Merge pull request #625 from nf-core/dev

Patch release 3.0.1
nf-core · Jun 10, 2024 · aac4962 · aac4962
2 parents a50117e + 402020b
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,26 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## 3.0.1 [2024-06-10]
+
+### `Added`
+
+### `Changed`
+
+- [#625](https://github.com/nf-core/mag/pull/625) - Updated link to geNomad database for downloading (reported by @amizeranschi, fix by @jfy133)
+
+### `Fixed`
+
+- [#618](https://github.com/nf-core/mag/pull/618) - Fix CENTRIFUGE mkfifo failures by using work directory /tmp (reported by @skrakau, fix by @jfy133)
+
+### `Dependencies`
+
+| Tool       | Previous version | New version |
+| ---------- | ---------------- | ----------- |
+| Centrifuge | 1.0.4_beta       | 1.0.4.1     |
+
+### `Deprecated`
+
 ## 3.0.0 - [2024-05-13]
 
 ### `Added`

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/mag/releases/tag/3.0.0" target="_blank">nf-core/mag</a>
+  This report has been generated by the <a href="https://github.com/nf-core/mag/releases/tag/3.0.1" target="_blank">nf-core/mag</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/mag/3.0.0/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/mag/3.0.1/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-mag-methods-description":
     order: -1000

diff --git a/conf/modules.config b/conf/modules.config
@@ -222,7 +222,16 @@ process {
         ]
     }
 
-    withName: CENTRIFUGE {
+    withName: CENTRIFUGE_CENTRIFUGE {
+        publishDir = [
+            path: { "${params.outdir}/Taxonomy/centrifuge/${meta.id}" },
+            mode: params.publish_dir_mode,
+            pattern: "*.txt"
+        ]
+    }
+
+    withName: CENTRIFUGE_KREPORT {
+        ext.prefix = { "${meta.id}_kreport" }
         publishDir = [
             path: { "${params.outdir}/Taxonomy/centrifuge/${meta.id}" },
             mode: params.publish_dir_mode,
@@ -239,7 +248,16 @@ process {
         ]
     }
 
-    withName: KRONA {
+    withName: KREPORT2KRONA_CENTRIFUGE {
+        publishDir = [
+            path: { "${params.outdir}/Taxonomy/${meta.classifier}/${meta.id}" },
+            mode: params.publish_dir_mode,
+            pattern: "*.txt",
+            enabled: false
+        ]
+    }
+
+    withName: KRONA_KTIMPORTTAXONOMY {
         publishDir = [
             path: { "${params.outdir}/Taxonomy/${meta.classifier}/${meta.id}" },
             mode: params.publish_dir_mode,

diff --git a/docs/output.md b/docs/output.md
@@ -170,9 +170,10 @@ More information on the [Centrifuge](https://ccb.jhu.edu/software/centrifuge/) w
 <summary>Output files</summary>
 
 - `Taxonomy/centrifuge/[sample]/`
-  - `report.txt`: Tab-delimited result file. See the [centrifuge manual](https://ccb.jhu.edu/software/centrifuge/manual.shtml#centrifuge-classification-output) for information about the fields
-  - `kreport.txt`: Classification in the Kraken report format. See the [kraken2 manual](https://github.com/DerrickWood/kraken2/wiki/Manual#output-formats) for more details
-  - `taxonomy.krona.html`: Interactive pie chart produced by [KronaTools](https://github.com/marbl/Krona/wiki)
+  - `[sample].kreport.txt`: Classification in the Kraken report format. See the [kraken2 manual](https://github.com/DerrickWood/kraken2/wiki/Manual#output-formats) for more details
+  - `[sample].report.txt`: Tab-delimited result file. See the [centrifuge manual](https://ccb.jhu.edu/software/centrifuge/manual.shtml#centrifuge-classification-output) for information about the fields
+  - `[sample].results.txt`: Per read taxonomic classification information. See the [centrifuge manual](https://ccb.jhu.edu/software/centrifuge/manual.shtml#centrifuge-classification-output) for more details
+  - `[sample].html`: Interactive pie chart produced by [KronaTools](https://github.com/marbl/Krona/wiki)
 
 </details>
 

diff --git a/modules.json b/modules.json
@@ -41,6 +41,17 @@
                         "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
                         "installed_by": ["modules"]
                     },
+                    "centrifuge/centrifuge": {
+                        "branch": "master",
+                        "git_sha": "9a07a1293d9b818d1e06d0f7b58152f74d462012",
+                        "installed_by": ["modules"]
+                    },
+                    "centrifuge/kreport": {
+                        "branch": "master",
+                        "git_sha": "9a07a1293d9b818d1e06d0f7b58152f74d462012",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/centrifuge/kreport/centrifuge-kreport.diff"
+                    },
                     "checkm/lineagewf": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
@@ -141,6 +152,21 @@
                         "git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57",
                         "installed_by": ["modules"]
                     },
+                    "krakentools/kreport2krona": {
+                        "branch": "master",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "installed_by": ["modules"]
+                    },
+                    "krona/kronadb": {
+                        "branch": "master",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "installed_by": ["modules"]
+                    },
+                    "krona/ktimporttaxonomy": {
+                        "branch": "master",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "installed_by": ["modules"]
+                    },
                     "maxbin2": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
@@ -205,6 +231,11 @@
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
+                    },
+                    "untar": {
+                        "branch": "master",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "installed_by": ["modules"]
                     }
                 }
             },

diff --git a/modules/nf-core/centrifuge/centrifuge/environment.yml b/modules/nf-core/centrifuge/centrifuge/environment.yml
diff --git a/modules/nf-core/centrifuge/centrifuge/main.nf b/modules/nf-core/centrifuge/centrifuge/main.nf
diff --git a/modules/nf-core/centrifuge/centrifuge/meta.yml b/modules/nf-core/centrifuge/centrifuge/meta.yml