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Tests

This directory contains tests for Tonkaz.

These test data are generated using sapporo-wes/sapporo-service, sapporo-wes/yevis-cli and Tonkaz.

The procedure of generating each data is as follows:

workflow -- (Sapporo-service/Yevis) --> execution_results + ro_crate -- (Tonkaz) --> comparison_results

Run tests

Several combinations of crates are available as follows:

# GATK (Linux, 1st) <-> GATK (Linux, 2nd)
# Use case: Same environment
# Result: ./comparison_results/gatk_same_env.log
$ deno test -A ./tests/gatk_test.ts

# GATK (Linux) <-> GATK (Mac)
# Use case: Different environment
# Result: ./comparison_results/gatk_diff_env.log
$ deno test -A ./tests/gatk_mac_test.ts

# JGA (Linux, 1st) <-> JGA (Linux, 2nd)
# Use case: Same environment
# Result: ./comparison_results/jga_same_env.log
$ deno test -A ./tests/jga_test.ts

# JGA (Linux) <-> JGA (Mac)
# Use case: Different environment
# Result: ./comparison_results/jga_diff_env.log
$ deno test -A ./tests/jga_mac_test.ts

# RNA-seq (Linux, 1st) <-> RNA-seq (Linux, 2nd)
# Use case: Same environment
# Result: ./comparison_results/rnaseq_same_env.log
$ deno test -A ./tests/rnaseq_test.ts

# RNA-seq (Linux) <-> RNA-seq (Mac)
# Use case: Different environment
# Result: ./comparison_results/rnaseq_diff_env.log
$ deno test -A ./tests/rnaseq_mac_test.ts

# RNA-seq (Linux, 1st) <-> RNA-seq (Linux, v3.6)
# Use case: Different version
# Result: ./comparison_results/rnaseq_diff_ver.log
$ deno test -A ./tests/rnaseq_v3.6_test.ts

# RNA-seq (Linux, 1st) <-> RNA-seq (Linux, small)
# Use case: Missing dataset
# Result: ./comparison_results/rnaseq_missing_data.log
$ deno test -A ./tests/rnaseq_small_test.ts

# RNA-seq (Linux, 1st) <-> RNA-seq (Linux, small)
# Use case: All files
# Result: ./comparison_results/rnaseq_all_files.log
$ deno test -A ./tests/rnaseq_all_files_test.ts

# RNA-seq (Linux, with yevis) <-> RNA-seq (Linux, only sapporo)
$ deno test -A ./tests/rnaseq_only_sapporo_test.ts

# Trimming (Linux) <-> Trimming (Mac)
$ deno test -A ./tests/trimming_mac_test.ts

About test data

The raw data of workflow execution results are stored in DOI.

The crate files contained in example_crate:

example_crate/
├── gatk_1st.json
├── gatk_2nd.json
├── gatk_mac.json
├── jga_1st.json
├── jga_2nd.json
├── jga_mac.json
├── rnaseq_1st.json
├── rnaseq_2nd.json
├── rnaseq_mac.json
├── rnaseq_only_sapporo.json
├── rnaseq_small.json
├── rnaseq_v3.6.json
├── trimming.json
└── trimming_mac.json

Executed environment

About the environment in which these crates were generated.

Field Linux env Mac Apple silicon env
OS Ubuntu 20.04.5 LTS macOS 12.5.1
CPU Intel(R) Xeon(R) CPU E5-2640 0 @ 2.50GHz Apple M1 Max
CPU cores 4 10
CPU Architecture x86_64 arm64
Memory 24.0 GiB 64.0 GiB
Docker version 20.10.8 20.10.16
Sapporo-service version 1.4.8 1.4.8
Yevis-cli version 0.5.4 0.5.4

GATK

  • Crate:
    • gatk_1st.json
      • Crate generated on Linux environment. (1st execution)
    • gatk_2nd.json
      • Crate generated on Linux environment. (2nd execution (same settings))
    • gatk_mac.json
      • Crate generated on Mac Apple silicon environment.

See https://github.com/sapporo-wes/test-workflow#broadinstitutegatkmitochondriapipeline for more details about the executed workflow.

Executed as follows:

yevis test --fetch-ro-crate https://raw.githubusercontent.com/sapporo-wes/test-workflow/main/yevis-metadata_gatk-workflows_mitochondria-pipeline.yml

JGA

  • Crate:
    • jga_1st.json
      • Crate generated on Linux environment. (1st execution)
    • jga_2nd.json
      • Crate generated on Linux environment. (2nd execution (same settings))
    • jga_mac.json
      • Crate generated on Mac Apple silicon environment.

See https://github.com/sapporo-wes/test-workflow#biosciencedbcjga-analysis---per-sample-workflow for more details about the executed workflow.

Executed as follows:

yevis test --fetch-ro-crate https://raw.githubusercontent.com/sapporo-wes/test-workflow/main/yevis-metadata_jga-workflow_per-sample.yml

RNA-seq

  • Crate:
    • rnaseq_1st.json
      • Crate generated on Linux environment. (1st execution)
    • rnaseq_2nd.json
      • Crate generated on Linux environment. (2nd execution (same settings))
    • rnaseq_mac.json
      • Crate generated on Mac Apple silicon environment.
    • rnaseq_small.json
      • Crate generated on Linux environment. (small dataset)
    • rnaseq_v3.6.json
      • Crate generated on Linux environment.
      • Using nf-core/rnaseq version is 3.6. (Normal one is 3.7)
    • rnaseq_only_sapporo.json
      • Crate generated on Linux environment.
      • Using nf-core/rnaseq version is 3.7.
      • Using Sapporo only. (Not using Yevis)

See https://github.com/sapporo-wes/test-workflow#nf-corernaseq for more details about the executed workflow.

Executed as follows:

# Normal one (v3.7)
$ yevis test --fetch-ro-crate https://raw.githubusercontent.com/sapporo-wes/test-workflow/main/yevis-metadata_nf-core_rnaseq.yml

# Small dataset
$ yevis test --fetch-ro-crate https://raw.githubusercontent.com/sapporo-wes/test-workflow/main/yevis-metadata_nf-core_rnaseq_small_test.yml

# v3.6
$ yevis test --fetch-ro-crate https://raw.githubusercontent.com/sapporo-wes/test-workflow/main/yevis-metadata_nf-core_rnaseq_v3.6.yml

Trimming

Workflow is https://github.com/sapporo-wes/yevis-cli/blob/main/tests/test-metadata-CWL.yml

Executed as follows:

yevis test --fetch-ro-crate https://raw.githubusercontent.com/sapporo-wes/yevis-cli/main/tests/test-metadata-CWL.yml