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CI 8aa5e10929 Build branch main_pipeline with version main_pipeline (d18fe81)

Build pipeline: viash-hub.htrnaseq.main-pipeline-skgbt

Source commit: d18fe81ef5

Source message: Add simple README and update integration_test script

2024-08-20 15:20:20 +00:00

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Viash-enabled HT-RNAseq pipeline

Introduction

TODO: Add a description of the pipeline here.

Test data

The pipeline can be run by creating a params.yaml file like this:

param_list:
  - input_r1: "test_resources/100k/SRR14730301/VH02001612_S9_R1_001.fastq"
    input_r2: "test_resources/100k/SRR14730301/VH02001612_S9_R2_001.fastq"
    genomeDir: "test_resources/genomeDir/gencode.v41.star.sparse"
    barcodesFasta: "test_resources/2-wells.fasta"
    id: sample_one
  - input_r1: "test_resources/100k/SRR14730302/VH02001614_S8_R1_001.fastq"
    input_r2: "test_resources/100k/SRR14730302/VH02001614_S8_R2_001.fastq"
    genomeDir: "test_resources/genomeDir/gencode.v41.star.sparse"
    barcodesFasta: "test_resources/2-wells.fasta"
    id: sample_two

and then:

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 \
  -publish_dir output \
  -resume

Or, by running src/workflows/htrnaseq/integration_test.sh.

1.1 KiB Raw Blame History

Viash-enabled HT-RNAseq pipeline

Introduction

Test data

1.1 KiB

Raw Blame History