template
Behavior:
- Creates directories, data files, and scripts for phylogenomic research.
- Generates materials for ASSEMBLY, BioSample, MinHash, Count, and Protein steps.
- Uses Tera templates to generate Bash scripts.
Input File Format:
.assembly.tsv is a TAB-delimited file to guide downloading and processing:
| Col | Type | Description |
|---|---|---|
| 1 | string | #name: species + infraspecific_name + assembly_accession |
| 2 | string | ftp_path |
| 3 | string | biosample |
| 4 | string | species |
| 5 | string | assembly_level |
Generated Materials:
-
--ass: ASSEMBLY/- One TSV file: url.tsv
- Five Bash scripts: rsync.sh, check.sh, n50.sh, collect.sh, finish.sh
-
--bs: BioSample/- One TSV file: sample.tsv
- Two Bash scripts: download.sh, collect.sh
-
--mh: MinHash/- One TSV file: species.tsv
- Five Bash scripts: compute.sh, species.sh, abnormal.sh, nr.sh, dist.sh
-
--count: Count/- One TSV file: species.tsv
- Three Bash scripts: strains.sh, rank.sh, lineage.sh
-
--pro: Protein/- One TSV file: species.tsv
- Bash scripts: collect.sh, info.sh, count.sh
Examples:
-
Generate ASSEMBLY materials
nwr template input.assembly.tsv --ass -
Generate all materials
nwr template input.assembly.tsv --ass --bs --mh --count --pro -
Specify output directory
nwr template input.assembly.tsv --ass -o output_dir -
Use parallel processing
nwr template input.assembly.tsv --mh --parallel 16