TODO: Add a description of the pipeline here.
As test data, we use a DRUGseq dataset from the NCBI Sequence Read Archive.
The original data has been (partly) subsampled to reduce the test runtime. We used seqtk for this with a seed of 1, e.g.:
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/:
❯ 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
18 directories, 37 files 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.
The 2-wells.fasta file contains the barcodes for 2 wells.
The pipeline can be run by creating a params.yaml file like this:
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 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 \
-resume \
--publish_dir output Or, by running src/workflows/htrnaseq/integration_test.sh.
Developed in collaboration with Data Intuitive and Open Analytics.
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17
License
MIT
Released at
Mar 20, 2025 (over 1 year ago)
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