Merge pull request #1008 from dialvarezs/gunc-update-output

Address review commentws on #1005

Author: dialvarezs

conf/modules.config

@@ -601,7 +601,7 @@ process {
 
     withName: GUNC_MERGECHECKM {
         publishDir = [
-            path: { "${params.outdir}/GenomeBinning/QC/GUNC/checkmmerged/${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}/${checkm_file.baseName}" },
+            path: { "${params.outdir}/GenomeBinning/QC/GUNC/checkmmerged/${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}/" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]

docs/output.md

@@ -739,9 +739,9 @@ Besides the reference files or output files created by CheckM, the following sum
 - `[gunc-database].dmnd`
 - `GUNC/`
   - `raw/`
-    - `[assembler]-[binner]-[domain]-[refinement]-[sample/group]/[fasta input file name]/GUNC_checkM.merged.tsv`: Per sample GUNC [output](https://grp-bork.embl-community.io/gunc/output.html) containing with taxonomic and completeness QC statistics.
+    - `[assembler]-[binner]-[domain]-[refinement]-[sample/group]/GUNC_checkM.merged.tsv`: Per sample GUNC [output](https://grp-bork.embl-community.io/gunc/output.html) containing with taxonomic and completeness QC statistics.
   - `checkmmerged/`
-    - `[assembler]-[binner]-[domain]-[refinement]-[sample/group]/[checkm input file name]/GUNC.progenomes_2.1.maxCSS_level.tsv`: Per sample GUNC output merged with output from [CheckM](#checkm)
+    - `[assembler]-[binner]-[domain]-[refinement]-[sample/group]/GUNC.progenomes_2.1.maxCSS_level.tsv`: Per sample GUNC output merged with output from [CheckM](#checkm)
 
 </details>