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[Read_Screen] skip_screen actually skips the screen (#699)
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* actually skip read screen

* remove extra input

* update v2.3.0 to vX.X.X

* make pr template more explicit

* fix tests and add default value to genome_length in theiaprok

* fix bug in genome_length

* update checks for theiaprok now that inputs are right

* provide additional clarification regarding theiaeuk-specific consequences of skip_screen

* indentation disasters averted

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Co-authored-by: Michal Babinski <[email protected]>
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sage-wright and Michal-Babins authored Jan 14, 2025

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kushti Alexander Chepurnoy
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2 changes: 1 addition & 1 deletion .github/PULL_REQUEST_TEMPLATE.md
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@@ -46,7 +46,7 @@ This PR uses an element that could cause duplicate runs to have different result
- [ ] The CI/CD has been adjusted and tests are passing (Theiagen developers)
- [ ] Code changes follow the [style guide](https://theiagen.notion.site/Style-Guide-WDL-Workflow-Development-51b66a47dde54c798f35d673fff80249)
- [ ] Documentation and/or workflow diagrams have been updated if applicable
- [ ] You have updated the latest version for any affected worklows in the respective workflow documentation page and for every entry in the three `workflows_overview` tables.
- [ ] You have updated the "Last Known Changes" field for any affected workflows in the respective workflow documentation page and for every entry in the three `workflows_overview` tables to be the tag for the next upcoming release. If you do not know the tag, please put "vX.X.X"

## 🎯 Reviewer Checklist
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4 changes: 2 additions & 2 deletions docs/workflows/genomic_characterization/theiaeuk.md
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@@ -170,7 +170,7 @@ All input reads are processed through "core tasks" in each workflow. The core ta
| theiaeuk_pe | **min_genome_size** | Int | Minimum genome size able to pass read screening | 100000 | Optional |
| theiaeuk_pe | **min_proportion** | Int | Minimum proportion of total reads in each read file to pass read screening | 50 | Optional |
| theiaeuk_pe | **min_reads** | Int | Minimum number of reads to pass read screening | 10000 | Optional |
| theiaeuk_pe | **skip_screen** | Boolean | Option to skip the read screening prior to analysis | FALSE | Optional |
| theiaeuk_pe | **skip_screen** | Boolean | Option to skip the read screening prior to analysis; if setting to true, please provide a value for the theiaeuk_pe `genome_length` optional input, OR set `call_rasusa` to false. Otherwise RASUSA will attempt to downsample to an expected genome size of 0 bp, and the workflow will fail. | FALSE | Optional |
| theiaeuk_pe | **subsample_coverage** | Float | Read depth for RASUSA task to subsample reads to | 150 | Optional |
| version_capture | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0" | Optional |
| version_capture | **timezone** | String | Set the time zone to get an accurate date of analysis (uses UTC by default) | | Optional |
@@ -212,7 +212,7 @@ All input reads are processed through "core tasks" in the TheiaEuk workflows. Th

| Variable | Rationale |
| --- | --- |
| `skip_screen` | Prevent the read screen from running |
| `skip_screen` | Prevent the read screen from running. If you set this value to true, please provide a value for the theiaeuk_pe `genome_length` optional input, OR set the theiaeuk_pe `call_rasusa` optional input to false. Otherwise RASUSA will attempt to downsample to an expected genome size of 0 bp, and the workflow will fail. |
| `min_reads` | Minimum number of base pairs for 20x coverage of _Hansenula polymorpha_ divided by 300 (longest Illumina read length) |
| `min_basepairs` | Greater than 10x coverage of _Hansenula polymorpha_ |
| `min_genome_size` | Based on the _Hansenula polymorpha_ genome - the smallest fungal genome as of 2015-04-02 (8.97 Mbp) |
4 changes: 2 additions & 2 deletions docs/workflows_overview/workflows_alphabetically.md
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| [**TBProfiler_tNGS**](../workflows/standalone/tbprofiler_tngs.md)| Performs in silico antimicrobial susceptibility testing on Mycobacterium tuberculosis targeted-NGS samples with TBProfiler and tbp-parser | Bacteria, TB | Sample-level | Yes | v2.3.0 | [TBProfiler_tNGS_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TBProfiler_tNGS_PHB:smw-tngs-tbprofiler-dev?tab=info) |
| [**Terra_2_GISAID**](../workflows/public_data_sharing/terra_2_gisaid.md)| Upload of assembly data to GISAID | SARS-CoV-2, Viral | Set-level | Yes | v1.2.1 | [Terra_2_GISAID_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Terra_2_GISAID_PHB:main?tab=info) |
| [**Terra_2_NCBI**](../workflows/public_data_sharing/terra_2_ncbi.md)| Upload of sequence data to NCBI | Bacteria, Mycotics, Viral | Set-level | No | v2.3.0 | [Terra_2_NCBI_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Terra_2_NCBI_PHB:main?tab=info) |
| [**TheiaCov Workflow Series**](../workflows/genomic_characterization/theiacov.md) | Viral genome assembly, QC and characterization from amplicon sequencing | HIV, Influenza, Monkeypox virus, RSV-A, RSV-B, SARS-CoV-2, Viral, WNV | Sample-level, Set-level | Some optional features incompatible, Yes | vX.X.X | [TheiaCoV_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_Illumina_PE_PHB:main?tab=info), [TheiaCoV_Illumina_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_Illumina_SE_PHB:main?tab=info), [TheiaCoV_ONT_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_ONT_PHB:main?tab=info), [TheiaCoV_ClearLabs_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_ClearLabs_PHB:main?tab=info), [TheiaCoV_FASTA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_FASTA_PHB:main?tab=info), [TheiaCoV_FASTA_Batch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_FASTA_Batch_PHB:main?tab=info) |
| [**TheiaEuk**](../workflows/genomic_characterization/theiaeuk.md) | Mycotic genome assembly, QC and characterization from WGS data | Mycotics | Sample-level | Some optional features incompatible, Yes | v2.3.0 | [TheiaEuk_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaEuk_Illumina_PE_PHB:main?tab=info) |
| [**TheiaCov Workflow Series**](../workflows/genomic_characterization/theiacov.md) | Viral genome assembly, QC and characterization from amplicon sequencing | HIV, Influenza, Monkeypox virus, RSV-A, RSV-B, SARS-CoV-2, Viral, WNV | Sample-level, Set-level | Some optional features incompatible, Yes | vX.X.X | [TheiaCoV_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_Illumina_PE_PHB:main?tab=info), [TheiaCoV_Illumina_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_Illumina_SE_PHB:main?tab=info), [TheiaCoV_ONT_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_ONT_PHB:main?tab=info), [TheiaCoV_ClearLabs_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_ClearLabs_PHB:main?tab=info), [TheiaCoV_FASTA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_FASTA_PHB:main?tab=info), [TheiaCoV_FASTA_Batch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_FASTA_Batch_PHB:main?tab=info)
| [**TheiaEuk**](../workflows/genomic_characterization/theiaeuk.md) | Mycotic genome assembly, QC and characterization from WGS data | Mycotics | Sample-level | Some optional features incompatible, Yes | vX.X.X | [TheiaEuk_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaEuk_Illumina_PE_PHB:main?tab=info) |
| [**TheiaMeta**](../workflows/genomic_characterization/theiameta.md) | Genome assembly and QC from metagenomic sequencing | Any taxa | Sample-level | Yes | v2.3.0 | [TheiaMeta_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaMeta_Illumina_PE_PHB:main?tab=info) |
| [**TheiaProk Workflow Series**](../workflows/genomic_characterization/theiaprok.md) | Bacterial genome assembly, QC and characterization from WGS data | Bacteria | Sample-level | Some optional features incompatible, Yes | vX.X.X | [TheiaProk_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_Illumina_PE_PHB:main?tab=info), [TheiaProk_Illumina_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_Illumina_SE_PHB:main?tab=info), [TheiaProk_ONT_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_ONT_PHB:main?tab=info), [TheiaProk_FASTA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_FASTA_PHB:main?tab=info) |
| [**TheiaValidate**](../workflows/standalone/theiavalidate.md)| This workflow performs basic comparisons between user-designated columns in two separate tables. | Any taxa | | No | v2.0.0 | [TheiaValidate_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaValidate_PHB:main?tab=info) |
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