[MycoSNP-WDL] Update README.md to delineate workflow I/O and usage #6
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| # MycoSNP-WDL Workflow Series | ||
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| ## Quick Facts | ||
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| | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | | ||
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| | mycosnp_variants | Fungi | v1.5 | Yes | Sample-level | | ||
| | mycosnp_tree | Fungi | v1.5 | Yes | Set-level | | ||
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| ## MycoSNP-WDL | ||
| WDL wrappers of [CDCGov/mycosnp-nf](https://github.com/CDCgov/mycosnp-nf) designed for [Terra.bio](https://terra.bio) integration. These workflows conduct *Candiozyma (Candida) auris* [variant calling](#wf_mycosnp_variants.wdl) and subsequent single nucleotide polymorphism (SNP) [phylogenetic tree reconstruction](#wf_mycosnp_treewdl). | ||
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| <br/> | ||
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| ### wf_mycosnp_variants.wdl | ||
| `mycosnp_variants` calls variants for inputted reads referencing the *C. auris* B11204 assembly accession [GCA_016772135](https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_016772135/) by default. Users can optionally reference a separate *C. auris* clade [data directory](https://github.com/theiagen/mycosnp-wdl/tree/main/data/reference), FASTA, or directory as described below. | ||
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| Note that `mycosnp_tree` requires at least 4 genomes that reference the same reference in `mycosnp_variants`. | ||
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| #### Inputs | ||
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| - **reference** optionally takes a presupplied reference clade directory depicted [here](https://github.com/theiagen/mycosnp-wdl/tree/main/data/reference). The default is `GCA_016772135`. | ||
| - **ref_fasta** optionally takes a reference FASTA (requires suffix `.fa`) that will be indexed via BWA and generate a reference directory. | ||
| - **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 | ||
| ├── B11221 # Prebuilt clade directory | ||
| ├── Clade1 | ||
| │ ├── bwa | ||
| | | ├── bwa # BWA index for alignment | ||
| | | | ├── reference.am | ||
| | | | ├── reference.ann | ||
| | | | ├── reference.bwt | ||
| | | | ├── reference.pac | ||
| | | | └── reference.sa | ||
| │ ├── dict | ||
| | | └── reference.dict # Picard dictionary | ||
| │ ├── fai | ||
| | | └── reference.fa.fai # FASTA index file | ||
| │ ├── masked | ||
| | | └── reference.fa # Masked reference sequence | ||
| │ └── Clade1.fasta | ||
| ├── Clade2 | ||
| ├── Clade3 | ||
| ├── Clade4 | ||
| ├── Clade5 | ||
| └── GCA_016772135 # Default reference | ||
| ``` | ||
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| - **strain** optionally delineates the strain name for VCF gene name annotation. MycoSNP currently only annotates with respect to the default strain, "B11205", so changing this option will simply bypass VCF annotation. | ||
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| <div class="searchable-table" markdown="1"> | ||
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| | **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** | | ||
| |---|---|---|---|---|---| | ||
| | mycosnp_variants | **read1** | File | Illumina forward read file in FASTQ format (compression optional) | | Required | | ||
| | mycosnp_variants | **read2** | File | Illumina reverse read file in FASTQ format (compression optional) | | Required | | ||
| | 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 | If true, keeps `.nextflow/` and `work/` directories | false | Optional | | ||
| | mycosnp | **disk_size** | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional | | ||
| | mycosnp | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/mycosnp:1.5" | Optional | | ||
| | mycosnp | **memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 64 | Optional | | ||
| | mycosnp | **min_depth** | Int | Min depth for a base to be called as the consensus sequence, otherwise it will be called as an N; set to 0 to disable | 10 | Optional | | ||
| | mycosnp | **reference** | String | Reference clade | "GCA_016772135" | Optional | | ||
| | mycosnp | **sample_ploidy** | Int | 1 | Ploidy of sample (GATK) | Optional | | ||
| | mycosnp | **strain** | String | Reference strain | "B11205" | Optional | | ||
| | mycosnp_variants | **ref_fasta** | File | Reference FASTA file | | Optional | | ||
| | mycosnp_variants | **ref_tar** | File | Reference gzipped compressed tarchive | | Optional | | ||
| | version_capture | **timezone** | String | Alternative timezone | | Optional | | ||
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| </div> | ||
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| #### Outputs | ||
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| <div class="searchable-table" markdown="1"> | ||
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| | **Variable** | **Type** | **Description** | | ||
| |---|---|---| | ||
| | analysis_date | String | Date of the analysis | | ||
| | assembly_size | Int | Size of the assembly | | ||
| | average_q_score_after_trimming | Float | Average quality score after trimming | | ||
| | average_q_score_before_trimming | Float | Average quality score before trimming | | ||
| | consensus_n_variant_min_depth | Int | Minimum depth for consensus N variant | | ||
| | full_results | File | Full results file | | ||
| | gc_after_trimming | Float | GC content after trimming | | ||
| | gc_before_trimming | Float | GC content before trimming | | ||
| | mean_coverage_depth | Float | Mean coverage depth | | ||
| | multiqc | File | MultiQC report | | ||
| | myco_bam | File | BAM file | | ||
| | myco_bam_bai | File | BAM index file | | ||
| | mycosnp_docker | String | Docker image used for MycoSNP | | ||
| | mycosnp_variants_analysis_date | String | Date of the MycoSNP variants analysis | | ||
| | mycosnp_variants_version | String | Version of the MycoSNP variants | | ||
| | mycosnp_version | String | Version of MycoSNP | | ||
| | number_n | Int | Number of N bases | | ||
| | paired_reads_after_trimming | Int | Number of paired reads after trimming | | ||
| | paired_reads_after_trimming_percent | String | Percentage of paired reads after trimming | | ||
| | percent_reference_coverage | Float | Percentage of reference coverage | | ||
| | reads_after_trimming | Int | Number of reads after trimming | | ||
| | reads_after_trimming_percent | String | Percentage of reads after trimming | | ||
| | reads_before_trimming | Int | Number of reads before trimming | | ||
| | 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 genome used | | ||
| | 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 | Compressed variant call format (VCF) file depicting SNPs | | ||
| | vcf_index | File | Compressed index file for the VCF | | ||
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| </div> | ||
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| <br/> | ||
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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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There was a problem hiding this comment. 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 |
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| NOTE: At least four samples, including reference, are required | ||
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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). | ||
| - **ref_fasta** optionally takes a reference FASTA (requires suffix `.fa`) that will be indexed via BWA and generate a reference directory. | ||
| - **strain** is passed to output but does not change workflow function. | ||
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| <div class="searchable-table" markdown="1"> | ||
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| | **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** | | ||
| |---|---|---|---|---|---| | ||
| | mycosnp_tree | **vcf** | Array[File] | VCF files (.vcf.gz) containing SNP data for phylogenetic analysis. These files can be generated from `wf_mycosnp_variants.wdl` | | Required | | ||
| | mycosnp_tree | **vcf_index** | Array[File] | Index files for the VCF files | | Required | | ||
| | mycosnp_tree | **ref_fasta** | File | Reference FASTA input | | Optional | | ||
| | mycosnptree | **cpu** | Int | Number of CPUs to allocate to the task | 8 | Optional | | ||
| | mycosnptree | **disk_size** | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional | | ||
| | mycosnptree | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/mycosnp:1.5" | Optional | | ||
| | mycosnptree | **memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 64 | Optional | | ||
| | mycosnptree | **reference** | String | Preexisting [reference directory](https://github.com/theiagen/mycosnp-wdl/tree/main/data/reference) | "GCA_016772135" | Optional | | ||
| | mycosnptree | **strain** | String | mycosnp-nf reference strain name | "B11205" | Optional | | ||
| | version_capture | **timezone** | String | Alternative timezone | | Optional | | ||
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| </div> | ||
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| #### Outputs | ||
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| <div class="searchable-table" markdown="1"> | ||
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| | **Variable** | **Type** | **Description** | | ||
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| | mycosnp_alignment | File | Concatenated SNP alignment file | | ||
| | mycosnp_docker | String | Docker image used for MycoSNP | | ||
| | mycosnp_fastree_tree | File | Phylogenetic tree inferred using FastTree (heuristic maximum likelihood) | | ||
| | mycosnp_iqtree_tree | File | Phylogenetic tree inferred using IQ-TREE (high quality maximum likelihood) | | ||
| | mycosnp_rapidnj_tree | File | Phylogenetic tree inferred using RapidNJ (neighbor-joining method) | | ||
| | mycosnp_tree_analysis_date | String | Date of the analysis | | ||
| | mycosnp_tree_full_results | File | Full results file | | ||
| | mycosnp_tree_vcf_csv | File | SNP variants formatted as a CSV table | | ||
| | mycosnp_tree_version | String | Version of the `mycosnp_tree` WDL workflow | | ||
| | mycosnp_version | String | Version of MycoSNP | | ||
| | mycosnptree_snpdists | File | SNP distances file | | ||
| | reference_name | String | Name of the reference | | ||
| | reference_strain | String | Reference strain used | | ||
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| </div> | ||
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recommend,