From 27110a72bc1ca013eda19e8b384a4f4130dfe569 Mon Sep 17 00:00:00 2001 From: cimendes Date: Thu, 5 Dec 2024 10:27:10 +0000 Subject: [PATCH] ops npw with docs update --- docs/workflows/standalone/ncbi_scrub.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/workflows/standalone/ncbi_scrub.md b/docs/workflows/standalone/ncbi_scrub.md index e82b3feea..65537070d 100644 --- a/docs/workflows/standalone/ncbi_scrub.md +++ b/docs/workflows/standalone/ncbi_scrub.md @@ -23,6 +23,7 @@ There are three Kraken2 workflows: | dehost_pe or dehost_se | **read1** | File | | | Required | PE, SE | | dehost_pe or dehost_se | **read2** | File | | | Required | PE | | dehost_pe or dehost_se | **samplename** | String | | | Required | PE, SE | +| dehost_pe or dehost_se | **target_organism** | String | Target organism for Kraken2 reporting | "Severe acute respiratory syndrome coronavirus 2" | Optional | PE, SE | | kraken2 | **cpu** | Int | Number of CPUs to allocate to the task | 4 | Optional | PE, SE | | kraken2 | **disk_size** | Int | Amount of storage (in GB) to allocate to the task. Increase this when using large (>30GB kraken2 databases such as the "k2_standard" database) | 100 | Optional | PE, SE | | kraken2 | **docker_image** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/staphb/kraken2:2.0.8-beta_hv | Optional | PE, SE |