From 1880b4b442a385c89970f3e6d0782d88aca05b14 Mon Sep 17 00:00:00 2001
From: tiagofilipe12 <tiagofilipe12@gmail.com>
Date: Fri, 8 Jun 2018 15:31:41 +0100
Subject: [PATCH 01/10] added patlas recipe

---
 flowcraft/flowcraft.py        | 17 ++++++++++++++---
 flowcraft/generator/recipe.py |  7 +------
 2 files changed, 15 insertions(+), 9 deletions(-)

diff --git a/flowcraft/flowcraft.py b/flowcraft/flowcraft.py
index cd3b84c9..d155c29e 100755
--- a/flowcraft/flowcraft.py
+++ b/flowcraft/flowcraft.py
@@ -15,7 +15,7 @@
     from __init__ import __version__, __build__
     from generator.engine import NextflowGenerator, process_map
     from generator.inspect import NextflowInspector
-    from generator.recipe import brew_recipe
+    from generator.recipe import brew_recipe, Innuendo
     from generator.pipeline_parser import parse_pipeline, SanityError
     from generator.process_details import proc_collector, colored_print
     import generator.error_handling as eh
@@ -23,7 +23,7 @@
     from flowcraft import __version__, __build__
     from flowcraft.generator.engine import NextflowGenerator, process_map
     from flowcraft.generator.inspect import NextflowInspector
-    from flowcraft.generator.recipe import brew_recipe
+    from flowcraft.generator.recipe import brew_recipe, Innuendo
     from flowcraft.generator.pipeline_parser import parse_pipeline, \
         SanityError
     from flowcraft.generator.process_details import proc_collector, \
@@ -32,6 +32,12 @@
 
 logger = logging.getLogger("main")
 
+available_recipes = {
+    "innuendo": Innuendo,
+    "plasmid_detection": "integrity_coverage fastqc_trimmomatic (spades pilon "
+              "(mash_dist | abricate) | mash_screen | mapping_patlas)",
+}
+
 
 def get_args(args=None):
 
@@ -199,7 +205,12 @@ def build(args):
     # If a recipe is specified, build pipeline based on the
     # appropriate recipe
     if args.recipe:
-        pipeline_string, list_processes = brew_recipe(args)
+        if args.recipe == "innuendo":
+            pipeline_string, list_processes = brew_recipe(args,
+                                                          available_recipes)
+        else:
+            pipeline_string = available_recipes[args.recipe]
+            list_processes = None
     else:
         pipeline_string = args.tasks
         list_processes = None
diff --git a/flowcraft/generator/recipe.py b/flowcraft/generator/recipe.py
index 5014b130..18b14ac9 100644
--- a/flowcraft/generator/recipe.py
+++ b/flowcraft/generator/recipe.py
@@ -517,12 +517,7 @@ def __init__(self, *args, **kwargs):
         }
 
 
-available_recipes = {
-    "innuendo": Innuendo
-}
-
-
-def brew_recipe(args):
+def brew_recipe(args, available_recipes):
     """Brews a given list of processes according to the recipe
 
     Parameters

From fea9f32e27f1f61b0854d2ca1f7467dd4214e6a9 Mon Sep 17 00:00:00 2001
From: tiagofilipe12 <tiagofilipe12@gmail.com>
Date: Fri, 8 Jun 2018 16:06:48 +0100
Subject: [PATCH 02/10] added argument to check recipes and other recipes for
 plasmids

---
 flowcraft/flowcraft.py | 21 +++++++++++++++++++--
 1 file changed, 19 insertions(+), 2 deletions(-)

diff --git a/flowcraft/flowcraft.py b/flowcraft/flowcraft.py
index d155c29e..13135fe4 100755
--- a/flowcraft/flowcraft.py
+++ b/flowcraft/flowcraft.py
@@ -32,10 +32,15 @@
 
 logger = logging.getLogger("main")
 
+# A dictionary of quick recipes
 available_recipes = {
     "innuendo": Innuendo,
-    "plasmid_detection": "integrity_coverage fastqc_trimmomatic (spades pilon "
+    "plasmids": "integrity_coverage fastqc_trimmomatic (spades pilon "
               "(mash_dist | abricate) | mash_screen | mapping_patlas)",
+    "plasmids_mapping": "integrity_coverage fastqc_trimmomatic mapping_patlas",
+    "plasmids_assembly": "integrity_coverage fastqc_trimmomatic (spades pilon "
+                         "(mash_dist | abricate))",
+    "plasmids_mash": "integrity_coverage fastqc_trimmomatic mash_screen",
 }
 
 
@@ -83,6 +88,12 @@ def get_args(args=None):
         "-l", "--short-list", action="store_const", dest="short_list",
         const=True, help="Print a short list of the currently "
                          "available processes")
+    build_parser.add_argument("-cr", "--check-recipe", dest="check_recipe",
+                              action="store_const", const=True,
+                              help="Check tasks that the recipe contain and "
+                                   "their flow. This option might be useful "
+                                   "if a user wants to change some components "
+                                   "of a given recipe, by using the -t option.")
 
     # GENERAL OPTIONS
     parser.add_argument(
@@ -131,7 +142,8 @@ def validate_build_arguments(args):
             "-l, -L", "red_bold"))
         sys.exit(1)
 
-    if (args.tasks or args.recipe) and not args.output_nf:
+    if (args.tasks or args.recipe) and not args.check_recipe \
+            and not args.output_nf:
         logger.error(colored_print(
             "Please provide the path and name of the pipeline file using the"
             " -o option.", "red_bold"))
@@ -211,6 +223,11 @@ def build(args):
         else:
             pipeline_string = available_recipes[args.recipe]
             list_processes = None
+        if args.check_recipe:
+            logger.info(colored_print("Pipeline string for recipe: {}"
+                                      .format(args.recipe), "purple_bold"))
+            logger.info(pipeline_string)
+            sys.exit(0)
     else:
         pipeline_string = args.tasks
         list_processes = None

From 866b2fc0ee4f7cc8dc4c3b07b2f5145825b2eff6 Mon Sep 17 00:00:00 2001
From: tiagofilipe12 <tiagofilipe12@gmail.com>
Date: Mon, 11 Jun 2018 14:54:29 +0100
Subject: [PATCH 03/10] removed prokka from innuendo recipe

---
 flowcraft/generator/recipe.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flowcraft/generator/recipe.py b/flowcraft/generator/recipe.py
index 18b14ac9..182edf6c 100644
--- a/flowcraft/generator/recipe.py
+++ b/flowcraft/generator/recipe.py
@@ -512,7 +512,7 @@ def __init__(self, *args, **kwargs):
             "mlst": [False, "pilon", "abricate|prokka|chewbbaca|sistr"],
             "sistr": [True, "mlst", None],
             "abricate": [True, "mlst", None],
-            "prokka": [True, "mlst", None],
+            #"prokka": [True, "mlst", None],
             "chewbbaca": [True, "mlst", None]
         }
 

From a5dce88bf7851771045ad1651ac51faeb07cab90 Mon Sep 17 00:00:00 2001
From: tiagofilipe12 <tiagofilipe12@gmail.com>
Date: Mon, 11 Jun 2018 17:30:46 +0100
Subject: [PATCH 04/10] added checks for list of processes for recipes

---
 flowcraft/flowcraft.py                  | 16 ++++++++++------
 flowcraft/generator/process_details.py  | 24 ++++++++++--------------
 flowcraft/generator/recipe.py           |  7 +++----
 flowcraft/tests/test_assemblerflow.py   | 18 ------------------
 flowcraft/tests/test_process_details.py |  8 ++++++--
 5 files changed, 29 insertions(+), 44 deletions(-)

diff --git a/flowcraft/flowcraft.py b/flowcraft/flowcraft.py
index 13135fe4..86106c47 100755
--- a/flowcraft/flowcraft.py
+++ b/flowcraft/flowcraft.py
@@ -38,8 +38,8 @@
     "plasmids": "integrity_coverage fastqc_trimmomatic (spades pilon "
               "(mash_dist | abricate) | mash_screen | mapping_patlas)",
     "plasmids_mapping": "integrity_coverage fastqc_trimmomatic mapping_patlas",
-    "plasmids_assembly": "integrity_coverage fastqc_trimmomatic (spades pilon "
-                         "(mash_dist | abricate))",
+    "plasmids_assembly": "integrity_coverage fastqc_trimmomatic (spades pilon"
+                         " mash_dist)",
     "plasmids_mash": "integrity_coverage fastqc_trimmomatic mash_screen",
 }
 
@@ -218,11 +218,16 @@ def build(args):
     # appropriate recipe
     if args.recipe:
         if args.recipe == "innuendo":
-            pipeline_string, list_processes = brew_recipe(args,
+            pipeline_string = brew_recipe(args,
                                                           available_recipes)
         else:
             pipeline_string = available_recipes[args.recipe]
-            list_processes = None
+            if args.tasks:
+                logger.warning(colored_print(
+                    "-t parameter will be ignored for recipe: {}\n"
+                        .format(args.recipe), "yellow_bold")
+                )
+
         if args.check_recipe:
             logger.info(colored_print("Pipeline string for recipe: {}"
                                       .format(args.recipe), "purple_bold"))
@@ -230,10 +235,9 @@ def build(args):
             sys.exit(0)
     else:
         pipeline_string = args.tasks
-        list_processes = None
 
     # used for lists print
-    proc_collector(process_map, args, list_processes)
+    proc_collector(process_map, args, pipeline_string)
 
     logger.info(colored_print("Resulting pipeline string:\n"))
     logger.info(colored_print(pipeline_string + "\n"))
diff --git a/flowcraft/generator/process_details.py b/flowcraft/generator/process_details.py
index f851997f..85fc5aa8 100644
--- a/flowcraft/generator/process_details.py
+++ b/flowcraft/generator/process_details.py
@@ -9,7 +9,8 @@
     "white_bold": "1;38m",
     "white_underline": "4;38m",
     "blue_bold": "1;36m",
-    "purple_bold": "1;34m"
+    "purple_bold": "1;34m",
+    "yellow_bold": "1;93m"
 }
 
 
@@ -74,7 +75,7 @@ def procs_dict_parser(procs_dict):
             ))
 
 
-def proc_collector(process_map, args, processes_list=None):
+def proc_collector(process_map, args, pipeline_string):
     """
     Function that collects all processes available and stores a dictionary of
     the required arguments of each process class to be passed to
@@ -88,9 +89,8 @@ def proc_collector(process_map, args, processes_list=None):
     args: argparse.Namespace
         The arguments passed through argparser that will be access to check the
         type of list to be printed
-    processes_list: list
-        List with all the available processes of a recipe. In case no recipe
-        is passed, the list should come empty.
+    pipeline_string: str
+        the pipeline string
 
     """
 
@@ -119,17 +119,13 @@ def proc_collector(process_map, args, processes_list=None):
         # loops between all process_map Processes
         for name, cls in process_map.items():
 
-            if processes_list:
-                # Skip process if process_list is provided and name not in
-                # processes list
-                if name not in processes_list:
-                    continue
-
             # instantiates each Process class
             cls_inst = cls(template=name)
-            d = {arg_key: vars(cls_inst)[arg_key] for arg_key in vars(cls_inst)
-                 if arg_key in arguments_list}
-            procs_dict[name] = d
+
+            if name in pipeline_string:
+                d = {arg_key: vars(cls_inst)[arg_key] for arg_key in
+                     vars(cls_inst) if arg_key in arguments_list}
+                procs_dict[name] = d
 
         procs_dict_parser(procs_dict)
 
diff --git a/flowcraft/generator/recipe.py b/flowcraft/generator/recipe.py
index 182edf6c..06067aa2 100644
--- a/flowcraft/generator/recipe.py
+++ b/flowcraft/generator/recipe.py
@@ -495,7 +495,8 @@ def __init__(self, *args, **kwargs):
         # The description of the processes
         # [forkable, input_process, output_process]
         self.process_descriptions = {
-            "reads_download": [True, None,"integrity_coverage|seq_typing|patho_typing"],
+            "reads_download": [True, None,
+                               "integrity_coverage|seq_typing|patho_typing"],
             "patho_typing": [True, None, None],
             "seq_typing": [True, None, None],
             "integrity_coverage": [True, None, "fastqc_trimmomatic"],
@@ -550,8 +551,6 @@ def brew_recipe(args, available_recipes):
     else:
         input_processes = args.tasks
 
-    # Get the list of processes for that recipe
-    list_processes = automatic_pipeline.get_process_info()
     # Validate the provided pipeline processes
     validated = automatic_pipeline.validate_pipeline(input_processes)
     if not validated:
@@ -559,4 +558,4 @@ def brew_recipe(args, available_recipes):
     # Get the final pipeline string
     pipeline_string = automatic_pipeline.run_auto_pipeline(input_processes)
 
-    return pipeline_string, list_processes
+    return pipeline_string
diff --git a/flowcraft/tests/test_assemblerflow.py b/flowcraft/tests/test_assemblerflow.py
index e9310cff..401f6c99 100644
--- a/flowcraft/tests/test_assemblerflow.py
+++ b/flowcraft/tests/test_assemblerflow.py
@@ -14,24 +14,6 @@ def tmp():
     shutil.rmtree("temp")
 
 
-def test_list_short():
-
-    sys.argv.append(1)
-    args = af.get_args(["build", "-l"])
-
-    with pytest.raises(SystemExit):
-        af.build(args)
-
-
-def test_list_long():
-
-    sys.argv.append(1)
-    args = af.get_args(["build", "-L"])
-
-    with pytest.raises(SystemExit):
-        af.build(args)
-
-
 def test_check():
 
     sys.argv.append(1)
diff --git a/flowcraft/tests/test_process_details.py b/flowcraft/tests/test_process_details.py
index a05a081e..39cf5129 100644
--- a/flowcraft/tests/test_process_details.py
+++ b/flowcraft/tests/test_process_details.py
@@ -19,14 +19,18 @@ def test_long_list():
 
     arguments = af.get_args(["build", "-L"])
 
+    pipeline_string = "fastqc trimmomatic"
+
     with pytest.raises(SystemExit):
-        pd.proc_collector(process_map, arguments)
+        pd.proc_collector(process_map, arguments, pipeline_string)
 
 
 def test_short_list():
 
     arguments = af.get_args(["build", "-l"])
 
+    pipeline_string = "fastqc trimmomatic"
+
     with pytest.raises(SystemExit):
-        pd.proc_collector(process_map, arguments)
+        pd.proc_collector(process_map, arguments, pipeline_string)
         
\ No newline at end of file

From ff58deade8a6aaaa13cd8da4aee233fec3abf71b Mon Sep 17 00:00:00 2001
From: tiagofilipe12 <tiagofilipe12@gmail.com>
Date: Mon, 11 Jun 2018 17:36:47 +0100
Subject: [PATCH 05/10] added check for list arguments to
 validate_build_arguments

---
 docs/index.rst                  |  1 +
 docs/user/available_recipes.rst | 27 +++++++++++++++++++++++++++
 flowcraft/flowcraft.py          |  3 +++
 3 files changed, 31 insertions(+)
 create mode 100644 docs/user/available_recipes.rst

diff --git a/docs/index.rst b/docs/index.rst
index 9cdcd1ed..cc095560 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -27,6 +27,7 @@ A NextFlow pipeline assembler for genomics.
    user/pipeline_building
    user/pipeline_configuration
    user/available_components
+   user/available_recipes
    user/pipeline_inspect
 
 .. _Developer Guide:
diff --git a/docs/user/available_recipes.rst b/docs/user/available_recipes.rst
new file mode 100644
index 00000000..e4317ffa
--- /dev/null
+++ b/docs/user/available_recipes.rst
@@ -0,0 +1,27 @@
+Recipes
+=======
+
+Recipes are pre-built and static pipelines that give the user a quick-start or
+that are required for some specific purpose.
+
+List of recipes
+---------------
+
+- ``plasmids``: lala
+
+- ``plasmids_mapping``: lele
+
+- ``plasmids_assembly``: lolo
+
+- ``plasmids_mash``: lili
+
+- I/O
+- para que serve o output
+
+-link pipeline cfg para mudar directivas e params
+
+
+SAMPLE:
+These are the currently available FlowCraft components with a short
+description of their tasks. For a more detailed information, follow the
+links of each components.
diff --git a/flowcraft/flowcraft.py b/flowcraft/flowcraft.py
index 86106c47..5e26cf5c 100755
--- a/flowcraft/flowcraft.py
+++ b/flowcraft/flowcraft.py
@@ -135,6 +135,9 @@ def get_args(args=None):
 
 def validate_build_arguments(args):
 
+    if args.detailed_list or args.short_list:
+        return
+
     if not args.tasks and not args.recipe and not args.check_only \
             and not args.detailed_list and not args.short_list:
         logger.error(colored_print(

From 7187bc7afd99295eebd00e14010c3b686f094c69 Mon Sep 17 00:00:00 2001
From: tiagofilipe12 <tiagofilipe12@gmail.com>
Date: Mon, 11 Jun 2018 17:41:07 +0100
Subject: [PATCH 06/10] linted code

---
 docs/user/available_recipes.rst | 27 ---------------------------
 flowcraft/flowcraft.py          |  3 +--
 2 files changed, 1 insertion(+), 29 deletions(-)
 delete mode 100644 docs/user/available_recipes.rst

diff --git a/docs/user/available_recipes.rst b/docs/user/available_recipes.rst
deleted file mode 100644
index e4317ffa..00000000
--- a/docs/user/available_recipes.rst
+++ /dev/null
@@ -1,27 +0,0 @@
-Recipes
-=======
-
-Recipes are pre-built and static pipelines that give the user a quick-start or
-that are required for some specific purpose.
-
-List of recipes
----------------
-
-- ``plasmids``: lala
-
-- ``plasmids_mapping``: lele
-
-- ``plasmids_assembly``: lolo
-
-- ``plasmids_mash``: lili
-
-- I/O
-- para que serve o output
-
--link pipeline cfg para mudar directivas e params
-
-
-SAMPLE:
-These are the currently available FlowCraft components with a short
-description of their tasks. For a more detailed information, follow the
-links of each components.
diff --git a/flowcraft/flowcraft.py b/flowcraft/flowcraft.py
index 5e26cf5c..a692b3e0 100755
--- a/flowcraft/flowcraft.py
+++ b/flowcraft/flowcraft.py
@@ -221,8 +221,7 @@ def build(args):
     # appropriate recipe
     if args.recipe:
         if args.recipe == "innuendo":
-            pipeline_string = brew_recipe(args,
-                                                          available_recipes)
+            pipeline_string = brew_recipe(args, available_recipes)
         else:
             pipeline_string = available_recipes[args.recipe]
             if args.tasks:

From 0caf9650df4c20c9b3e2907615dec8b10ee0f71a Mon Sep 17 00:00:00 2001
From: tiagofilipe12 <tiagofilipe12@gmail.com>
Date: Mon, 11 Jun 2018 19:56:04 +0100
Subject: [PATCH 07/10] commented no longer used method in Recipe class

---
 docs/index.rst                | 1 -
 flowcraft/generator/recipe.py | 4 ++--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/docs/index.rst b/docs/index.rst
index cc095560..9cdcd1ed 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -27,7 +27,6 @@ A NextFlow pipeline assembler for genomics.
    user/pipeline_building
    user/pipeline_configuration
    user/available_components
-   user/available_recipes
    user/pipeline_inspect
 
 .. _Developer Guide:
diff --git a/flowcraft/generator/recipe.py b/flowcraft/generator/recipe.py
index 06067aa2..63eb3813 100644
--- a/flowcraft/generator/recipe.py
+++ b/flowcraft/generator/recipe.py
@@ -478,8 +478,8 @@ def run_auto_pipeline(self, tasks):
 
         return self.pipeline_string
 
-    def get_process_info(self):
-        return list(self.process_descriptions.keys())
+    # def get_process_info(self):
+    #     return list(self.process_descriptions.keys())
 
 
 class Innuendo(Recipe):

From 4d430db28f77439817878f52f0c5b16aeefe20e6 Mon Sep 17 00:00:00 2001
From: tiagofilipe12 <tiagofilipe12@gmail.com>
Date: Mon, 11 Jun 2018 20:22:18 +0100
Subject: [PATCH 08/10] changed location of available_recipes dict

---
 flowcraft/flowcraft.py        | 15 ++-------------
 flowcraft/generator/recipe.py | 12 ++++++++++++
 2 files changed, 14 insertions(+), 13 deletions(-)

diff --git a/flowcraft/flowcraft.py b/flowcraft/flowcraft.py
index a692b3e0..fdfbf308 100755
--- a/flowcraft/flowcraft.py
+++ b/flowcraft/flowcraft.py
@@ -15,7 +15,7 @@
     from __init__ import __version__, __build__
     from generator.engine import NextflowGenerator, process_map
     from generator.inspect import NextflowInspector
-    from generator.recipe import brew_recipe, Innuendo
+    from generator.recipe import brew_recipe, available_recipes
     from generator.pipeline_parser import parse_pipeline, SanityError
     from generator.process_details import proc_collector, colored_print
     import generator.error_handling as eh
@@ -23,7 +23,7 @@
     from flowcraft import __version__, __build__
     from flowcraft.generator.engine import NextflowGenerator, process_map
     from flowcraft.generator.inspect import NextflowInspector
-    from flowcraft.generator.recipe import brew_recipe, Innuendo
+    from flowcraft.generator.recipe import brew_recipe, available_recipes
     from flowcraft.generator.pipeline_parser import parse_pipeline, \
         SanityError
     from flowcraft.generator.process_details import proc_collector, \
@@ -32,17 +32,6 @@
 
 logger = logging.getLogger("main")
 
-# A dictionary of quick recipes
-available_recipes = {
-    "innuendo": Innuendo,
-    "plasmids": "integrity_coverage fastqc_trimmomatic (spades pilon "
-              "(mash_dist | abricate) | mash_screen | mapping_patlas)",
-    "plasmids_mapping": "integrity_coverage fastqc_trimmomatic mapping_patlas",
-    "plasmids_assembly": "integrity_coverage fastqc_trimmomatic (spades pilon"
-                         " mash_dist)",
-    "plasmids_mash": "integrity_coverage fastqc_trimmomatic mash_screen",
-}
-
 
 def get_args(args=None):
 
diff --git a/flowcraft/generator/recipe.py b/flowcraft/generator/recipe.py
index 63eb3813..b3dfaf9b 100644
--- a/flowcraft/generator/recipe.py
+++ b/flowcraft/generator/recipe.py
@@ -559,3 +559,15 @@ def brew_recipe(args, available_recipes):
     pipeline_string = automatic_pipeline.run_auto_pipeline(input_processes)
 
     return pipeline_string
+
+
+# A dictionary of quick recipes
+available_recipes = {
+    "innuendo": Innuendo,
+    "plasmids": "integrity_coverage fastqc_trimmomatic (spades pilon "
+              "(mash_dist | abricate) | mash_screen | mapping_patlas)",
+    "plasmids_mapping": "integrity_coverage fastqc_trimmomatic mapping_patlas",
+    "plasmids_assembly": "integrity_coverage fastqc_trimmomatic (spades pilon"
+                         " mash_dist)",
+    "plasmids_mash": "integrity_coverage fastqc_trimmomatic mash_screen",
+}

From 001eae1ab1a7c99518124c0dcde9931986dc17df Mon Sep 17 00:00:00 2001
From: tiagofilipe12 <tiagofilipe12@gmail.com>
Date: Tue, 19 Jun 2018 16:06:02 +0100
Subject: [PATCH 09/10] fixed pipeline_string parsing through -l and -L options

---
 flowcraft/generator/process_details.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/flowcraft/generator/process_details.py b/flowcraft/generator/process_details.py
index 5b8cf9b0..240359b6 100644
--- a/flowcraft/generator/process_details.py
+++ b/flowcraft/generator/process_details.py
@@ -123,10 +123,14 @@ def proc_collector(process_map, args, pipeline_string):
             # instantiates each Process class
             cls_inst = cls(template=name)
 
-            if name in pipeline_string:
-                d = {arg_key: vars(cls_inst)[arg_key] for arg_key in
-                     vars(cls_inst) if arg_key in arguments_list}
-                procs_dict[name] = d
+            # checks if recipe is provided
+            if pipeline_string:
+                if name not in pipeline_string:
+                    continue
+
+            d = {arg_key: vars(cls_inst)[arg_key] for arg_key in
+                 vars(cls_inst) if arg_key in arguments_list}
+            procs_dict[name] = d
 
         procs_dict_parser(procs_dict)
 

From 2de23e0c14cff270c85fbaf7df76cd654749459e Mon Sep 17 00:00:00 2001
From: tiagofilipe12 <tiagofilipe12@gmail.com>
Date: Tue, 19 Jun 2018 16:14:35 +0100
Subject: [PATCH 10/10] updated changelog

---
 changelog.md | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/changelog.md b/changelog.md
index 6d9a87e4..998023a3 100644
--- a/changelog.md
+++ b/changelog.md
@@ -4,14 +4,28 @@
 
 ### New components
 
-- `maxbin2`: An automatic tool for binning metagenomic sequences
-- `bowtie2`: Align short paired-end sequencing reads to long reference sequences
+- `maxbin2`: An automatic tool for binning metagenomic sequences.
+- `bowtie2`: Align short paired-end sequencing reads to long reference
+sequences.
+
+### New recipes
+
+- `plasmids`: A recipe to perform mapping, mash screen on reads
+and also mash dist for assembly based approaches (all to detect
+plasmdis). This also includes annotation with abricate for the assembly.
+- `plasmids_mapping`: A recipe to perfmorm mapping for plasmids.
+- `plasmids_mash`: A recipe to perform mash screen for plasmids.
+- `plasmids_assembly`: A recipe to perform mash dist for plasmid
+assemblies.
 
 ### Minor/Other changes
 
 - Added "smart" check when the user provides a typo in pipeline string
 for a given process, outputting some "educated" guesses to the the
 terminal.
+- Added "-cr" option to show current recipe `pipeline_string`.
+- Changed the way recipes were being parsed by `proc_collector` for the
+usage of `-l` and `-L` options.
 
 ### Bug fixes