Commit bd285b6f authored by Mathieu Giraud's avatar Mathieu Giraud

doc/vidjil-algo.md: --gz makes all three output files compressed

closes #4270
parent 387db5b2
Pipeline #140740 passed with stages
in 43 minutes and 3 seconds
......@@ -544,13 +544,9 @@ The main output of Vidjil-algo (with the default `-c clones` command) are the th
setup or in a immunological study).
Please see the [web application user manual](http://www.vidjil.org/doc/user) for more information.
With the `--gz` option, this file is output as a compressed `.vidjil.gz` file.
- The `.tsv` file is the AIRR output, for compatibility with other software
using the same format. See [below](#airr-tsv-output) for details.
With the `--gz` option, this file is output as a compressed `.tsv.gz` file.
- The `.vdj.fa` file is *a FASTA file for further processing by other bioinformatics tools*.
Even if it is advised to rather use the full information in the `.vijdil` file,
the `.vdj.fa` is a convenient way to have sequences of clones for further processing.
......@@ -570,6 +566,8 @@ By default, the three output files are named
- `out` is the directory where all the outputs are stored (can be changed with the `--dir` option).
- `basename` is the basename of the input `.fasta/.fastq` file (can be overriden with the `--base` option)
With the `--gz` option, the three files are output
as compressed `.vidjil.gz`, `.tsv.gz`, and `.vdj.fa.gz` files.
Vidjil-algo also outputs the first 50 clones on the standard output.
More data can be printed on the standard output with the `-v` option.
......
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