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fixing parameters multiline tables
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@hariszaf
hariszaf committed Jul 26, 2023
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7 changes: 3 additions & 4 deletions docs/args_and_params.rst
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Expand Up @@ -65,7 +65,6 @@ The steps to be performed are selected by setting ``True`` or ``False`` the foll
.. Attention:: The intermediate files produced in a complete run of ``metaGOflow`` depending
on the sample size, may reach 1 TB of storage.
.. tip:: If you want to run only the first steps and at a later point the rest of those, you do not need to use the ``-b`` parameter.
It is the end products of each step that are required for any following step.
Expand Down Expand Up @@ -96,7 +95,7 @@ as well as, some resources-to-be-used related ones.
|``disable_trim_poly_g`` | Enables the detection of polyG in read tails and trims them |
+---------------------------------+------------------------------------------------------------------------------------------------------------+
|``overlap_len_require`` | The minimum length to detect overlapped region of PE reads. This will affect overlap analysis based |
| | merge, adapter trimming and correction. 30 by default. (int [=30]) |
| | merge, adhttps://apptainer.orgapter trimming and correction. 30 by default. (int [=30]) |
+---------------------------------+------------------------------------------------------------------------------------------------------------+
|``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. |
Expand All @@ -110,7 +109,7 @@ Finally, a number of syst
+---------------------------------+------------------------------------------------------------------------------------------------------------+
|**Parameter** |**Description** |
+---------------------------------+------------------------------------------------------------------------------------------------------------+
|``memory`` | Memory to run assembly. When 0 < ``memory`` < 1, fraction of all available memory of the machine is used,
|``memory`` | Memory to run assembly. When 0 < ``memory`` < 1, fraction of all available memory of the machine is used, |
| | otherwise it specifies the memory in BYTE. |
+---------------------------------+------------------------------------------------------------------------------------------------------------+
|``threads`` | Number of threads to be used in all tasks of the steps to be performed except of the InterProScan |
Expand Down Expand Up @@ -159,7 +158,7 @@ certain files that were produced (in the first run) are required, based on the s
| ``count_faa_from_previous_run`` | Number of the sequences included in the ``*merged_CDS.faa`` file. Mandatory for the |
| | ``reads_functional_annotation`` step; You may get this by running: ``grep -c ">" <*..merged_CDS.faa>`` |
+-----------------------------------+------------------------------------------------------------------------------------------------------------+
|``predicted_faa_from_previous_run``| Mandatory for the functional annotation step; file suffix: ``.merged_CDS.faa`` |
|``predicted_faa_from_previous_run``| Mandatory for the functional annotation step; file suffix: ``.merged_CDS.faa`` | |
+-----------------------------------+------------------------------------------------------------------------------------------------------------+
| ``processed_read_files`` | Forward and reverse files with unmergerd filteres sequences. Mandatory for running the assembly step; |
| | file suffix: ``clean.fastq.trimmed.fasta`` |
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