Merge pull request #520 from nf-core/tiara-publish-fix

Fix Tiara publishing files

CHANGELOG.md

@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#514](https://github.com/nf-core/mag/pull/514) - Fix missing CONCOCT files in downstream output (reported by @maxibor, fix by @jfy133)
 - [#515](https://github.com/nf-core/mag/pull/515) - Fix overwriting of GUNC output directories when running with domain classification (reported by @maxibor, fix by @jfy133)
 - [#516](https://github.com/nf-core/mag/pull/516) - Fix edge-case bug where MEGAHIT re-uses previous work directory on resume and fails (reported by @husensofteng, fix by @prototaxites)
+- [#520](https://github.com/nf-core/mag/pull/520) - Fix missing Tiara output files (fix by @jfy133)
 
 ### `Dependencies`
 

conf/modules.config

@@ -698,17 +698,10 @@ process {
 
     withName: TIARA_TIARA {
         publishDir = [
-            [
-                path: { "${params.outdir}/Taxonomy/Tiara" },
+                path: { "${params.outdir}/Taxonomy/Tiara/" },
                 mode: params.publish_dir_mode,
-                pattern: { "${meta.assembler}-${meta.id}.tiara.{txt}" }
-            ],
-            [
-                path: { "${params.outdir}/Taxonomy/Tiara/log" },
-                mode: params.publish_dir_mode,
-                pattern: { "log_${meta.assembler}-${meta.id}.tiara.{txt}" }
+                pattern: "*.txt"
             ]
-        ]
         ext.args = { "--min_len ${params.tiara_min_length} --probabilities" }
         ext.prefix = { "${meta.assembler}-${meta.id}.tiara" }
     }
@@ -720,7 +713,7 @@ process {
 
     withName: TIARA_SUMMARY {
         publishDir = [
-            path: { "${params.outdir}/Taxonomy/" },
+            path: { "${params.outdir}/GenomeBinning/Tiara" },
             mode: params.publish_dir_mode,
             pattern: "tiara_summary.tsv"
         ]

docs/output.md

@@ -434,12 +434,12 @@ Tiara is a contig classifier that identifies the domain (prokarya, eukarya) of c
 
 - `Taxonomy/Tiara/`
   - `[assembler]-[sample/group].tiara.txt` - Tiara output classifications (with probabilities) for all contigs within the specified sample/group assembly
-  - `log/log_[assembler]-[sample/group].txt` - log file detailing the parameters used by the Tiara model for contig classification.
+  - `log_[assembler]-[sample/group].txt` - log file detailing the parameters used by the Tiara model for contig classification.
 - `GenomeBinning/tiara_summary.tsv` - Summary of Tiara domain classification for all bins.
 
 </details>
 
-Typically, you would use `tiara_summary.tsv` as the primary file to see which bins or unbins have been classified to which domains at a glance, whereas `[assembler]-[sample/group].tiara.txt` provides classifications for each contig.
+Typically, you would use `tiara_summary.tsv` as the primary file to see which bins or unbins have been classified to which domains at a glance, whereas the files in `Taxonomy/Tiara` provide classifications for each contig.
 
 ### Bin sequencing depth