From 4be3a5b363dd760a43d75f461b545dea158f33ce Mon Sep 17 00:00:00 2001 From: fraser-combe Date: Fri, 25 Oct 2024 11:05:31 -0500 Subject: [PATCH] moved task snippy variants up a few lines --- .../snippy_streamline_fasta.md | 16 ++++++++-------- .../phylogenetic_construction/snippy_tree.md | 6 ++++++ 2 files changed, 14 insertions(+), 8 deletions(-) diff --git a/docs/workflows/phylogenetic_construction/snippy_streamline_fasta.md b/docs/workflows/phylogenetic_construction/snippy_streamline_fasta.md index c7667806c..f03695d44 100644 --- a/docs/workflows/phylogenetic_construction/snippy_streamline_fasta.md +++ b/docs/workflows/phylogenetic_construction/snippy_streamline_fasta.md @@ -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** | @@ -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** | diff --git a/docs/workflows/phylogenetic_construction/snippy_tree.md b/docs/workflows/phylogenetic_construction/snippy_tree.md index 574fffabf..400376292 100644 --- a/docs/workflows/phylogenetic_construction/snippy_tree.md +++ b/docs/workflows/phylogenetic_construction/snippy_tree.md @@ -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** |