Merge pull request #385 from nf-core/cat-unbinnned

Run CAT on unbinnned contigs as well as binned contigs

CHANGELOG.md

@@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#353](https://github.com/nf-core/mag/pull/353) - Added the busco_clean parameter to optionally clean each BUSCO directory after a successful (by @prototaxites)
 - [#361](https://github.com/nf-core/mag/pull/361) - Added the skip_clipping parameter to skip read preprocessing with fastp or adapterremoval. Running the pipeline with skip_clipping, keep_phix and without specifying a host genome or fasta file skips the FASTQC_TRIMMED process (by @prototaxites)
-- [#365](https://github.com/nf-core/mag/pull/365) - Adds CONCOCT as an additional (optional) binning tool (by @jfy133)
+- [#365](https://github.com/nf-core/mag/pull/365) - Added CONCOCT as an additional (optional) binning tool (by @jfy133)
 - [#366](https://github.com/nf-core/mag/pull/366) - Added CAT_SUMMARISE process and cat_official_taxonomy parameter (by @prototaxites)
 - [#372](https://github.com/nf-core/mag/pull/372) - Allow CAT_DB to take an extracted database as well as a tar.gz file.
 - [#380](https://github.com/nf-core/mag/pull/380) - Added support for saving processed reads (clipped, host removed etc.) to results directory (by @jfy133)
@@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#340](https://github.com/nf-core/mag/pull/340),[#368](https://github.com/nf-core/mag/pull/368),[#373](https://github.com/nf-core/mag/pull/373) - Update to nf-core 2.7.2 `TEMPLATE` (by @jfy133, @d4straub, @skrakau)
 - [#373](https://github.com/nf-core/mag/pull/373) - Removed parameter `--enable_conda`. Updated local modules to new conda syntax and updated nf-core modules (by @skrakau)
 - [#350](https://github.com/nf-core/mag/pull/350) - Adds support for CheckM as alternative bin completeness and QC tool (added by @jfy133 and @skrakau)
+- [#385](https://github.com/nf-core/mag/pull/385) - CAT also now runs on unbinned contigs as well as binned contigs (added by @jfy133)
 
 ### `Fixed`
 

workflows/mag.nf

@@ -668,7 +668,7 @@ workflow MAG {
             ch_cat_db = CAT_DB_GENERATE.out.db
         }
         CAT (
-            ch_input_for_postbinning_bins,
+            ch_input_for_postbinning_bins_unbins,
             ch_cat_db
         )
         CAT_SUMMARY(