diff --git a/HISTORY.md b/HISTORY.md index 225d4b0..1ceba45 100644 --- 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 index 4cfd3e3..f355cff 100644 --- 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 index cf84a6e..6cf6c69 100644 --- 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