Merge branch 'dev' into bouncy-basenji

CHANGELOG.md

@@ -9,23 +9,31 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#417](https://github.com/nf-core/taxprofiler/pull/417) - Added reference-free metagenome estimation with Nonpareil (added by @jfy133)
 
-## v1.1.8dev - Augmented Akita Patch []
+### `Fixed`
+
+### `Dependencies`
+
+### `Deprecated`
+
+## v1.1.8 - Augmented Akita Patch [2024-06-20]
 
 ### `Added`
 
-- [#487](https://github.com/nf-core/taxprofiler/pull/487) Updated to nf-core pipeline template v2.14.1 (added by jfy133)
+- [#487](https://github.com/nf-core/taxprofiler/pull/487) Updated to nf-core pipeline template v2.14.1 (added by @jfy133)
 
 ### `Fixed`
 
 - [#484](https://github.com/nf-core/taxprofiler/pull/484) Improved input validation to immediately fail if run accession IDs within a given sample ID are not unique (❤️ to @sofstam for reporting, fixed by @jfy133)
 - [#491](https://github.com/nf-core/taxprofiler/pull/491) Added flag to publish intermediate bracken files (❤️ to @ewissel for reporting, fixed by @sofstam and @jfy133)
-- [489](https://github.com/nf-core/taxprofiler/pull/489) Fix KrakenUniq classified reads output format mismatch (❤️ to @SannaAb for reporting, fixed by @jfy133)
+- [#489](https://github.com/nf-core/taxprofiler/pull/489) Fix KrakenUniq classified reads output format mismatch (❤️ to @SannaAb for reporting, fixed by @jfy133)
+- [#495](https://github.com/nf-core/taxprofiler/pull/495) Stop TAXPASTA failures when profiles do not have exact compositionality (fixes by @Midnighter, @jfy133)
 
 ### `Dependencies`
 
-| Tool | Previous version | New version |
-| ---- | ---------------- | ----------- |
-| KMCP | 0.9.1            | 0.9.4       |
+| Tool     | Previous version | New version |
+| -------- | ---------------- | ----------- |
+| KMCP     | 0.9.1            | 0.9.4       |
+| TAXPASTA | 0.6.1            | 0.7.0       |
 
 ### `Deprecated`
 

conf/modules.config

@@ -782,15 +782,14 @@ process {
 
     withName: TAXPASTA_MERGE {
         tag = { "${meta.tool}|${meta.id}" }
+        ext.prefix = { "${meta.tool}_${meta.id}" }
         ext.args =  {
             [
-                "-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}",
                 params.taxpasta_add_name ?  "--add-name" : "",
                 params.taxpasta_add_rank ? "--add-rank" : "",
                 params.taxpasta_add_lineage ? "--add-lineage" : "",
                 params.taxpasta_add_idlineage ? "--add-id-lineage" : "",
                 params.taxpasta_add_ranklineage ? "--add-rank-lineage" : "",
-                params.taxpasta_ignore_errors ? "--ignore-errors" : ""
             ].join(' ').trim()
             }
         publishDir = [
@@ -802,14 +801,15 @@ process {
 
     withName: TAXPASTA_STANDARDISE {
         tag = { "${meta.tool}|${meta.id}" }
+        ext.prefix = { "${meta.tool}_${meta.id}" }
         ext.args =  {
-            [
-                "-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}",
-                params.taxpasta_add_name ?  "--add-name" : "",
-                params.taxpasta_add_rank ? "--add-rank" : "",
-                params.taxpasta_add_lineage ? "--add-lineage" : "",
-                params.taxpasta_add_idlineage ? "--add-id-lineage" : ""
-            ].join(' ').trim()
+                [
+                    params.taxpasta_add_name ?  "--add-name" : "",
+                    params.taxpasta_add_rank ? "--add-rank" : "",
+                    params.taxpasta_add_lineage ? "--add-lineage" : "",
+                    params.taxpasta_add_idlineage ? "--add-id-lineage" : "",
+                    params.taxpasta_add_ranklineage ? "--add-rank-lineage" : ""
+                ].join(' ').trim()
             }
         publishDir = [
             path: { "${params.outdir}/taxpasta/" },

modules.json

@@ -243,12 +243,12 @@
                     },
                     "taxpasta/merge": {
                         "branch": "master",
-                        "git_sha": "48019785051ba491e82dce910273c2eca61bd5b7",
+                        "git_sha": "4fd9089d3cf904e0b870d5a6a7ab903ee5e1004d",
                         "installed_by": ["modules"]
                     },
                     "taxpasta/standardise": {
                         "branch": "master",
-                        "git_sha": "48019785051ba491e82dce910273c2eca61bd5b7",
+                        "git_sha": "4fd9089d3cf904e0b870d5a6a7ab903ee5e1004d",
                         "installed_by": ["modules"]
                     },
                     "untar": {