Merge pull request #83 from fmalmeida/82-fix-canu-hifi-choice-for-pacbio

82 fix canu hifi choice for pacbio

Author: fmalmeida

docs/manual.md

@@ -135,7 +135,7 @@ However, they can also be set in a sample-specific manner. If a sample has a val
 | `--wtdbg2_technology`    | :material-close: | ont/sq           | It tells the pipeline which technology the long reads are, which is required for wtdbg2. Options are: `ont` for Nanopore reads, `rs` for PacBio RSII, `sq` for PacBio Sequel, `ccs` for PacBio CCS reads. With not wanted, consider using `--skip_wtdbg2` |
 | `--shasta_config`        | :material-close: | Nanopore-Oct2021 | It tells the pipeline which shasta pre-set configuration to use when assembling nanopore reads. Please read the [shasta configuration manual page](https://chanzuckerberg.github.io/shasta/Configurations.html) to know the available models |
 | `--corrected_longreads` | :material-check: | False            | It tells the pipeline to interpret the input long reads as "corrected". This will activate (if available) the options for corrected reads in the assemblers. For example: `-corrected` (in canu), `--pacbio-corr|--nano-corr` (in flye), etc. Be cautious when using this parameter. If your reads are not corrected, and you use this parameter, you will probably do not generate any contig |
-| `--high_quality_longreads` | :material-check: | False          | It tells the pipeline to interpret the input long reads as "(high quality - hifi)". This will activate (if available) the options for high quality (hifi) reads in the assemblers. For example: `-corrected` (in canu), `--pacbio-hifi|--nano-hq` (in flye), etc. Be cautious when using this parameter. If your reads are not corrected, and you use this parameter, you will probably do not generate any contig |
+| `--high_quality_longreads` | :material-check: | False          | It tells the pipeline to interpret the input long reads as "(high quality - hifi)". This will activate (if available) the options for high quality (hifi) reads in the assemblers. For example: `-pacbio-hifi|-nanopore -corrected` (in canu), `--pacbio-hifi|--nano-hq` (in flye), etc. Be cautious when using this parameter. If your reads are not corrected, and you use this parameter, you will probably do not generate any contig |
 
 ### Long reads polishers
 

markdown/CHANGELOG.md

@@ -2,6 +2,11 @@
 
 The tracking for changes started in v2.
 
+## v3.2.2 -- TBD
+
+* [#82](https://github.com/fmalmeida/MpGAP/issues/82)
+  * Small fix to allow canu to use `-pacbio-hifi` parameter when using `--high_quality_longreads` pipeline parameter. For nanopore it stays using `-corrected` since canu does not have a special option for high-quality nanopore data.
+
 ## v3.2.1 -- [2024-Jul-24]
 
 * [#77](https://github.com/fmalmeida/MpGAP/issues/77)

modules/local/LongReads/canu.nf

@@ -109,5 +109,5 @@ manifest {
   homePage        = "https://github.com/fmalmeida/mpgap"
   mainScript      = "main.nf"
   nextflowVersion = "!>=21.10.3"
-  version         = "3.2.1"
+  version         = "3.2.2"
 }