Terra - Kincekara/C-BIRD GitHub Wiki
Installation
Install C-BIRD to your workspace using Dockstore
Download required databases and add them to your workspace without decompressing. Kraken2/Bracken database: Download CheckM2 database: Download
Inputs
Required inputs
| Input | Description |
|---|---|
read1 |
Path to the first FASTQ file (paired-end) |
read2 |
Path to the second FASTQ file (paired-end) |
samplename |
Name of the sample being processed |
kraken2_db |
Kraken2/Bracken database |
checkm2_db |
CheckM2 database |
Optional inputs
| Input | Description |
|---|---|
adapters |
FastP detects and removes adapters automatically without needing a file. However, you can still use a multi-fasta input if you wish |
mash_reference |
C-BIRD uses a custom curated database for identification. If you want to use your own database, you can provide it as a .msh file. |
target_genes_fasta |
a protein fasta file for additional gene search |
minimum_total_reads |
Minimum total reads required for starting analysis (default: 30000). The samples that have lower read counts will be omitted. |
Report related inputs
The inputs below are related to the plain report, which will be desired in certain situations. labid is required to create a plain .docx report. Each logo and header line is optional and they can be used in various ways to create desired style. HTML reports are independent of these inputs and will be created even if labid does not exist.
| Input | Description |
|---|---|
labid |
Laboratory ID which will be placed on plain report. It is required for plain report creation. |
report_logo1 |
logo that will be placed on the left side of the header 1.15"x1.15" (optional) |
report_logo2 |
logo that will be placed on the right side of the header 1.15"x1.15" (optional) |
header_line1 |
First line of the plain report header (optional) |
header_line2 |
Second line of the plain report header (optional) |
header_line3 |
Third line of the plain report header (optional) |
header_line4 |
Fourth line of the plain report header (optional) |
header_line5 |
Fifth line of the plain report header (optional) |
header_line6 |
Sixth line of the plain report header (optional) |
report_disclaimer |
A disclaimer text to be placed on the plain report. It should be a .txt file (optional) |