Merge pull request #467 from nf-core/LilyAnderssonLee-merge_dev_into_…

…bouncy

Lily andersson lee merge dev into bouncy

.github/workflows/ci.yml

@@ -64,7 +64,7 @@ jobs:
         run: |
           if [[ "${{ matrix.tags }}" == "test_motus" ]]; then
             wget https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py
-            python downloadDB.py > download_db_log.txt
+            python downloadDB.py --no-download-progress
             echo 'tool,db_name,db_params,db_path' > 'database_motus.csv'
             echo "motus,db_mOTU,,db_mOTU" >> 'database_motus.csv'
             nextflow run ${GITHUB_WORKSPACE} -profile docker,${{ matrix.tags }} --databases ./database_motus.csv --outdir ./results_${{ matrix.tags }};

CHANGELOG.md

@@ -7,12 +7,22 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#417](https://github.com/nf-core/taxprofiler/pull/417) - Added reference-free metagenome estimation with Nonpareil (added by @jfy133)
+
+## v1.1.6dev - [unreleased]
+
+### `Added`
+
 - [#417](https://github.com/nf-core/taxprofiler/pull/417) - Added reference-free metagenome estimation with Nonpareil (added by @jfy133)
 - [#454](https://github.com/nf-core/taxprofiler/pull/454) Updated to nf-core pipeline template v2.13.1 (added by @LilyAnderssonLee & @sofstam)
+- [#461](https://github.com/nf-core/taxprofiler/pull/461) Turned on 'strict' Nextflow evaluation runs (added by @jfy133)
+- [#461](https://github.com/nf-core/taxprofiler/pull/461) Optimised database compression so each compressed input database is untarred once, and shared amongst each run with different parameters (added by @jfy133)
+- [#461](https://github.com/nf-core/taxprofiler/pull/461) Added new parameter to optionally save uncompressed databases (added by @jfy133)
 
 ### `Fixed`
 
 - [#336](https://github.com/nf-core/taxprofiler/issues/336) Replace samplesheet check with nf-validation for both sample and database input sheets (fix by @LilyAnderssonLee)
+- [#460](https://github.com/nf-core/taxprofiler/issues/460) corrected the channel transformations to combine Kaiju and mOTUs reports with their reference databases (fix by @Midnighter)
 
 ### `Dependencies`
 

conf/modules.config

@@ -18,6 +18,15 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
+    withName: UNTAR {
+        ext.prefix = { "${archive.simpleName}" }
+        publishDir = [
+            path: { "${params.outdir}/untar/databases" },
+            mode: params.publish_dir_mode,
+            enabled: params.save_untarred_databases
+        ]
+    }
+
     withName: FASTQC {
         ext.args = '--quiet'
         ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }
@@ -521,7 +530,7 @@ process {
     }
 
     withName: KRAKENTOOLS_COMBINEKREPORTS_KRAKEN {
-        ext.prefix = { "kraken2_${meta.db_name}_combined_reports" }
+        ext.prefix = { "kraken2_${meta.id}_combined_reports" }
         publishDir = [
             path: { "${params.outdir}/kraken2/" },
             mode: params.publish_dir_mode,
@@ -540,6 +549,14 @@ process {
         ]
     }
 
+    withName: KRAKENTOOLS_KREPORT2KRONA {
+        publishDir = [
+            enabled: false,
+            mode: params.publish_dir_mode,
+            pattern: '*.txt'
+        ]
+    }
+
     withName: KRONA_CLEANUP {
         ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}" }
         publishDir = [