Merge branch 'dev' into template_tests

Author: tiagofilipe12

changelog.md

@@ -2,22 +2,38 @@
 
 ## Changes in upcoming release (`dev` branch) 
 
+### New features
+
+- Added new `recipe` system to flowcraft along with 6 starting recipes.
+Recipes are pre-made and curated pipelines that address specific questions.
+To create a recipe, the `-r <recipe_name>` can be used. To list available
+recipes, the `--recipe-list` and `--recipe-list-short` options were added. 
+
 ### Components changes
 
 - Added new `disableRR` param in the `spades` component that disables repeat
 resolution
+- The `abyss` and `spades` components emit GFA in a secondary channel.
+- The new `bandage` component can accept either FASTA from a primary channel
+  or GFA from a secondary channel.
 
 ### New components
 
 - Added component `abyss`.
+- Added component `bandage`.
+- Added component `unicycler`.
+- Added component `prokka`.
+- Added component `bcalm`.
 
 ### Minor/Other changes
 
 - Added removal of duplicate IDs from `reads_download` component input.
 - Added seed parameter to `downsample_fastq` component.
+- Added bacmet database to `abricate` component.
 - Added default docker option to avoid docker permission errors.
 - Added tests for `mash_screen`, `mash_dist`, `mapping_patlas` related python 
 templates
+- Changed the default URL generated by inspect and report commands. 
 
 ### Bug fixes
 

docs/dev/create_recipe.rst

@@ -0,0 +1,116 @@
+Recipe creation guidelines
+===========================
+
+Recipes are pre-made pipeline strings that may be associated with specific
+parameters and directives and are used to rapidly build a certain type of
+pipeline.
+
+Instead of building a pipeline like::
+
+    -t "integrity_coverage fastqc_trimmomatic fastqc spades pilon"
+
+The user simply can specific a recipe with that pipeline::
+
+    -r assembly
+
+Recipe creation
+---------------
+
+The creation of new recipes is a very simple and straightforward process.
+You need to create a new file in the ``flowcraft/generator/recipes`` folder
+with any name and create a basic class with three attributes::
+
+    try:
+        from generator.recipe import Recipe
+    except ImportError:
+        from flowcraft.generator.recipe import Recipe
+
+
+    class Innuca(Recipe):
+
+        def __init__(self):
+            super().__init__()
+
+            # Recipe name
+            self.name = "innuca"
+
+            # Recipe pipeline
+            self.pipeline_str = <pipeline string>
+
+            # Recipe parameters and directives
+            self.directives = { <directives> }
+
+And that's it! Now there is a new recipe available with the ``innuca`` name and
+we can build this pipeline using the option ``-r innuca``.
+
+Name
+^^^^
+
+This is the name of the recipe, which is used to make a match with the recipe
+name provided by the user via the ``-r`` option.
+
+Pipeline_str
+^^^^^^^^^^^^
+
+The pipeline string as if provided via the ``-t`` option.
+
+Directives
+^^^^^^^^^^
+
+A dictionary containing the parameters and directives for each process in the
+pipeline string. **Setting this attribute is optional and components
+that are not specified here will assume their default values**. In general, each
+element in this dictionary should have the following format::
+
+    self.directives = {
+        "component_name": {
+            "params": {
+                "paramA": "value"
+            },
+            "directives": {
+                "directiveA": "value"
+            }
+        }
+    }
+
+This will set the provided parameters and directives to the component, but it is
+possible to provide only one.
+
+A more concrete example of a real component and directives follows::
+
+    self.pipeline_str = "integrity_coverage fastqc"
+
+    # Set parameters and directives only for integrity_coverage
+    # and leave fastqc with the defaults
+    self.directives = {
+        "integrity_coverage": {
+            "params": {
+                "minCoverage": 20
+            },
+            "directives": {
+                "memory": "1GB"
+            }
+        }
+    }
+
+Duplicate components
+~~~~~~~~~~~~~~~~~~~~
+
+In some cases, the same component may be present multiple times in the pipeline
+string of a recipe. In these cases, directives can be assigned to each individual
+component by adding a ``#<id>`` suffix to the component::
+
+    self.pipeline_str = "integrity_coverage ( trimmomatic spades#1 | spades#2)"
+
+    self.directives = {
+        "spades#1": {
+            "directives": {
+                "memory": "10GB"
+            }
+        },
+        "spades#2": {
+            "directives": {
+                "version": "3.7.0"
+            }
+        }
+    }

docs/index.rst

@@ -44,6 +44,7 @@ A NextFlow pipeline assembler for genomics.
    dev/general_orientation
    dev/create_process
    dev/create_template
+   dev/create_recipe
    dev/containers
    dev/process_dotfiles
    dev/pipeline_reporting

docs/resources/reports/mash_dist_table.png

@@ -393,7 +393,7 @@ Local visualization
 :::::::::::::::::::
 
 The FlowCraft report JSON file can also be visualized locally by drag and dropping
-it into the FlowCraft web application page, currently hosted at http://192.92.149.169/reports
+it into the FlowCraft web application page, currently hosted at http://www.flowcraft.live/reports
 
 Offline visualization
 :::::::::::::::::::::

docs/resources/reports/sliding_window_mash_dist.png

@@ -1,11 +1,11 @@
 mash_screen
-==============
+===========
 
 Purpose
 -------
 
 This component performes mash screen to find plasmids
-contained in high throughoput sequencing data, using as inputs read files
+contained in high throughout sequencing data, using as inputs read files
 (FastQ files). Then, the resulting file can
 be imported into `pATLAS <http://www.patlas.site/>`_.
 This component searches for containment of a given sequence in read sequencing

docs/user/basic_usage.rst

@@ -1,4 +1,54 @@
 prokka
 ======
 
-**Building...**
+
+Purpose
+-------
+
+This component performs annotations using the annotations available in
+`prokka <https://github.com/tseemann/prokka>`_.
+
+
+Input/Output type
+-----------------
+
+- Input type: ``fasta``
+- Output type: ``None``
+
+.. note::
+    - Although the component doesn't have an output channel it writes the results into the ``publishDir``.
+
+
+Parameters
+----------
+
+- ``centre``: sets the center to which the sequencing center id.
+  Default: 'UMMI'.
+
+- ``kingdom``: Selects the annotation mode between Archaea, Bacteria,
+  Mitochondria, Viruses. Default: Bacteria).
+
+- ``genus``: Allows user to select a genus name. Default: 'Genus' (same
+  as prokka). This also adds the use of the --usegenus flag to prokka.
+
+
+Published results
+-----------------
+
+- ``results/annotation/prokka_<pid>/<sample_id>``: All the outputs from prokka
+  will be available in these directories.
+
+
+Published reports
+-----------------
+
+None.
+
+
+Default directives
+------------------
+
+- ``prokka``:
+    - ``cpus``: 2
+    - ``container``: ummidock/prokka
+    - ``version``: 1.12

docs/user/components/mash_screen.rst

@@ -9,6 +9,7 @@ Pipeline reports
 .. include:: reports/fastqc.rst
 .. include:: reports/fastqc_trimmomatic.rst
 .. include:: reports/integrity_coverage.rst
+.. include:: reports/mash_dist.rst
 .. include:: reports/mlst.rst
 .. include:: reports/patho_typing.rst
 .. include:: reports/pilon.rst
@@ -18,6 +19,7 @@ Pipeline reports
 .. include:: reports/process_spades.rst
 .. include:: reports/process_viral_assembly.rst
 .. include:: reports/seq_typing.rst
+.. include:: reports/sistr.rst
 .. include:: reports/trimmomatic.rst
 .. include:: reports/true_coverage.rst
 

docs/user/components/prokka.rst

@@ -0,0 +1,20 @@
+mash_dist
+---------
+
+Table data
+^^^^^^^^^^
+
+Plasmids table:
+    - **Mash Dist**: Number of plasmid hits
+
+.. image:: ../resources/reports/mash_dist_table.png
+    :align: center
+
+Plot data
+^^^^^^^^^
+
+- **Sliding window Plasmid annotation**: Provides annotation of plasmid
+  hits along the genome assembly. This report component is only available
+  when the ``mash_dist`` component is used.
+
+.. image:: ../resources/reports/sliding_window_mash_dist.png