Merge pull request #618 from nf-core/fix-centrifuge

Fix centrifuge
nf-core · May 23, 2024 · 333caeb · 333caeb
2 parents f48a1fd + b44e0f5
commit 333caeb
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Showing 32 changed files with 1,208 additions and 65 deletions.
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
diff --git a/modules/nf-core/centrifuge/centrifuge/tests/main.nf.test b/modules/nf-core/centrifuge/centrifuge/tests/main.nf.test