From 0a41d1f5c801c2c94cd83f18bebff08272f39827 Mon Sep 17 00:00:00 2001 From: "Andrew G. McArthur" Date: Tue, 6 Feb 2024 12:28:05 -0500 Subject: [PATCH] code block wrap --- docs/rgi_main.rst | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/docs/rgi_main.rst b/docs/rgi_main.rst index 890ade7..1cee542 100644 --- a/docs/rgi_main.rst +++ b/docs/rgi_main.rst @@ -155,7 +155,8 @@ The default settings for RGI main will include Perfect or Strict predictions via .. code-block:: sh - rgi main --input_sequence /path/to/nucleotide_input.fasta --output_file /path/to/output_file --local --clean + rgi main --input_sequence /path/to/nucleotide_input.fasta --output_file /path/to/output_file + --local --clean For AMR gene discovery, this can be expanded to include all Loose matches: @@ -190,7 +191,9 @@ This same analysis can be threaded over many processors if high-performance comp .. code-block:: sh - rgi main --input_sequence /path/to/nucleotide_input.fasta --output_file /path/to/output_file --local --clean -a DIAMOND --low_quality --include_nudge --num_threads 40 --split_prodigal_jobs + rgi main --input_sequence /path/to/nucleotide_input.fasta + --output_file /path/to/output_file --local --clean -a DIAMOND --low_quality + --include_nudge --num_threads 40 --split_prodigal_jobs Running RGI main with Protein Sequences ```````````````````````````````````````