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Add AWS Megatest #130

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Feb 14, 2024
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Add AWS Megatest #130

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3 changes: 0 additions & 3 deletions .github/workflows/awsfulltest.yml
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Expand Up @@ -15,9 +15,6 @@ jobs:
steps:
- name: Launch workflow via tower
uses: seqeralabs/action-tower-launch@v2
# TODO nf-core: You can customise AWS full pipeline tests as required
# Add full size test data (but still relatively small datasets for few samples)
# on the `test_full.config` test runs with only one set of parameters
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [ec24cfb](https://github.com/nf-core/nascent/commit/ec24cfb2646904bcc78379a071b50b53a855b9a9) - Update pipeline template to [nf-core/tools 2.11.1](https://github.com/nf-core/tools/releases/tag/2.11.1)
- [15b8ff3](https://github.com/nf-core/nascent/commit/15b8ff31cd43ec2e330ce7958bd6d7d65529b4d3) - Update pipeline template to [nf-core/tools 2.11](https://github.com/nf-core/tools/releases/tag/2.11)
- [9712163](https://github.com/nf-core/nascent/commit/97121638eb77e175b912ff45a669426e532c5d7f) - Update pipeline template to [nf-core/tools 2.10](https://github.com/nf-core/tools/releases/tag/2.10)
- [[#130](https://github.com/nf-core/nascent/pull/130)] - AWS Mega Tests

## v2.1.1 - 2023-02-17

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3 changes: 0 additions & 3 deletions README.md
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Expand Up @@ -21,9 +21,6 @@

The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!

<!-- TODO nf-core: Add full-sized test dataset and amend the paragraph below if applicable -->
<!-- https://github.com/nf-core/nascent/issues/66 -->

On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/nascent/results).

## Pipeline summary
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12 changes: 12 additions & 0 deletions assets/samplesheet_full.csv
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@@ -0,0 +1,12 @@
sample,fastq_1,fastq_2
GM_0h,ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR211/ERR2114683/GM0h.fastq.gz,
GM_30min,ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR211/ERR2114684/GM30min.fastq.gz,
GM_1h,ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR211/ERR2114685/GM1h.fastq.gz,
GM_2h,ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR211/ERR2114686/GM2h.fastq.gz,
GM_4h,ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR211/ERR2114687/GM4h.fastq.gz,
GM_6h,ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR211/ERR2114688/GM6h.fastq.gz,
GM_9h,ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR211/ERR2114689/GM9h.fastq.gz,
GM_12h,ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR211/ERR2114690/GM12h.fastq.gz,
GM_18h,ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR211/ERR2114691/GM18h.fastq.gz,
GM_48h,ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR211/ERR2114693/GM48h.fastq.gz,
GM_72h,ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR211/ERR2114694/GM72h.fastq.gz,
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if download is an issue we can also move this data to the megatest bucket.

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Oh good point I hadn't thought of that... Might be more expensive due to the slow download, but it should just be the head node...

7 changes: 3 additions & 4 deletions conf/test_full.config
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Expand Up @@ -15,10 +15,9 @@ params {
config_profile_description = 'Full test dataset to check pipeline function'

// Input data for full size test
// TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
// TODO nf-core: Give any required params for the test so that command line flags are not needed
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
input = "${projectDir}/assets/samplesheet_full.csv"

// Genome references
genome = 'R64-1-1'
genome = 'hg38'
assay_type = 'GROseq'
}
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