This article contains additional details about the workflows found in the COVID-19 workspace. You'll find a table outlining example inputs and outputs for each of the workflows listed in the workspace dashboard below. For more information about this workspace, see COVID-19 workspaces, data, and tools in Terra.
Getting Data into your workspace
| genbank_ingest | |
| Pull fasta files and metadata from NCBI Virus for SARS-CoV-2 and formats metadata for NextStrain workflows. | |
| Input | Output |
| Google_maps_api_key | Seqs_fasta |
| User_email | seqs_metadata |
| Fetch_sra_to_bam | |
|
This workflow downloads .fastq files from SRA, given an SRA_ID as input. Specifically, the output of the workflow will produce the unaligned BAM file that is needed for viral assembly. |
|
| Inputs | Outputs |
|
Sra_accession |
biosample_accession |
|
library_id |
|
|
run_date |
|
|
sample_collected_by |
|
|
sample_collection_date |
|
|
sample_geo_loc |
|
|
sample_strain |
|
|
sequencing_center |
|
|
sequencing_platform |
|
|
sequencing_platform_model |
|
|
sra_metadata |
|
| reads_uBAM | |
Sequence Data processing and assembly
| Fastq_to_ubam | |
|
This workflow accepts paired-end or single-end fastq files and converts them to uBAM files. |
|
|
Input |
Output |
|
fastq_1 |
unmapped_bam |
| fastq_2 | |
| library_name | |
| platform_name | |
| platform_unit | |
| readgroup_name | |
| run_date | |
| sample_name | |
| sequencing_center | |
| Demux_deplete | |
|
Picard-based demultiplexing and basecalling from a tarball of a raw bcl directory, followed by QC metrics and depletion. |
|
| Input | Output |
| Assemble_refbased | |
| This takes a raw read file (uBAM) and assembles a viral genome by aligning to a reference genome. | |
| Input | Output |
|
reads_unmapped_bams |
|
|
reference_fasta |
|
Calling Lineages and Clades
|
Sarscov2_lineages |
|
| Call NextClade and PANGOlin on a single SARS-CoV-2 genome | |
| Input | Output |
| genome_fasta | |
|
Sarscov2_nextclade_multi |
|
|
Create NextClade visualizations on many SARS-CoV-2 genomes |
|
| Input | Output |
| basename | auspice_json |
| genome_fastas | nextclas_json |
| nextclade_tsv | |
NextStrain Phylogenetic Analysis
|
Sarscov2_nexstrain |
|
| aligns assemblies, build trees and produces a json representation for NextStrain visualziation | |
| Input | Output |
| build_name | |
| builds_yaml | |
|
genbank_curate |
|
| Pulls fasta files and metadata from NCBI Virus and formats metadata to use in Nexstrain workvlows | |
| Input | Output |
All-in-one Workflows
| Sarscov2_illumina_full | |
|
This workflow is a combination of several workflows, as illustrated in the diagram above. |
|
|
Input |
Explanation |
|
samplesheet |
Custom formatted tsv samplesheet |
|
spikein_db |
Spike-in fasta file |
|
author_template_sbt |
List of authors for submission to NCBI |
|
spuid_namespace |
Defaulted to Broad_GCID |
|
amplicon_bed_prefix |
Amplicon primers to trim in reference coordinate space |
|
biosample_attributes |
The post-submission attributes file that is generated by NCBI after BioSample submission |
|
flowcell_tgz |
gs:// path to flowcell.tar.gz |
|
instrument_model |
Controlled vocabulary text field for instrument model |
|
reference_fasta |
Reference genome to align reads to |
|
sra_title |
Title that will appear in NCBI SRA packed file (free text) |
|
sample_rename_map |
Two column tsv that links the sample id assigned to sample upon receipt in lab to a reformatted sample id acceptable to NCBI |
|
submitting_lab_name |
|
|
account_name |
|
|
bioproject |
|
|
ftp_config_js |
|
|
id_salt |
|
|
sarscov2_sra_to_genbank |
|
| Full SARS-CoV-2 analysis workflow starting from SRA data and metadata and performing assembly, spike-in analysis, qc, lineage assignment, and packaging assemblies for data release. | |
| Input | Output |
| submitting_lab_name | |
| account_name | |
| author_template_sbt | |
| spuid_namespace | |
| submission_name | |
| submission_uid | |
| amplicon_bed_default | |
| reference_fasta | |
| spikein_db | |
| SRA_accessions | |
|
sarscov2_genbank |
|
| Workflow to prepare SARS-CoV-2 assemblies for Genbank submission. This includes QC checks with NCBI's VADR tool and filters out genomes that do not pass its tests. | |
| Input | Output |
| submitting_lab_name | gisaid_fasta |
| account_name | gisaid_meta_csv |
| assemblies_fasta | num_input |
| spuid_namespace | num_successful |
| submission_name | num_weird |
| submission_uid | submission_xml |
| assembly_stats_tsv | submission_zip |
| author_sbt_defaults_yaml | submit_ready |
| author_sbt_j2_template | vadr_output |
| biosample_attributes | weird_genbank_xml |
| weird_genbank_zip | |
| weird_gisaid_fasta | |
| weird_gisaid_meta_csv | |