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Added parameter hic_samtools_ext_args #165

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Oct 25, 2024
Merged

Added parameter hic_samtools_ext_args #165

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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
4. Now using nf-test for pipeline level testing [#153](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/153)
5. Added `text/html` as content mime type for the report file [#146](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/146)
6. Added a sequence labels table below the HiC contact map [#147](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/147)
7. Added parameter `hic_samtools_ext_args` and set its default value to `-F 3852` [#159](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/159)

### `Fixed`

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5 changes: 4 additions & 1 deletion conf/modules.config
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Expand Up @@ -328,7 +328,10 @@ process {

withName: '.*:FQ2HIC:FASTQ_BWA_MEM_SAMBLASTER:SAMBLASTER' {
ext.prefix = { "${meta.id}.on.${meta.ref_id}.samblaster" }
ext.args3 = '-h -F 2316'
ext.args3 = [
'-h',
params.hic_samtools_ext_args ? params.hic_samtools_ext_args.split("\\s(?=-+)") : ''
].flatten().unique(false).join(' ').trim()
}

withName: '.*:FQ2HIC:AGP2ASSEMBLY' {
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13 changes: 7 additions & 6 deletions docs/parameters.md
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Expand Up @@ -67,12 +67,13 @@ A Nextflow pipeline which evaluates assembly quality with multiple QC tools and

## HiC options

| Parameter | Description | Type | Default | Required | Hidden |
| -------------------- | ---------------------------------------------------------------------------------------- | --------- | ------------------------------------------------- | -------- | ------ |
| `hic` | HiC reads path provided as a SRA ID or as paired reads such as 'hic_reads{1,2}.fastq.gz' | `string` | | | |
| `hic_skip_fastp` | Skip HiC read trimming | `boolean` | | | |
| `hic_skip_fastqc` | Skip HiC read QC | `boolean` | | | |
| `hic_fastp_ext_args` | Additional parameters for fastp trimming | `string` | --qualified_quality_phred 20 --length_required 50 | | |
| Parameter | Description | Type | Default | Required | Hidden |
| ----------------------- | ---------------------------------------------------------------------------------------- | --------- | ------------------------------------------------- | -------- | ------ |
| `hic` | HiC reads path provided as a SRA ID or as paired reads such as 'hic_reads{1,2}.fastq.gz' | `string` | | | |
| `hic_skip_fastp` | Skip HiC read trimming | `boolean` | | | |
| `hic_skip_fastqc` | Skip HiC read QC | `boolean` | | | |
| `hic_fastp_ext_args` | Additional parameters for fastp trimming | `string` | --qualified_quality_phred 20 --length_required 50 | | |
| `hic_samtools_ext_args` | Additional parameters for samtools view command run after samblaster | `string` | -F 3852 | | |

## Synteny options

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1 change: 1 addition & 0 deletions nextflow.config
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Expand Up @@ -53,6 +53,7 @@ params {
hic_skip_fastp = false
hic_skip_fastqc = false
hic_fastp_ext_args = '--qualified_quality_phred 20 --length_required 50'
hic_samtools_ext_args = '-F 3852'

// Synteny options
synteny_skip = true
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6 changes: 6 additions & 0 deletions nextflow_schema.json
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Expand Up @@ -237,6 +237,12 @@
"default": "--qualified_quality_phred 20 --length_required 50",
"description": "Additional parameters for fastp trimming",
"fa_icon": "fas fa-terminal"
},
"hic_samtools_ext_args": {
"type": "string",
"default": "-F 3852",
"fa_icon": "fas fa-terminal",
"description": "Additional parameters for samtools view command run after samblaster"
}
}
},
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6 changes: 5 additions & 1 deletion tests/README.md
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Expand Up @@ -16,7 +16,11 @@ nextflow run plant-food-research-open/assemblyqc -r main -profile singularity,te

## nf-test and Continuous Integration (CI)

The GitHub [CI action](../.github/workflows/ci.yml) included with the pipeline continuously tests the pipeline using [nf-test](https://www.nf-test.com).
The GitHub [CI action](../.github/workflows/ci.yml) included with the pipeline continuously tests the pipeline using [nf-test](https://www.nf-test.com). Many components included with the pipeline such as [minimap2/align](../modules/nf-core/minimap2/align) include their own [tests](../modules/nf-core/minimap2/align/tests/main.nf.test) with test data from nf-core.

## Testing with a Large Dataset at Plant&Food

Before each release, the functionality of the entire pipeline is tested with a large dataset on the on-prem SLURM-based HPC at The New Zealand Institute of Plant and Food Research.

## Testing Merqury Datasets

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