Skip to content

Commit

Permalink
moved task snippy variants up a few lines
Browse files Browse the repository at this point in the history
  • Loading branch information
fraser-combe committed Oct 25, 2024
1 parent b45dde6 commit 4be3a5b
Show file tree
Hide file tree
Showing 2 changed files with 14 additions and 8 deletions.
Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,14 @@ The `Snippy_Streamline_FASTA` workflow is an all-in-one approach to generating a

**If reference genomes have multiple contigs, they will not be compatible with using Gubbins** to mask recombination in the phylogenetic tree. The automatic selection of a reference genome by the workflow may result in a reference with multiple contigs. In this case, an alternative reference genome should be sought.

### Workflow Tasks

??? task "snippy_variants" (qc_metrics output)

##### snippy_variants {#snippy_variants}

This task runs Snippy to perform SNP analysis on individual samples. It extracts QC metrics from the Snippy output for each sample and saves them in per-sample TSV files (`snippy_variants_qc_metrics`). These per-sample QC metrics are then combined into a single file (`snippy_combined_qc_metrics`) in the downstream `snippy_tree_wf` workflow.

### Inputs

| **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** |
Expand Down Expand Up @@ -107,14 +115,6 @@ The `Snippy_Streamline_FASTA` workflow is an all-in-one approach to generating a
| 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 |

### Workflow Tasks

??? task "snippy_variants" (qc_metrics output)

##### snippy_variants {#snippy_variants}

This task runs Snippy to perform SNP analysis on individual samples. It extracts QC metrics from the Snippy output for each sample and saves them in per-sample TSV files (`snippy_variants_qc_metrics`). These per-sample QC metrics are then combined into a single file (`snippy_combined_qc_metrics`) in the downstream `snippy_tree_wf` workflow.

### Outputs

| **Variable** | **Type** | **Description** |
Expand Down
6 changes: 6 additions & 0 deletions docs/workflows/phylogenetic_construction/snippy_tree.md
Original file line number Diff line number Diff line change
Expand Up @@ -306,6 +306,12 @@ Sequencing data used in the Snippy_Tree workflow must:
| Task | task_shared_variants.wdl |
| Software Source Code | [task_shared_variants.wdl](https://github.com/theiagen/public_health_bioinformatics/blob/main/tasks/phylogenetic_inference/utilities/task_shared_variants.wdl) |

??? task "snippy_variants" (qc_metrics output)

##### snippy_variants {#snippy_variants}

This task runs Snippy to perform SNP analysis on individual samples. It extracts QC metrics from the Snippy output for each sample and saves them in per-sample TSV files (`snippy_variants_qc_metrics`). These per-sample QC metrics are then combined into a single file (`snippy_combined_qc_metrics`) in the downstream `snippy_tree_wf` workflow.

### Outputs

| **Variable** | **Type** | **Description** |
Expand Down

0 comments on commit 4be3a5b

Please sign in to comment.