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https://github.com/apetkau/from-samplesheet-test-nf

https://github.com/apetkau/from-samplesheet-test-nf

Science Score: 13.0%

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    Low similarity (6.0%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: apetkau
  • Language: Nextflow
  • Default Branch: main
  • Size: 14.6 KB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
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Created almost 3 years ago · Last pushed almost 3 years ago
Metadata Files
Readme

README.md

Repostiory for testing fromSamplesheet

This repository is used to test out fromSamplesheet with paired/single-end fastq data for comparing running times.

In order to run, first do nextflow pull to download the pipeline files:

bash nextflow pull apetkau/from-samplesheet-test-nf

Now, you can follow the below instructions to test out different cases.

Paired-end

Case: 30 paired-end samples

To extract running times for paired-end data:

bash time nextflow run apetkau/from-samplesheet-test-nf -r main --input https://raw.githubusercontent.com/apetkau/from-samplesheet-test-nf/main/samplesheet.pe.30.csv

For me, this takes ~6 seconds.

To determine time spent validating the samplesheet.

```bash $ grep 'Starting validation' -A1 .nextflow.log

Sep-06 10:43:29.713 [main] DEBUG nextflow.validation.SchemaValidator - Starting validation: 'input': '/apetkau/from-samplesheet-test-nf/main/samplesheet.pe.30.csv' with 'assets/schema_input.json'

Sep-06 10:43:29.878 [main] DEBUG nextflow.validation.SchemaValidator - Validation passed: 'input': '/apetkau/from-samplesheet-test-nf/main/samplesheet.pe.30.csv' with 'assets/schema_input.json'

Sep-06 10:43:29.903 [main] DEBUG nextflow.validation.SchemaValidator - Starting validation: '/apetkau/from-samplesheet-test-nf/main/samplesheet.pe.30.csv' with 'assets/schemainput.json' Sep-06 10:43:29.952 [main] DEBUG nextflow.validation.SchemaValidator - Validation passed: '/apetkau/from-samplesheet-test-nf/main/samplesheet.pe.30.csv' with 'assets/schemainput.json' ```

That is it takes < 1 second for validation, however, this is repeated twice.

Or, in summary: * Total runtime: 6 seconds * Validation time: < 1 second (x2)

Case: 60 paired-end samples

Repeating above with the file https://raw.githubusercontent.com/apetkau/from-samplesheet-test-nf/main/samplesheet.pe.60.csv gives:

  • Total runtime: 6 seconds
  • Validation time: < 1 second (x2)

Single-end

Compare the above run-times to the single-end cases.

Case: 30 single-end samples

bash time nextflow run apetkau/from-samplesheet-test-nf -r main --input https://raw.githubusercontent.com/apetkau/from-samplesheet-test-nf/main/samplesheet.se.30.csv

``` $ grep 'Starting validation' -A1 .nextflow.log

Sep-06 10:45:47.894 [main] DEBUG nextflow.validation.SchemaValidator - Starting validation: 'input': '/apetkau/from-samplesheet-test-nf/main/samplesheet.se.30.csv' with 'assets/schema_input.json'

Sep-06 10:46:11.016 [main] DEBUG nextflow.validation.SchemaValidator - Validation passed: 'input': '/apetkau/from-samplesheet-test-nf/main/samplesheet.se.30.csv' with 'assets/schema_input.json'

Sep-06 10:46:11.035 [main] DEBUG nextflow.validation.SchemaValidator - Starting validation: '/apetkau/from-samplesheet-test-nf/main/samplesheet.se.30.csv' with 'assets/schemainput.json' Sep-06 10:46:34.027 [main] DEBUG nextflow.validation.SchemaValidator - Validation passed: '/apetkau/from-samplesheet-test-nf/main/samplesheet.se.30.csv' with 'assets/schemainput.json' ```

Summary: * Total runtime: 52 seconds * Validationt time: 24 + 13 seconds

Case: 60 single-end samples

Use https://raw.githubusercontent.com/apetkau/from-samplesheet-test-nf/main/samplesheet.se.60.csv.

  • Total runtime: 12 minutes 14 seconds (734 seconds)
  • Validation time: 368 + 360 seconds

Owner

  • Name: Aaron Petkau
  • Login: apetkau
  • Kind: user
  • Company: Public Health Agency of Canada

Bioinformatician with the Public Health Agency of Canada.

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