Merge branch 'master' into fix_haplotyper

nf-core · Aug 1, 2024 · 00f0ca3 · 00f0ca3
2 parents 7bedd59 + a16e02e
commit 00f0ca3
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diff --git a/subworkflows/nf-core/fastq_extract_kraken_krakentools/main.nf b/subworkflows/nf-core/fastq_extract_kraken_krakentools/main.nf
@@ -18,8 +18,8 @@ workflow FASTQ_EXTRACT_KRAKEN_KRAKENTOOLS {
     ch_versions = ch_versions.mix( KRAKENTOOLS_EXTRACTKRAKENREADS.out.versions.first() )
 
     emit:
-    kraken2_report = KRAKEN2_KRAKEN2.out.report                                          // channel: [ val(meta), path ]
+    kraken2_report          = KRAKEN2_KRAKEN2.out.report                                 // channel: [ val(meta), path ]
     extracted_kraken2_reads = KRAKENTOOLS_EXTRACTKRAKENREADS.out.extracted_kraken2_reads // channel: [ val(meta), [ fastq/fasta ] ]
-    multiqc_files = KRAKEN2_KRAKEN2.out.report                                           // channel: [ val(meta), path ]
-    versions = ch_versions                                                               // channel: [ versions.yml ]
+    multiqc_files           = KRAKEN2_KRAKEN2.out.report.map{it[1]}                      // channel: [ path ]
+    versions                = ch_versions                                                // channel: [ versions.yml ]
 }
diff --git a/subworkflows/nf-core/fastq_extract_kraken_krakentools/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_extract_kraken_krakentools/tests/main.nf.test.snap
@@ -21,13 +21,7 @@
                     ]
                 ],
                 "2": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test.kraken2.report.txt:md5,4227755fe40478b8d7dc8634b489761e"
-                    ]
+                    "test.kraken2.report.txt:md5,4227755fe40478b8d7dc8634b489761e"
                 ],
                 "3": [
                     "versions.yml:md5,0cbacd88674c22fcac104444bb04a386",
@@ -52,13 +46,7 @@
                     ]
                 ],
                 "multiqc_files": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test.kraken2.report.txt:md5,4227755fe40478b8d7dc8634b489761e"
-                    ]
+                    "test.kraken2.report.txt:md5,4227755fe40478b8d7dc8634b489761e"
                 ],
                 "versions": [
                     "versions.yml:md5,0cbacd88674c22fcac104444bb04a386",
@@ -70,7 +58,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.1"
         },
-        "timestamp": "2024-05-22T10:38:59.172878312"
+        "timestamp": "2024-07-31T17:33:41.289766041"
     },
     "sarscov2 illumina paired end with fastq output [fastq]": {
         "content": [
@@ -97,13 +85,7 @@
                     ]
                 ],
                 "2": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.kraken2.report.txt:md5,4227755fe40478b8d7dc8634b489761e"
-                    ]
+                    "test.kraken2.report.txt:md5,4227755fe40478b8d7dc8634b489761e"
                 ],
                 "3": [
                     "versions.yml:md5,0cbacd88674c22fcac104444bb04a386",
@@ -131,13 +113,7 @@
                     ]
                 ],
                 "multiqc_files": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.kraken2.report.txt:md5,4227755fe40478b8d7dc8634b489761e"
-                    ]
+                    "test.kraken2.report.txt:md5,4227755fe40478b8d7dc8634b489761e"
                 ],
                 "versions": [
                     "versions.yml:md5,0cbacd88674c22fcac104444bb04a386",
@@ -149,7 +125,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.1"
         },
-        "timestamp": "2024-05-22T10:39:11.065987706"
+        "timestamp": "2024-07-31T17:33:56.26437485"
     },
     "sarscov2 illumina paired end with parents [fastq]": {
         "content": [
@@ -176,13 +152,7 @@
                     ]
                 ],
                 "2": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.kraken2.report.txt:md5,4227755fe40478b8d7dc8634b489761e"
-                    ]
+                    "test.kraken2.report.txt:md5,4227755fe40478b8d7dc8634b489761e"
                 ],
                 "3": [
                     "versions.yml:md5,0cbacd88674c22fcac104444bb04a386",
@@ -210,13 +180,7 @@
                     ]
                 ],
                 "multiqc_files": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.kraken2.report.txt:md5,4227755fe40478b8d7dc8634b489761e"
-                    ]
+                    "test.kraken2.report.txt:md5,4227755fe40478b8d7dc8634b489761e"
                 ],
                 "versions": [
                     "versions.yml:md5,0cbacd88674c22fcac104444bb04a386",
@@ -228,6 +192,6 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.1"
         },
-        "timestamp": "2024-05-22T10:39:24.121519717"
+        "timestamp": "2024-07-31T17:34:16.269626373"
     }
 }