From 752282c92c8e649989d404e1402dc0254e3d1444 Mon Sep 17 00:00:00 2001 From: Haris Zafeiropoulos Date: Wed, 26 Jul 2023 11:14:16 +0200 Subject: [PATCH] fix args console --- docs/args_and_params.rst | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/docs/args_and_params.rst b/docs/args_and_params.rst index abacfc7e..d7331e75 100644 --- a/docs/args_and_params.rst +++ b/docs/args_and_params.rst @@ -12,7 +12,9 @@ Arguments ``metaGOflow`` has 2 levels where the user sets arguments. Inline, a few technical arguments are provided as described below: -.. code-block:: bash + +.. code-block:: console + -f Forward reads fasta file path (mandatory if and olny if -e not used). -r Reverse reads fasta file path (mandatory if and olny if -e not used). -e ENA run accession number. Its raw data will be fetched and then analysed (if used, -f and -r should not me set). @@ -100,11 +102,16 @@ as well as, some resources-to-be-used related ones. |``cut_right`` | Moves a sliding window from front to tail, if meet one window with mean quality < threshold, drops the | | | bases in the window and the right part, and then stop. | +---------------------------------+------------------------------------------------------------------------------------------------------------+ +|``min-contig-len`` | Minimum length of a contig to be returned | ++---------------------------------+------------------------------------------------------------------------------------------------------------+ For more information about how the different analysis of ``fastp`` is performed, you may have a look at its `GitHub repository `_. -Finally, a number of syst +Finally, a number of system related parameters need to be set. +These parameters do not affect the final data products but they play a crucial role in the time efficiency +of ``metaGOflow``. The size of the sample and the computing resources available need to be taken into account +for the best tuning of those. +---------------------------------+------------------------------------------------------------------------------------------------------------+ |**Parameter** |**Description** | @@ -116,8 +123,6 @@ Finally, a number of syst +---------------------------------+------------------------------------------------------------------------------------------------------------+ |``interproscan_threads`` | Number of threads to be used for the InterProScan task. | +---------------------------------+------------------------------------------------------------------------------------------------------------+ -|``min-contig-len`` | Minimum length of a contig to be returned | -+---------------------------------+------------------------------------------------------------------------------------------------------------+ |``cgc_chunk_size`` | Size of each chunk to which filtered sequences will be split to to perform the ``cgc_step`` | +---------------------------------+------------------------------------------------------------------------------------------------------------+ |``protein_chunk_size_IPS`` | Size of each chunk to which the filtered sequences will be split to to perform the InterProScan task |