diff --git a/LICENSE b/LICENSE new file mode 100644 index 00000000..f5b784fa --- /dev/null +++ b/LICENSE @@ -0,0 +1,21 @@ +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. diff --git a/README.md b/README.md index 20d55213..5a36d937 100644 --- a/README.md +++ b/README.md @@ -1,129 +1,207 @@ -# 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. \ No newline at end of file +Other contributions are welcome. diff --git a/README.qmd b/README.qmd new file mode 100644 index 00000000..ccb24557 --- /dev/null +++ b/README.qmd @@ -0,0 +1,149 @@ +--- +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. diff --git a/_viash.yaml b/_viash.yaml index a7e29d98..d20439a7 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -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 diff --git a/assets/htrnaseq-launch-small.png b/assets/htrnaseq-launch-small.png new file mode 100644 index 00000000..c0872d6f Binary files /dev/null and b/assets/htrnaseq-launch-small.png differ diff --git a/assets/htrnaseq-launch.png b/assets/htrnaseq-launch.png new file mode 100644 index 00000000..bcbd2f25 Binary files /dev/null and b/assets/htrnaseq-launch.png differ diff --git a/assets/launch-parameters-1-small.png b/assets/launch-parameters-1-small.png new file mode 100644 index 00000000..6fa7ef94 Binary files /dev/null and b/assets/launch-parameters-1-small.png differ diff --git a/assets/launch-parameters-1.png b/assets/launch-parameters-1.png new file mode 100644 index 00000000..5a76b1fd Binary files /dev/null and b/assets/launch-parameters-1.png differ diff --git a/assets/launch-parameters-2-small.png b/assets/launch-parameters-2-small.png new file mode 100644 index 00000000..7c4a9eff Binary files /dev/null and b/assets/launch-parameters-2-small.png differ diff --git a/assets/launch-parameters-2.png b/assets/launch-parameters-2.png new file mode 100644 index 00000000..3d8dc5b5 Binary files /dev/null and b/assets/launch-parameters-2.png differ diff --git a/assets/launch-parameters-3-small.png b/assets/launch-parameters-3-small.png new file mode 100644 index 00000000..7e23730b Binary files /dev/null and b/assets/launch-parameters-3-small.png differ diff --git a/assets/launch-parameters-3.png b/assets/launch-parameters-3.png new file mode 100644 index 00000000..cdb842c5 Binary files /dev/null and b/assets/launch-parameters-3.png differ diff --git a/assets/launch-parameters-4-small.png b/assets/launch-parameters-4-small.png new file mode 100644 index 00000000..4f9b7703 Binary files /dev/null and b/assets/launch-parameters-4-small.png differ diff --git a/assets/launch-parameters-4.png b/assets/launch-parameters-4.png new file mode 100644 index 00000000..2289f7c6 Binary files /dev/null and b/assets/launch-parameters-4.png differ diff --git a/assets/launch-parameters-5-small.png b/assets/launch-parameters-5-small.png new file mode 100644 index 00000000..a6e2700c Binary files /dev/null and b/assets/launch-parameters-5-small.png differ diff --git a/assets/launch-parameters-5.png b/assets/launch-parameters-5.png new file mode 100644 index 00000000..abbc1f75 Binary files /dev/null and b/assets/launch-parameters-5.png differ diff --git a/target/executable/eset/create_eset/.config.vsh.yaml b/target/executable/eset/create_eset/.config.vsh.yaml index 3268babe..39f6d78a 100644 --- a/target/executable/eset/create_eset/.config.vsh.yaml +++ b/target/executable/eset/create_eset/.config.vsh.yaml @@ -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: diff --git a/target/executable/eset/create_eset/create_eset b/target/executable/eset/create_eset/create_eset index f6fe2e69..469be369 100755 --- a/target/executable/eset/create_eset/create_eset +++ b/target/executable/eset/create_eset/create_eset @@ -456,9 +456,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component eset create_eset" -LABEL org.opencontainers.image.created="2025-04-30T10:35:22Z" +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 diff --git a/target/executable/eset/create_fdata/.config.vsh.yaml b/target/executable/eset/create_fdata/.config.vsh.yaml index 902bc37b..5d164f75 100644 --- a/target/executable/eset/create_fdata/.config.vsh.yaml +++ b/target/executable/eset/create_fdata/.config.vsh.yaml @@ -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: diff --git a/target/executable/eset/create_fdata/create_fdata b/target/executable/eset/create_fdata/create_fdata index 529c3c00..af733309 100755 --- a/target/executable/eset/create_fdata/create_fdata +++ b/target/executable/eset/create_fdata/create_fdata @@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component eset create_fdata" -LABEL org.opencontainers.image.created="2025-04-30T10:35:21Z" +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 diff --git a/target/executable/eset/create_pdata/.config.vsh.yaml b/target/executable/eset/create_pdata/.config.vsh.yaml index cd00db86..e246a78a 100644 --- a/target/executable/eset/create_pdata/.config.vsh.yaml +++ b/target/executable/eset/create_pdata/.config.vsh.yaml @@ -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: diff --git a/target/executable/eset/create_pdata/create_pdata b/target/executable/eset/create_pdata/create_pdata index 4f0127d5..3b7c6f22 100755 --- a/target/executable/eset/create_pdata/create_pdata +++ b/target/executable/eset/create_pdata/create_pdata @@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component eset create_pdata" -LABEL org.opencontainers.image.created="2025-04-30T10:35:22Z" +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 diff --git a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml index eee7dfcd..8d1fc670 100644 --- a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml +++ b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml @@ -152,12 +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: diff --git a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset index a47747ba..5614634a 100755 --- a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset +++ b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset @@ -455,9 +455,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/htrnaseq check_eset" -LABEL org.opencontainers.image.created="2025-04-30T10:35:21Z" +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 diff --git a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml index e252155b..4965a3d6 100644 --- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml +++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml @@ -161,12 +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: diff --git a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output index 61c593b6..fab77460 100755 --- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output +++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output @@ -457,9 +457,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/well_demultiplexing check_cutadapt_output" -LABEL org.opencontainers.image.created="2025-04-30T10:35:23Z" +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 diff --git a/target/executable/io/publish_fastqs/.config.vsh.yaml b/target/executable/io/publish_fastqs/.config.vsh.yaml index fbaeb220..d19f1656 100644 --- a/target/executable/io/publish_fastqs/.config.vsh.yaml +++ b/target/executable/io/publish_fastqs/.config.vsh.yaml @@ -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: diff --git a/target/executable/io/publish_fastqs/publish_fastqs b/target/executable/io/publish_fastqs/publish_fastqs index e7fdd5c3..b7b4479b 100755 --- a/target/executable/io/publish_fastqs/publish_fastqs +++ b/target/executable/io/publish_fastqs/publish_fastqs @@ -450,9 +450,9 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component io publish_fastqs" -LABEL org.opencontainers.image.created="2025-04-30T10:35:21Z" +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 diff --git a/target/executable/io/publish_results/.config.vsh.yaml b/target/executable/io/publish_results/.config.vsh.yaml index 82b085fd..4f93c844 100644 --- a/target/executable/io/publish_results/.config.vsh.yaml +++ b/target/executable/io/publish_results/.config.vsh.yaml @@ -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: diff --git a/target/executable/io/publish_results/publish_results b/target/executable/io/publish_results/publish_results index 4bec0928..b336f8e5 100755 --- a/target/executable/io/publish_results/publish_results +++ b/target/executable/io/publish_results/publish_results @@ -450,9 +450,9 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component io publish_results" -LABEL org.opencontainers.image.created="2025-04-30T10:35:21Z" +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 diff --git a/target/executable/parallel_map/.config.vsh.yaml b/target/executable/parallel_map/.config.vsh.yaml index da910c48..b7de1f96 100644 --- a/target/executable/parallel_map/.config.vsh.yaml +++ b/target/executable/parallel_map/.config.vsh.yaml @@ -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: diff --git a/target/executable/parallel_map/parallel_map b/target/executable/parallel_map/parallel_map index c0483956..a44ee9d5 100755 --- a/target/executable/parallel_map/parallel_map +++ b/target/executable/parallel_map/parallel_map @@ -461,9 +461,9 @@ ENV STAR_BINARY=STAR COPY STAR /usr/local/bin/$STAR_BINARY LABEL org.opencontainers.image.authors="Dries Schaumont, Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component parallel_map" -LABEL org.opencontainers.image.created="2025-04-30T10:35:22Z" +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 diff --git a/target/executable/report/create_report/.config.vsh.yaml b/target/executable/report/create_report/.config.vsh.yaml index 5aa7bcb3..2a642b30 100644 --- a/target/executable/report/create_report/.config.vsh.yaml +++ b/target/executable/report/create_report/.config.vsh.yaml @@ -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: diff --git a/target/executable/report/create_report/create_report b/target/executable/report/create_report/create_report index 98088cce..8ae3d94b 100755 --- a/target/executable/report/create_report/create_report +++ b/target/executable/report/create_report/create_report @@ -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 diff --git a/target/executable/stats/combine_star_logs/.config.vsh.yaml b/target/executable/stats/combine_star_logs/.config.vsh.yaml index 3336f8bd..d1cf23f8 100644 --- a/target/executable/stats/combine_star_logs/.config.vsh.yaml +++ b/target/executable/stats/combine_star_logs/.config.vsh.yaml @@ -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: diff --git a/target/executable/stats/combine_star_logs/combine_star_logs b/target/executable/stats/combine_star_logs/combine_star_logs index 62cf361c..2a260a61 100755 --- a/target/executable/stats/combine_star_logs/combine_star_logs +++ b/target/executable/stats/combine_star_logs/combine_star_logs @@ -457,9 +457,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component stats combine_star_logs" -LABEL org.opencontainers.image.created="2025-04-30T10:35:21Z" +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 diff --git a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml index 5923dd44..e8532e50 100644 --- a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml +++ b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml @@ -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: diff --git a/target/executable/stats/generate_pool_statistics/generate_pool_statistics b/target/executable/stats/generate_pool_statistics/generate_pool_statistics index f10e2e08..97cc8fda 100755 --- a/target/executable/stats/generate_pool_statistics/generate_pool_statistics +++ b/target/executable/stats/generate_pool_statistics/generate_pool_statistics @@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component stats generate_pool_statistics" -LABEL org.opencontainers.image.created="2025-04-30T10:35:21Z" +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 diff --git a/target/executable/stats/generate_well_statistics/.config.vsh.yaml b/target/executable/stats/generate_well_statistics/.config.vsh.yaml index a348db12..94d20fa4 100644 --- a/target/executable/stats/generate_well_statistics/.config.vsh.yaml +++ b/target/executable/stats/generate_well_statistics/.config.vsh.yaml @@ -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: diff --git a/target/executable/stats/generate_well_statistics/generate_well_statistics b/target/executable/stats/generate_well_statistics/generate_well_statistics index 087bf7b5..62d02484 100755 --- a/target/executable/stats/generate_well_statistics/generate_well_statistics +++ b/target/executable/stats/generate_well_statistics/generate_well_statistics @@ -461,9 +461,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component stats generate_well_statistics" -LABEL org.opencontainers.image.created="2025-04-30T10:35:21Z" +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 diff --git a/target/nextflow/eset/create_eset/.config.vsh.yaml b/target/nextflow/eset/create_eset/.config.vsh.yaml index cf406bdb..4e7fa577 100644 --- a/target/nextflow/eset/create_eset/.config.vsh.yaml +++ b/target/nextflow/eset/create_eset/.config.vsh.yaml @@ -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: diff --git a/target/nextflow/eset/create_eset/main.nf b/target/nextflow/eset/create_eset/main.nf index ed0684f4..b81b634e 100644 --- a/target/nextflow/eset/create_eset/main.nf +++ b/target/nextflow/eset/create_eset/main.nf @@ -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", diff --git a/target/nextflow/eset/create_fdata/.config.vsh.yaml b/target/nextflow/eset/create_fdata/.config.vsh.yaml index 27394886..75e41023 100644 --- a/target/nextflow/eset/create_fdata/.config.vsh.yaml +++ b/target/nextflow/eset/create_fdata/.config.vsh.yaml @@ -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: diff --git a/target/nextflow/eset/create_fdata/main.nf b/target/nextflow/eset/create_fdata/main.nf index df7e814d..48a1d0bc 100644 --- a/target/nextflow/eset/create_fdata/main.nf +++ b/target/nextflow/eset/create_fdata/main.nf @@ -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", diff --git a/target/nextflow/eset/create_pdata/.config.vsh.yaml b/target/nextflow/eset/create_pdata/.config.vsh.yaml index 4fb3343e..f193275a 100644 --- a/target/nextflow/eset/create_pdata/.config.vsh.yaml +++ b/target/nextflow/eset/create_pdata/.config.vsh.yaml @@ -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: diff --git a/target/nextflow/eset/create_pdata/main.nf b/target/nextflow/eset/create_pdata/main.nf index 2e0b982c..d1afddd8 100644 --- a/target/nextflow/eset/create_pdata/main.nf +++ b/target/nextflow/eset/create_pdata/main.nf @@ -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", diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml index b5da1f9a..c3a915d9 100644 --- a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml +++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml @@ -152,12 +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: diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf index 1129628a..72b19a8c 100644 --- a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf +++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf @@ -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", diff --git a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml index 5ac44c37..51f8200b 100644 --- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml +++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml @@ -161,12 +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: diff --git a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf index 11eca22d..abfca083 100644 --- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf +++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf @@ -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", diff --git a/target/nextflow/io/publish_fastqs/.config.vsh.yaml b/target/nextflow/io/publish_fastqs/.config.vsh.yaml index 75ee2e6b..9326440e 100644 --- a/target/nextflow/io/publish_fastqs/.config.vsh.yaml +++ b/target/nextflow/io/publish_fastqs/.config.vsh.yaml @@ -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: diff --git a/target/nextflow/io/publish_fastqs/main.nf b/target/nextflow/io/publish_fastqs/main.nf index 768321bc..3e241b91 100644 --- a/target/nextflow/io/publish_fastqs/main.nf +++ b/target/nextflow/io/publish_fastqs/main.nf @@ -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", diff --git a/target/nextflow/io/publish_results/.config.vsh.yaml b/target/nextflow/io/publish_results/.config.vsh.yaml index cc9017f8..7dc67196 100644 --- a/target/nextflow/io/publish_results/.config.vsh.yaml +++ b/target/nextflow/io/publish_results/.config.vsh.yaml @@ -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: diff --git a/target/nextflow/io/publish_results/main.nf b/target/nextflow/io/publish_results/main.nf index 8acbd860..3d4f062f 100644 --- a/target/nextflow/io/publish_results/main.nf +++ b/target/nextflow/io/publish_results/main.nf @@ -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", diff --git a/target/nextflow/parallel_map/.config.vsh.yaml b/target/nextflow/parallel_map/.config.vsh.yaml index 9f9cefff..f23f78f3 100644 --- a/target/nextflow/parallel_map/.config.vsh.yaml +++ b/target/nextflow/parallel_map/.config.vsh.yaml @@ -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: diff --git a/target/nextflow/parallel_map/main.nf b/target/nextflow/parallel_map/main.nf index 625b7ca5..433476cf 100644 --- a/target/nextflow/parallel_map/main.nf +++ b/target/nextflow/parallel_map/main.nf @@ -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", diff --git a/target/nextflow/report/create_report/.config.vsh.yaml b/target/nextflow/report/create_report/.config.vsh.yaml index 195b597a..83db5603 100644 --- a/target/nextflow/report/create_report/.config.vsh.yaml +++ b/target/nextflow/report/create_report/.config.vsh.yaml @@ -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: diff --git a/target/nextflow/report/create_report/main.nf b/target/nextflow/report/create_report/main.nf index 2e468397..fc9afd75 100644 --- a/target/nextflow/report/create_report/main.nf +++ b/target/nextflow/report/create_report/main.nf @@ -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", diff --git a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml index 9c85b875..323a03ec 100644 --- a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml +++ b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml @@ -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: diff --git a/target/nextflow/stats/combine_star_logs/main.nf b/target/nextflow/stats/combine_star_logs/main.nf index 16c20370..ecddd77a 100644 --- a/target/nextflow/stats/combine_star_logs/main.nf +++ b/target/nextflow/stats/combine_star_logs/main.nf @@ -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", diff --git a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml index 607e2280..49da4286 100644 --- a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml +++ b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml @@ -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: diff --git a/target/nextflow/stats/generate_pool_statistics/main.nf b/target/nextflow/stats/generate_pool_statistics/main.nf index 80683f04..6c0f1e5e 100644 --- a/target/nextflow/stats/generate_pool_statistics/main.nf +++ b/target/nextflow/stats/generate_pool_statistics/main.nf @@ -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", diff --git a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml index 72913418..6932c92f 100644 --- a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml +++ b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml @@ -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: diff --git a/target/nextflow/stats/generate_well_statistics/main.nf b/target/nextflow/stats/generate_well_statistics/main.nf index d6263b43..5b3160ab 100644 --- a/target/nextflow/stats/generate_well_statistics/main.nf +++ b/target/nextflow/stats/generate_well_statistics/main.nf @@ -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", diff --git a/target/nextflow/utils/concatRuns/.config.vsh.yaml b/target/nextflow/utils/concatRuns/.config.vsh.yaml index 1e35513b..e5d1f6e2 100644 --- a/target/nextflow/utils/concatRuns/.config.vsh.yaml +++ b/target/nextflow/utils/concatRuns/.config.vsh.yaml @@ -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: diff --git a/target/nextflow/utils/concatRuns/main.nf b/target/nextflow/utils/concatRuns/main.nf index 7f24493f..25d4cdab 100644 --- a/target/nextflow/utils/concatRuns/main.nf +++ b/target/nextflow/utils/concatRuns/main.nf @@ -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", diff --git a/target/nextflow/utils/listInputDir/.config.vsh.yaml b/target/nextflow/utils/listInputDir/.config.vsh.yaml index fdf8035c..35e5f7cf 100644 --- a/target/nextflow/utils/listInputDir/.config.vsh.yaml +++ b/target/nextflow/utils/listInputDir/.config.vsh.yaml @@ -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: diff --git a/target/nextflow/utils/listInputDir/main.nf b/target/nextflow/utils/listInputDir/main.nf index 5797919c..f1ec8d1c 100644 --- a/target/nextflow/utils/listInputDir/main.nf +++ b/target/nextflow/utils/listInputDir/main.nf @@ -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", diff --git a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml index 84594210..8340a23e 100644 --- a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml +++ b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml @@ -328,7 +328,7 @@ build_info: output: "target/nextflow/workflows/htrnaseq" executable: "target/nextflow/workflows/htrnaseq/main.nf" viash_version: "0.9.4" - 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: diff --git a/target/nextflow/workflows/htrnaseq/main.nf b/target/nextflow/workflows/htrnaseq/main.nf index 9a978898..4e6efdc8 100644 --- a/target/nextflow/workflows/htrnaseq/main.nf +++ b/target/nextflow/workflows/htrnaseq/main.nf @@ -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", diff --git a/target/nextflow/workflows/runner/.config.vsh.yaml b/target/nextflow/workflows/runner/.config.vsh.yaml index 2b9e7f06..8c100f3b 100644 --- a/target/nextflow/workflows/runner/.config.vsh.yaml +++ b/target/nextflow/workflows/runner/.config.vsh.yaml @@ -221,7 +221,7 @@ build_info: output: "target/nextflow/workflows/runner" executable: "target/nextflow/workflows/runner/main.nf" viash_version: "0.9.4" - 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: diff --git a/target/nextflow/workflows/runner/main.nf b/target/nextflow/workflows/runner/main.nf index 533cabd0..fb6e32f1 100644 --- a/target/nextflow/workflows/runner/main.nf +++ b/target/nextflow/workflows/runner/main.nf @@ -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", diff --git a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml index 5c96ead6..40d70dca 100644 --- a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml +++ b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml @@ -214,7 +214,7 @@ build_info: output: "target/nextflow/workflows/well_demultiplex" executable: "target/nextflow/workflows/well_demultiplex/main.nf" viash_version: "0.9.4" - 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: diff --git a/target/nextflow/workflows/well_demultiplex/main.nf b/target/nextflow/workflows/well_demultiplex/main.nf index 6fca264e..dcb07dce 100644 --- a/target/nextflow/workflows/well_demultiplex/main.nf +++ b/target/nextflow/workflows/well_demultiplex/main.nf @@ -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", diff --git a/target/nextflow/workflows/well_metadata/.config.vsh.yaml b/target/nextflow/workflows/well_metadata/.config.vsh.yaml index 98d17b7a..46136624 100644 --- a/target/nextflow/workflows/well_metadata/.config.vsh.yaml +++ b/target/nextflow/workflows/well_metadata/.config.vsh.yaml @@ -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: diff --git a/target/nextflow/workflows/well_metadata/main.nf b/target/nextflow/workflows/well_metadata/main.nf index c50ae702..6c217c13 100644 --- a/target/nextflow/workflows/well_metadata/main.nf +++ b/target/nextflow/workflows/well_metadata/main.nf @@ -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",