline",
"workflow"
],
"license" : "MIT",
"organization" : "vsh",

24
target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
View File

@@ -161,12 +161,28 @@ 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: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -183,11 +199,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

11
target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf
View File

@@ -3239,13 +3239,14 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
"viash_version" : "0.9.4",
"git_commit" : "a62a15edd24e20595ec87bc641f1d829bd1e60d0",
"git_commit" : "28e59b1fb79832767993f62358551f8aafafc3cf",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "main",
"description" : "High-throughput pipeline [WIP]\n",
"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" : {
"test_resources" : [
{
@@ -3265,11 +3266,13 @@ meta = [
],
"keywords" : [
"bioinformatics",
"sequence",
"sequencing",
"high-throughput",
"RNAseq",
"mapping",
"counting",
"pipeline"
"pipeline",
"workflow"
],
"license" : "MIT",
"organization" : "vsh",

24
target/nextflow/io/publish_fastqs/.config.vsh.yaml
View File

@@ -136,12 +136,28 @@ build_info:
output: "target/nextflow/io/publish_fastqs"
executable: "target/nextflow/io/publish_fastqs/main.nf"
viash_version: "0.9.4"
git_commit: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -158,11 +174,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

11
target/nextflow/io/publish_fastqs/main.nf
View File

@@ -3202,13 +3202,14 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/publish_fastqs",
"viash_version" : "0.9.4",
"git_commit" : "a62a15edd24e20595ec87bc641f1d829bd1e60d0",
"git_commit" : "28e59b1fb79832767993f62358551f8aafafc3cf",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "main",
"description" : "High-throughput pipeline [WIP]\n",
"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" : {
"test_resources" : [
{
@@ -3228,11 +3229,13 @@ meta = [
],
"keywords" : [
"bioinformatics",
"sequence",
"sequencing",
"high-throughput",
"RNAseq",
"mapping",
"counting",
"pipeline"
"pipeline",
"workflow"
],
"license" : "MIT",
"organization" : "vsh",

24
target/nextflow/io/publish_results/.config.vsh.yaml
View File

@@ -190,12 +190,28 @@ build_info:
output: "target/nextflow/io/publish_results"
executable: "target/nextflow/io/publish_results/main.nf"
viash_version: "0.9.4"
git_commit: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -212,11 +228,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

11
target/nextflow/io/publish_results/main.nf
View File

@@ -3262,13 +3262,14 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/publish_results",
"viash_version" : "0.9.4",
"git_commit" : "a62a15edd24e20595ec87bc641f1d829bd1e60d0",
"git_commit" : "28e59b1fb79832767993f62358551f8aafafc3cf",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "main",
"description" : "High-throughput pipeline [WIP]\n",
"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" : {
"test_resources" : [
{
@@ -3288,11 +3289,13 @@ meta = [
],
"keywords" : [
"bioinformatics",
"sequence",
"sequencing",
"high-throughput",
"RNAseq",
"mapping",
"counting",
"pipeline"
"pipeline",
"workflow"
],
"license" : "MIT",
"organization" : "vsh",

24
target/nextflow/parallel_map/.config.vsh.yaml
View File

@@ -282,12 +282,28 @@ build_info:
output: "target/nextflow/parallel_map"
executable: "target/nextflow/parallel_map/main.nf"
viash_version: "0.9.4"
git_commit: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -304,11 +320,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

11
target/nextflow/parallel_map/main.nf
View File

@@ -3374,13 +3374,14 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/parallel_map",
"viash_version" : "0.9.4",
"git_commit" : "a62a15edd24e20595ec87bc641f1d829bd1e60d0",
"git_commit" : "28e59b1fb79832767993f62358551f8aafafc3cf",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "main",
"description" : "High-throughput pipeline [WIP]\n",
"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" : {
"test_resources" : [
{
@@ -3400,11 +3401,13 @@ meta = [
],
"keywords" : [
"bioinformatics",
"sequence",
"sequencing",
"high-throughput",
"RNAseq",
"mapping",
"counting",
"pipeline"
"pipeline",
"workflow"
],
"license" : "MIT",
"organization" : "vsh",

24
target/nextflow/report/create_report/.config.vsh.yaml
View File

@@ -212,12 +212,28 @@ build_info:
output: "target/nextflow/report/create_report"
executable: "target/nextflow/report/create_report/main.nf"
viash_version: "0.9.4"
git_commit: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -234,11 +250,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

11
target/nextflow/report/create_report/main.nf
View File

@@ -3318,13 +3318,14 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/report/create_report",
"viash_version" : "0.9.4",
"git_commit" : "a62a15edd24e20595ec87bc641f1d829bd1e60d0",
"git_commit" : "28e59b1fb79832767993f62358551f8aafafc3cf",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "main",
"description" : "High-throughput pipeline [WIP]\n",
"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" : {
"test_resources" : [
{
@@ -3344,11 +3345,13 @@ meta = [
],
"keywords" : [
"bioinformatics",
"sequence",
"sequencing",
"high-throughput",
"RNAseq",
"mapping",
"counting",
"pipeline"
"pipeline",
"workflow"
],
"license" : "MIT",
"organization" : "vsh",

24
target/nextflow/stats/combine_star_logs/.config.vsh.yaml
View File

@@ -201,12 +201,28 @@ 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: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -223,11 +239,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

11
target/nextflow/stats/combine_star_logs/main.nf
View File

@@ -3290,13 +3290,14 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/combine_star_logs",
"viash_version" : "0.9.4",
"git_commit" : "a62a15edd24e20595ec87bc641f1d829bd1e60d0",
"git_commit" : "28e59b1fb79832767993f62358551f8aafafc3cf",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "main",
"description" : "High-throughput pipeline [WIP]\n",
"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" : {
"test_resources" : [
{
@@ -3316,11 +3317,13 @@ meta = [
],
"keywords" : [
"bioinformatics",
"sequence",
"sequencing",
"high-throughput",
"RNAseq",
"mapping",
"counting",
"pipeline"
"pipeline",
"workflow"
],
"license" : "MIT",
"organization" : "vsh",

24
target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
View File

@@ -185,12 +185,28 @@ 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: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -207,11 +223,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

11
target/nextflow/stats/generate_pool_statistics/main.nf
View File

@@ -3274,13 +3274,14 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/generate_pool_statistics",
"viash_version" : "0.9.4",
"git_commit" : "a62a15edd24e20595ec87bc641f1d829bd1e60d0",
"git_commit" : "28e59b1fb79832767993f62358551f8aafafc3cf",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "main",
"description" : "High-throughput pipeline [WIP]\n",
"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" : {
"test_resources" : [
{
@@ -3300,11 +3301,13 @@ meta = [
],
"keywords" : [
"bioinformatics",
"sequence",
"sequencing",
"high-throughput",
"RNAseq",
"mapping",
"counting",
"pipeline"
"pipeline",
"workflow"
],
"license" : "MIT",
"organization" : "vsh",

24
target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
View File

@@ -267,12 +267,28 @@ 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: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -289,11 +305,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

11
target/nextflow/stats/generate_well_statistics/main.nf
View File

@@ -3369,13 +3369,14 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/generate_well_statistics",
"viash_version" : "0.9.4",
"git_commit" : "a62a15edd24e20595ec87bc641f1d829bd1e60d0",
"git_commit" : "28e59b1fb79832767993f62358551f8aafafc3cf",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "main",
"description" : "High-throughput pipeline [WIP]\n",
"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" : {
"test_resources" : [
{
@@ -3395,11 +3396,13 @@ meta = [
],
"keywords" : [
"bioinformatics",
"sequence",
"sequencing",
"high-throughput",
"RNAseq",
"mapping",
"counting",
"pipeline"
"pipeline",
"workflow"
],
"license" : "MIT",
"organization" : "vsh",

24
target/nextflow/utils/concatRuns/.config.vsh.yaml
View File

@@ -157,14 +157,30 @@ build_info:
output: "target/nextflow/utils/concatRuns"
executable: "target/nextflow/utils/concatRuns/main.nf"
viash_version: "0.9.4"
git_commit: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
dependencies:
- "target/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/concat_text"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -181,11 +197,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

11
target/nextflow/utils/concatRuns/main.nf
View File

@@ -3224,13 +3224,14 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/utils/concatRuns",
"viash_version" : "0.9.4",
"git_commit" : "a62a15edd24e20595ec87bc641f1d829bd1e60d0",
"git_commit" : "28e59b1fb79832767993f62358551f8aafafc3cf",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "main",
"description" : "High-throughput pipeline [WIP]\n",
"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" : {
"test_resources" : [
{
@@ -3250,11 +3251,13 @@ meta = [
],
"keywords" : [
"bioinformatics",
"sequence",
"sequencing",
"high-throughput",
"RNAseq",
"mapping",
"counting",
"pipeline"
"pipeline",
"workflow"
],
"license" : "MIT",
"organization" : "vsh",

24
target/nextflow/utils/listInputDir/.config.vsh.yaml
View File

@@ -168,12 +168,28 @@ build_info:
output: "target/nextflow/utils/listInputDir"
executable: "target/nextflow/utils/listInputDir/main.nf"
viash_version: "0.9.4"
git_commit: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -190,11 +206,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

11
target/nextflow/utils/listInputDir/main.nf
View File

@@ -3234,13 +3234,14 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/utils/listInputDir",
"viash_version" : "0.9.4",
"git_commit" : "a62a15edd24e20595ec87bc641f1d829bd1e60d0",
"git_commit" : "28e59b1fb79832767993f62358551f8aafafc3cf",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "main",
"description" : "High-throughput pipeline [WIP]\n",
"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" : {
"test_resources" : [
{
@@ -3260,11 +3261,13 @@ meta = [
],
"keywords" : [
"bioinformatics",
"sequence",
"sequencing",
"high-throughput",
"RNAseq",
"mapping",
"counting",
"pipeline"
"pipeline",
"workflow"
],
"license" : "MIT",
"organization" : "vsh",

24
target/nextflow/workflows/htrnaseq/.config.vsh.yaml
View File

@@ -328,7 +328,7 @@ build_info:
output: "target/nextflow/workflows/htrnaseq"
executable: "target/nextflow/workflows/htrnaseq/main.nf"
viash_version: "0.9.4"
git_commit: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
dependencies:
- "target/nextflow/stats/combine_star_logs"
@@ -345,7 +345,23 @@ build_info:
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -362,11 +378,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

11
target/nextflow/workflows/htrnaseq/main.nf
View File

@@ -3460,13 +3460,14 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/htrnaseq",
"viash_version" : "0.9.4",
"git_commit" : "a62a15edd24e20595ec87bc641f1d829bd1e60d0",
"git_commit" : "28e59b1fb79832767993f62358551f8aafafc3cf",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "main",
"description" : "High-throughput pipeline [WIP]\n",
"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" : {
"test_resources" : [
{
@@ -3486,11 +3487,13 @@ meta = [
],
"keywords" : [
"bioinformatics",
"sequence",
"sequencing",
"high-throughput",
"RNAseq",
"mapping",
"counting",
"pipeline"
"pipeline",
"workflow"
],
"license" : "MIT",
"organization" : "vsh",

24
target/nextflow/workflows/runner/.config.vsh.yaml
View File

@@ -221,7 +221,7 @@ build_info:
output: "target/nextflow/workflows/runner"
executable: "target/nextflow/workflows/runner/main.nf"
viash_version: "0.9.4"
git_commit: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
dependencies:
- "target/nextflow/utils/listInputDir"
@@ -231,7 +231,23 @@ build_info:
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -248,11 +264,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

11
target/nextflow/workflows/runner/main.nf
View File

@@ -3312,13 +3312,14 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/runner",
"viash_version" : "0.9.4",
"git_commit" : "a62a15edd24e20595ec87bc641f1d829bd1e60d0",
"git_commit" : "28e59b1fb79832767993f62358551f8aafafc3cf",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "main",
"description" : "High-throughput pipeline [WIP]\n",
"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" : {
"test_resources" : [
{
@@ -3338,11 +3339,13 @@ meta = [
],
"keywords" : [
"bioinformatics",
"sequence",
"sequencing",
"high-throughput",
"RNAseq",
"mapping",
"counting",
"pipeline"
"pipeline",
"workflow"
],
"license" : "MIT",
"organization" : "vsh",

24
target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
View File

@@ -214,7 +214,7 @@ build_info:
output: "target/nextflow/workflows/well_demultiplex"
executable: "target/nextflow/workflows/well_demultiplex/main.nf"
viash_version: "0.9.4"
git_commit: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/cutadapt"
@@ -222,7 +222,23 @@ build_info:
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -239,11 +255,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

11
target/nextflow/workflows/well_demultiplex/main.nf
View File

@@ -3314,13 +3314,14 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/well_demultiplex",
"viash_version" : "0.9.4",
"git_commit" : "a62a15edd24e20595ec87bc641f1d829bd1e60d0",
"git_commit" : "28e59b1fb79832767993f62358551f8aafafc3cf",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "main",
"description" : "High-throughput pipeline [WIP]\n",
"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" : {
"test_resources" : [
{
@@ -3340,11 +3341,13 @@ meta = [
],
"keywords" : [
"bioinformatics",
"sequence",
"sequencing",
"high-throughput",
"RNAseq",
"mapping",
"counting",
"pipeline"
"pipeline",
"workflow"
],
"license" : "MIT",
"organization" : "vsh",

24
target/nextflow/workflows/well_metadata/.config.vsh.yaml
View File

@@ -212,12 +212,28 @@ build_info:
output: "target/nextflow/workflows/well_metadata"
executable: "target/nextflow/workflows/well_metadata/main.nf"
viash_version: "0.9.4"
git_commit: "a62a15edd24e20595ec87bc641f1d829bd1e60d0"
git_commit: "28e59b1fb79832767993f62358551f8aafafc3cf"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
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)\n\
supplemented 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:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -234,11 +250,13 @@ package_config:
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "sequencing"
- "high-throughput"
- "RNAseq"
- "mapping"
- "counting"
- "pipeline"
- "workflow"
license: "MIT"
organization: "vsh"
links:

11
target/nextflow/workflows/well_metadata/main.nf
View File

@@ -3294,13 +3294,14 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/well_metadata",
"viash_version" : "0.9.4",
"git_commit" : "a62a15edd24e20595ec87bc641f1d829bd1e60d0",
"git_commit" : "28e59b1fb79832767993f62358551f8aafafc3cf",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
"version" : "main",
"description" : "High-throughput pipeline [WIP]\n",
"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" : {
"test_resources" : [
{
@@ -3320,11 +3321,13 @@ meta = [
],
"keywords" : [
"bioinformatics",
"sequence",
"sequencing",
"high-throughput",
"RNAseq",
"mapping",
"counting",
"pipeline"
"pipeline",
"workflow"
],
"license" : "MIT",
"organization" : "vsh",