Update publishdir and docs for bakta output

CHANGELOG.md

@@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#343](https://github.com/nf-core/funcscan/pull/343) Standardized the resulting workflow summary tables to always start with 'sample_id\tcontig_id\t..'. Reformatted the output of `hamronization/summarize` module. (by @darcy220606)
 - [#348](https://github.com/nf-core/funcscan/pull/348) Updated samplesheet for pipeline tests to 'samplesheet_reduced.csv' with smaller datasets to reduce resource consumption. Updated prodigal module to fix pigz issue. Removed `tests/` from `.gitignore`. (by @darcy220606)
+- [#362](https://github.com/nf-core/funcscan/pull/362) Save annotations from bakta in subdirectories per sample. (by @jasmezz)
 
 | Tool          | Previous version | New version |
 | ------------- | ---------------- | ----------- |

conf/modules.config

@@ -146,7 +146,7 @@ process {
 
     withName: BAKTA_BAKTA {
         publishDir = [
-            path: { "${params.outdir}/annotation/bakta" },
+            path: { "${params.outdir}/annotation/bakta/${meta.id}" },
             mode: params.publish_dir_mode,
             enabled: params.save_annotations,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }

docs/output.md

@@ -28,7 +28,7 @@ results/
 |   └── mmseqs_createtsv/
 ├── annotation/
 |   ├── bakta/
-|   ├── prodigal
+|   ├── prodigal/
 |   ├── prokka/
 |   └── pyrodigal/
 ├── amp/
@@ -209,18 +209,19 @@ Output Summaries:
 <summary>Output files</summary>
 
 - `bakta/`
-  - `<samplename>.gff3`: annotations & sequences in GFF3 format
-  - `<samplename>.gbff`: annotations & sequences in (multi) GenBank format
-  - `<samplename>.ffn`: feature nucleotide sequences as FASTA
-  - `<samplename>.fna`: replicon/contig DNA sequences as FASTA
-  - `<samplename>.embl`: annotations & sequences in (multi) EMBL format
-  - `<samplename>.faa`: CDS/sORF amino acid sequences as FASTA
-  - `<samplename>_hypothetical.faa`: further information on hypothetical protein CDS as simple human readble tab separated values
-  - `<samplename>_hypothetical.tsv`: hypothetical protein CDS amino acid sequences as FASTA
-  - `<samplename>.tsv`: annotations as simple human readble TSV
-  - `<samplename>.txt`: summary in TXT format
-
-> Descriptions directly from the [Bakta documentation](https://github.com/oschwengers/bakta#output).
+  - `<samplename>`
+    - `<samplename>.gff3`: annotations & sequences in GFF3 format
+    - `<samplename>.gbff`: annotations & sequences in (multi) GenBank format
+    - `<samplename>.ffn`: feature nucleotide sequences as FASTA
+    - `<samplename>.fna`: replicon/contig DNA sequences as FASTA
+    - `<samplename>.embl`: annotations & sequences in (multi) EMBL format
+    - `<samplename>.faa`: CDS/sORF amino acid sequences as FASTA
+    - `<samplename>_hypothetical.faa`: further information on hypothetical protein CDS as simple human readble tab separated values
+    - `<samplename>_hypothetical.tsv`: hypothetical protein CDS amino acid sequences as FASTA
+    - `<samplename>.tsv`: annotations as simple human readble TSV
+    - `<samplename>.txt`: summary in TXT format
+
+> Descriptions taken from the [Bakta documentation](https://github.com/oschwengers/bakta#output).
 
 </details>