Merge pull request #533 from nf-core/fix-metabat2-publishing

Fix metaBAT2 bin publishing

CHANGELOG.md

@@ -11,7 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
-- [#489](https://github.com/nf-core/mag/pull/489) Fix file name collision clashes for CHECKM, CAT, GTDBTK, and QUAST (by @maxibor)
+- [#489](https://github.com/nf-core/mag/pull/489) Fix file name collision clashes for CHECKM, CAT, GTDBTK, and QUAST (reported by @tillenglert and @maxibor, fix by @maxibor)
+- [#527](https://github.com/nf-core/mag/pull/489) Fix glob pattern for publishing MetaBAT2 bins in results (reported by @patriciatran, fix by @jfy133)
 
 ### `Dependencies`
 

conf/modules.config

@@ -570,9 +570,9 @@ process {
     withName: METABAT2_METABAT2 {
         publishDir = [
             [
-                path: { "${params.outdir}/GenomeBinning/MetaBAT2/" },
+                path: { "${params.outdir}/GenomeBinning/MetaBAT2/bins/" },
                 mode: params.publish_dir_mode,
-                pattern: 'bins/*.fa.gz'
+                pattern: '*[!lowDepth|tooShort|unbinned].fa.gz'
             ],
             [
                 path: { "${params.outdir}/GenomeBinning/MetaBAT2/discarded" },

docs/output.md

@@ -333,6 +333,8 @@ These depth files are used for downstream binning steps.
 
 All the files and contigs in these folders will be assessed by QUAST and BUSCO.
 
+All other files that were discarded by the tool, or from the low-quality unbinned contigs , can be found here.
+
 <details markdown="1">
 <summary>Output files</summary>