kfukuta/wf-transcriptomes-v202
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Remove demo data to avoid breaking production demo

Browse Source
This commit is contained in:
Sarah Griffiths 2026-05-28 07:15:20 +00:00 committed by Sam Nicholls
parent 334173d613
commit 30a9880bf7
3 changed files with 0 additions and 38 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

18
README.md
View File

@ -108,24 +108,6 @@ the following command:
nextflow pull epi2me-labs/wf-transcriptomes nextflow pull epi2me-labs/wf-transcriptomes
``` ```
A demo dataset is provided for testing of the workflow.
It can be downloaded and unpacked using the following commands:
```
wget https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-transcriptomes/wf-transcriptomes-demo.tar.gz
tar -xzvf wf-transcriptomes-demo.tar.gz
```
The workflow can then be run with the downloaded demo data using:
```
nextflow run epi2me-labs/wf-transcriptomes \
--de_analysis \
--direct_rna \
--fastq 'wf-transcriptomes-demo/differential_expression_fastq' \
--ref_annotation 'wf-transcriptomes-demo/gencode.v22.annotation.chr20.gtf' \
--ref_genome 'wf-transcriptomes-demo/hg38_chr20.fa' \
--sample_sheet 'wf-transcriptomes-demo/sample_sheet.csv' \
-profile standard
```

18
docs/04_install_and_run.md
View File

@ -37,21 +37,3 @@ the following command:
``` ```
nextflow pull epi2me-labs/wf-transcriptomes nextflow pull epi2me-labs/wf-transcriptomes
``` ```
A demo dataset is provided for testing of the workflow.
It can be downloaded and unpacked using the following commands:
```
wget https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-transcriptomes/wf-transcriptomes-demo.tar.gz
tar -xzvf wf-transcriptomes-demo.tar.gz
```
The workflow can then be run with the downloaded demo data using:
```
nextflow run epi2me-labs/wf-transcriptomes \
--de_analysis \
--direct_rna \
--fastq 'wf-transcriptomes-demo/differential_expression_fastq' \
--ref_annotation 'wf-transcriptomes-demo/gencode.v22.annotation.chr20.gtf' \
--ref_genome 'wf-transcriptomes-demo/hg38_chr20.fa' \
--sample_sheet 'wf-transcriptomes-demo/sample_sheet.csv' \
-profile standard
```

2
nextflow_schema.json
View File

@ -4,8 +4,6 @@
"title": "epi2me-labs/wf-transcriptomes", "title": "epi2me-labs/wf-transcriptomes",
"workflow_title": "Transcriptomes", "workflow_title": "Transcriptomes",
"description": "Long-read transcriptome analysis using bambu with optional SQANTI3 QC, DESeq2, and DEXSeq.", "description": "Long-read transcriptome analysis using bambu with optional SQANTI3 QC, DESeq2, and DEXSeq.",
"demo_url": "https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-transcriptomes/wf-transcriptomes-demo.tar.gz",
"aws_demo_url": "https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-transcriptomes/wf-transcriptomes-demo/aws.nextflow.config",
"url": "https://github.com/epi2me-labs/wf-transcriptomes", "url": "https://github.com/epi2me-labs/wf-transcriptomes",
"type": "object", "type": "object",
"definitions": { "definitions": {