DOC Update documentation examples

Author: luispedro

docs/sources/Organisms.rst

@@ -81,33 +81,4 @@ When attempting to install an organism if is returned **True** it means that
 the organism is already installed, and there is no reason to install again.
 Otherwise, a progress bar is displayed to provide information on the download.
 
-Data Set Structure
--------------------
-
-This section provides the technical details necessary if you wish to build your
-own reference for others to use automatically. For most users, it will likely
-be easier to directly specify the references in the ngless script.
-
-The archives provided by NGLess contain BWA index files, the genome reference
-file and a gene annotation file.
-
-::
-
- Name.tar.gz
-  |
-  |--- Sequence
-  |     |
-  |     |-- BWAIndex
-  |             |-- genome.fa.gz
-  |             |-- genome.fa.gz.amb
-  |             |-- genome.fa.gz.ann
-  |             |-- genome.fa.gz.bwt
-  |             |-- genome.fa.gz.pac
-  |             |-- genome.fa.gz.sa
-  |
-  |--- Annotation
-        |-- annot.gtf.gz
-
-The basename of Description.tar.gz (Description) will have the description name
-of the respective organism (i.e, Mus_musculus.tar.gz).
 

docs/sources/conf.py

@@ -49,20 +49,14 @@
 
 # General information about the project.
 project = u'NGLess'
-copyright = u'2013-2020, NGLess Authors'
+copyright = u'2013-2022, NGLess Authors'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
-#
-p = subprocess.run(['./build-scripts/read-version.sh'],
-                    cwd='../../',
-                    stdout=subprocess.PIPE)
-# The full version, including alpha/beta/rc tags.
-release = p.stdout.decode('utf-8').strip()
-
-# The short X.Y version.
-version = release.split('-')[0]
+
+release = '1.4.0-beta1'
+version = '1.4'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/sources/default.nix

@@ -29,7 +29,6 @@ let
         meta = {
           homepage = "https://github.com/guzzle/guzzle_sphinx_theme";
           description = "Sphinx theme";
-          license = pkgs.licenses.mit;
           maintainers = with pkgs.maintainers; [ fridh ];
         };
       };

docs/sources/index.rst

@@ -31,7 +31,7 @@ NGLess
 
 NGLess is best illustrated by an example::
 
-    ngless "1.0"
+    ngless "1.4"
     input = paired('ctrl1.fq', 'ctrl2.fq', singles='ctrl-singles.fq')
     input = preprocess(input) using |read|:
         read = read[5:]

docs/sources/software.md

@@ -4,9 +4,10 @@ NGLess internally uses a few other packages to implement specific
 functionality. As we believe in giving appropriate credit, these pacakges are
 printed in the citation list of any script that uses them.
 
-NGLess version 0.6 uses the following software tools:
-
-- Samtools (used for SAM/BAM handling as well as in the [samtools module](Modules.html): version 1.6
-- BWA (used for [map](Functions.html#map)): version 0.7.15
-- Prodigal (used for [orf\_find](Functions.html#orf_find)): version 2.6.3 (with a patch to fix a bug [submitted upstream])
+NGLess version 1.4 uses the following software tools:
 
+- Samtools (used for SAM/BAM handling as well as in the [samtools module](Modules.html): version 2.13
+- BWA (used for [map](Functions.html#map)): version 0.7.17
+- Minimap (used for [map](Functions.html#map) as an alternative to bwa): version 2.24
+- Prodigal (used for [orf\_find](Functions.html#orf_find)): version 2.6.3
+- Megahit (used for [assemble](Functions.html#assemble)): version 1.2.9

docs/sources/tutorial-assembly-gp.rst

@@ -26,21 +26,17 @@ of that tutorial before starting this one.
 
 To run ngless, we need write a script. We start with a few imports::
 
-    ngless "0.6"
+    ngless "1.4"
 
 
-.. _`profiling tutorial`: tutorial-ocean-metagenomics.html
-
 3. Preprocessing
 
-This is as in the `profiling tutorial`_, except that we will be working with a
-single sample. You could also use the parallel module to make it easier to work
-on all samples::
+First, we want to trim the reads based on quality::
 
     sample = 'SAMEA2621155.sampled'
     input = load_mocat_sample(sample)
 
-    preprocess(input, keep_singles=False) using |read|:
+    input = preprocess(input, keep_singles=False) using |read|:
         read = substrim(read, min_quality=25)
         if len(read) < 45:
             discard
@@ -62,13 +58,12 @@ Full script
 
 ::
 
-    ngless "0.6"
-
+    ngless "1.4"
 
     sample = 'SAMEA2621155.sampled'
     input = load_mocat_sample(sample)
 
-    preprocess(input, keep_singles=False) using |read|:
+    input = preprocess(input, keep_singles=False) using |read|:
         read = substrim(read, min_quality=25)
         if len(read) < 45:
             discard

docs/sources/tutorial-ocean-metagenomics.rst

@@ -34,9 +34,9 @@ expand the data to a directory called ``ocean-short``.
 This is a toy dataset. It is based on real data, but the samples were trimmed
 so that they contains only 250k paired-end reads.
 
-The dataset is organized in classical MOCAT style. Ngless does not require this
-structure, but this tutorial also demonstrates how to upgrade from your
-existing MOCAT-based projects.::
+The dataset is organized in so that each directory contains a sample with
+multiple fastq files). NGLess does not require this structure, but it is
+convenient::
 
     $ find
     ./SAMEA2621229.sampled
@@ -63,10 +63,9 @@ The rest of this tutorial is an explanation of the steps in this script.
 
 To run ngless, we need write a script. We start with a few imports::
 
-    ngless "0.7"
-    import "parallel" version "0.6"
-    import "mocat" version "0.0"
-    import "omrgc" version "0.0"
+    ngless "1.4"
+    import "parallel" version "1.0"
+    import "omrgc" version "1.0"
 
 These will all be used in the tutorial.
 
@@ -94,7 +93,7 @@ sample.
 
 First, we load the data (the FastQ files)::
 
-    input = load_mocat_sample(sample)
+    input = load_fastq_directory(sample)
 
 And, now, we preprocess the data::
 
@@ -153,15 +152,14 @@ Full script
 
 Here is the full script::
 
-    ngless "0.8"
+    ngless "1.4"
     import "parallel" version "0.0"
-    import "mocat" version "0.0"
-    import "omrgc" version "0.0"
+    import "omrgc" version "1.0"
 
 
     samples = readlines('tara.demo.short')
     sample = lock1(samples)
-    input = load_mocat_sample(sample)
+    input = load_fastq_directory(sample)
 
     input = preprocess(input, keep_singles=False) using |read|:
         read = substrim(read, min_quality=25)