Fixing merge conflicts on #435

CHANGELOG.md

@@ -17,7 +17,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 
 ### Enhancements & fixes
 
-- [[#299](https://github.com/nf-core/viralrecon/issues/299)] - Add the freyja pipeline as a subworkflow
+- [[PR #375](https://github.com/nf-core/viralrecon/pull/375)] - Add the freyja pipeline as a subworkflow
 - [[PR #387](https://github.com/nf-core/viralrecon/pull/387)] - Software closes gracefully when encountering an error
 - [[PR #395](https://github.com/nf-core/viralrecon/pull/395)] - Remove minia from default assemblers because it is unreliable
 - [[PR #393](https://github.com/nf-core/viralrecon/pull/393)] - Changed primer set to params
@@ -27,6 +27,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [[PR #417](https://github.com/nf-core/viralrecon/pull/417)] - Allow skipping of Freyja bootstrapping module & freyja module update
 - [[PR #434](https://github.com/nf-core/viralrecon/pull/434)] - Add blast result filtering through `min_contig_length` and `min_perc_contig_aligned`.
 - [[PR #435](https://github.com/nf-core/viralrecon/pull/435)] - Changed cutadapt to use nf-core modules, added `skip_noninternal_primers` param to allow users to process primers inside the pipeline.
+- [[PR #438](https://github.com/nf-core/viralrecon/pull/438)] - Update fastp container to 0.23.4
 
 ### Parameters
 
@@ -53,9 +54,11 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 
 | Dependency | Old version | New version |
 | ---------- | ----------- | ----------- |
+| `cutadapt` |             | 4.6         |
+| `fastp`    | 0.23.2      | 0.23.4      |
 | `freyja`   |             | 1.5.0       |
 | `multiqc`  | 1.14        | 1.19        |
-| `cutadapt` |             | 4.6         |
+| `fastp`    | 0.23.2      | 0.23.4      |
 
 > **NB:** Dependency has been **updated** if both old and new version information is present.
 >

modules.json

@@ -112,7 +112,7 @@
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "95cf5fe0194c7bf5cb0e3027a2eb7e7c89385080",
+                        "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {