[MycoSNP-WDL] Update README.md to delineate workflow I/O and usage #6
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… for MycoSNP-WDL; Terra task delineation needs to be updated
| - **ref_tar** optionally takes a gzipped tarchive (`.tar.gz`) with the same directory structure as the provided reference clades: | ||
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| ``` | ||
| data/reference |
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recommend,
data/reference
├── B11221 # Prebuilt clade directory
├── Clade1
│ ├── bwa # BWA index for alignment
│ ├── dict # Picard dictionary
│ ├── fai # FASTA index file
│ ├── masked # Masked reference sequence
│ └── Clade1.fasta # Main reference FASTA
├── Clade2
├── Clade3
├── Clade4
├── Clade5
└── GCA_016772135 # Default reference
```
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| ### wf_mycosnp_tree.wdl | ||
| `mycosnp_tree` reconstructs an IQ-TREE SNP phylogenetic tree that incorporates representative genomes of Clade1-Clade5 *C. auris*. VCF data generated from [wf_mycosnp_variants.wdl](#wf_mycosnp_variantswdl) are used as inputs. | ||
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Tree will fail with less than 4 samples so I think we should add this in. IQ tree wont run if less than 4 samples are in the file I saw in the log output
README.md
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| #### Inputs | ||
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| - **reference** optionally takes a presupplied reference clade directory delineated [here](https://github.com/theiagen/mycosnp-wdl/tree/main/data/reference). Currently, this option will fail the workflow with "GCA_016772135" set as the reference - use "B11205" instead. |
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We can update this. i have successful runs using the default settings for variants and tree. -- reference optionally takes a presupplied reference clade directory delineated here. The default reference GCA_016772135 is fully supported, but users may specify an alternative reference, such as B11205 or other clade specific reference, if desired.
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| | mycosnp_variants | **samplename** | String | Name of sample to be analyzed | | Required | | ||
| | mycosnp | **coverage** | Int | Coverage is used to calculate a down-sampling rate that results in the specified coverage. For example, if coverage is 70, then FASTQ files are down-sampled such that, when aligned to the reference, the result is approximately 70x coverage | 0 | Optional | | ||
| | mycosnp | **cpu** | Int | Number of CPUs to allocate to the task | 8 | Optional | | ||
| | mycosnp | **debug** | Boolean | Keeps `.nextflow/` and `work/` directories | false | Optional | |
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If true, keeps .nextflow/ and work/ directories for debugging purposes.
README.md
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| | reference_strain | String | Reference strain used | | ||
| | unpaired_reads_after_trimming | Int | Number of unpaired reads after trimming | | ||
| | unpaired_reads_after_trimming_percent | String | Percentage of unpaired reads after trimming | | ||
| | vcf | File | VCF file | |
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Final variant call format (VCF) file containing SNPs.
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| | reads_mapped | Int | Number of reads mapped | | ||
| | reference_length_coverage_after_trimming | Float | Reference length coverage after trimming | | ||
| | reference_length_coverage_before_trimming | Float | Reference length coverage before trimming | | ||
| | reference_name | String | Name of the reference | |
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Name of the reference genome used.
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| | **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** | | ||
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| | mycosnp_tree | **vcf** | Array[File] | VCF files for analysis | | Required | |
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Maybe add above inputs,
Compressed VCF files (.vcf.gz) containing SNP data for phylogenetic analysis. These files should be generated from wf_mycosnp_variants.wdl.
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| | **Variable** | **Type** | **Description** | | ||
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| | mycosnp_alignment | File | Alignment file | |
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Concatenated SNP alignment used for tree inference.
README.md
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| | mycosnp_rapidnj_tree | File | RapidNJ tree file | | ||
| | mycosnp_tree_analysis_date | String | Date of the analysis | | ||
| | mycosnp_tree_full_results | File | Full results file | | ||
| | mycosnp_tree_vcf_csv | File | VCF to CSV file | |
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SNP variants formatted as a CSV table for external analysis
For the tree methods:
mycosnp_fastree_tree | File | Phylogenetic tree inferred using FastTree.
mycosnp_iqtree_tree | File | Phylogenetic tree inferred using IQ-TREE (maximum likelihood method).
mycosnp_rapidnj_tree | File | Phylogenetic tree inferred using RapidNJ (neighbor-joining method).
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these changes have been incorporated into the most recent commit (ec553ca) - thank you for the suggestions
This PR updates the main repository README.md to delineate workflow I/O and usage.
🗑️ This dev branch should be deleted after merging to main.
🧠 Summary
Delineate workflow I/O and usage in the README
⚡ Impacted Workflows/Tasks
None
This PR may lead to different results in pre-existing outputs: No
This PR uses an element that could cause duplicate runs to have different results: No
🛠️ Changes
Delineate workflow I/O and usage in README.md
⚙️ Algorithm
n/a
➡️ Inputs
n/a
⬅️ Outputs
n/a
🧪 Testing
n/a
Suggested Scenarios for Reviewer to Test
n/a
🔬 Final Developer Checklist
workflows_overviewtables.🎯 Reviewer Checklist