Merge pull request #104 from gbouras13/dev

update docs
gbouras13 · Oct 18, 2024 · 9bf944a · 9bf944a
2 parents 8348d42 + 80829d9
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diff --git a/HISTORY.md b/HISTORY.md
@@ -1,11 +1,11 @@
 # History
 
-## v0.10.0 Updates (17 October 2024)
+## v0.10.0 Updates (18 October 2024)
 
 * Updates Medaka to v2.0.1, implementing the `--bacteria` option by default.
 * This is based on the recommendations of Ryan Wick [here](https://rrwick.github.io/2024/10/17/medaka-v2.html) who found it improved assemblies due to (likely) enhanced methylation error correction.
 * If you still want to specify a Medaka model, the flag `--medaka_override` has been added. You need to include this along with your model via `--medakaModel`. This is most likely useful for older R9 data.
-* 
+* Adds `--extra_params_flye` parameter if you want to specify extra commands for the Flye assembly step thanks @pdobbler.
 
 ## v0.9.1 Updates (8 October 2024)
 

diff --git a/README.md b/README.md
@@ -178,6 +178,7 @@ To summarise the conclusions:
 * Updates Medaka to v2.0.1, implementing the `--bacteria` option by default.
 * This is based on the recommendations of Ryan Wick [here](https://rrwick.github.io/2024/10/17/medaka-v2.html) who found it improved assemblies due to (likely) enhanced methylation error correction.
 * If you still want to specify a Medaka model, the flag `--medaka_override` has been added. You need to include this along with your model via `--medakaModel`. This is most likely useful for older R9 data.
+* * Adds `--extra_params_flye` parameter if you want to specify extra commands for the Flye assembly step.
 
 ### v0.9.0 Updates (18 September 2024)
 

diff --git a/docs/run.md b/docs/run.md
@@ -121,6 +121,8 @@ Options:
   --medaka_override               Use this if you do NOT want to use the
                                   --bacteria option with Medaka. Instead your
                                   specified --medakaModel will be used.
+  --extra_params_flye TEXT        Use this if want to add extra parameters to
+                                  Flye.
   --use-conda / --no-use-conda    Use conda for Snakemake rules  [default:
                                   use-conda]
   --conda-prefix PATH             Custom conda env directory
@@ -209,6 +211,8 @@ Options:
   --medaka_override               Use this if you do NOT want to use the
                                   --bacteria option with Medaka. Instead your
                                   specified --medakaModel will be used.
+  --extra_params_flye TEXT        Use this if want to add extra parameters to
+                                  Flye.
   --use-conda / --no-use-conda    Use conda for Snakemake rules  [default:
                                   use-conda]
   --conda-prefix PATH             Custom conda env directory
@@ -301,6 +305,8 @@ Options:
   --medaka_override               Use this if you do NOT want to use the
                                   --bacteria option with Medaka. Instead your
                                   specified --medakaModel will be used.
+  --extra_params_flye TEXT        Use this if want to add extra parameters to
+                                  Flye.
   --use-conda / --no-use-conda    Use conda for Snakemake rules  [default:
                                   use-conda]
   --conda-prefix PATH             Custom conda env directory
@@ -381,6 +387,8 @@ Options:
   --medaka_override               Use this if you do NOT want to use the
                                   --bacteria option with Medaka. Instead your
                                   specified --medakaModel will be used.
+  --extra_params_flye TEXT        Use this if want to add extra parameters to
+                                  Flye.
   --use-conda / --no-use-conda    Use conda for Snakemake rules  [default:
                                   use-conda]
   --conda-prefix PATH             Custom conda env directory