diff --git a/docs/workflows/public_data_sharing/fetch_srr_accession.md b/docs/workflows/public_data_sharing/fetch_srr_accession.md index eb9ccac22..134406893 100644 --- a/docs/workflows/public_data_sharing/fetch_srr_accession.md +++ b/docs/workflows/public_data_sharing/fetch_srr_accession.md @@ -21,6 +21,8 @@ The workflow uses the fastq-dl tool to fetch metadata from SRA and specifically | fetch_srr_metadata | **docker**| String | Docker image for metadata retrieval. | `us-docker.pkg.dev/general-theiagen/biocontainers/fastq-dl:2.0.4--pyhdfd78af_0` | Optional | | fetch_srr_metadata | **memory** | Int | Memory in GB allocated for the task. | 8 | Optional | | fetch_srr_metadata | **sample_accession** | String | SRA-compatible accession, such as a **BioSample ID** (e.g., "SAMN00000000") or **SRA Experiment ID** (e.g., "SRX000000"), used to retrieve SRR metadata. | | Required | +| 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 diff --git a/mkdocs.yml b/mkdocs.yml index 2b2bf4808..613f81b15 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -43,7 +43,7 @@ nav: - Samples_to_Ref_Tree: workflows/phylogenetic_placement/samples_to_ref_tree.md - Usher_PHB: workflows/phylogenetic_placement/usher.md - Public Data Sharing: - - Fetch_SRR_Accession: workflows/public_data_sharing/fetch_srr_accessions.md + - Fetch_SRR_Accession: workflows/public_data_sharing/fetch_srr_accession.md - Mercury_Prep_N_Batch: workflows/public_data_sharing/mercury_prep_n_batch.md - Terra_2_GISAID: workflows/public_data_sharing/terra_2_gisaid.md - Terra_2_NCBI: workflows/public_data_sharing/terra_2_ncbi.md