Update the module: nanoq (#5964)

* update nanoq module * update nf-test
nf-core · Jul 11, 2024 · cf05b61 · cf05b61
1 parent 0c827c3
commit cf05b61
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Showing 3 changed files with 31 additions and 30 deletions.
diff --git a/modules/nf-core/nanoq/main.nf b/modules/nf-core/nanoq/main.nf
@@ -12,18 +12,19 @@ process NANOQ {
     val(output_format) //One of the following: fastq, fastq.gz, fastq.bz2, fastq.lzma, fasta, fasta.gz, fasta.bz2, fasta.lzma.
 
     output:
-    tuple val(meta), path("*.stats")                                                  , emit: stats
-    tuple val(meta), path("*_nanoq.${output_format}")                                 , emit: reads
+    tuple val(meta), path("*.{stats,json}")                                           , emit: stats
+    tuple val(meta), path("*_filtered.${output_format}")                              , emit: reads
     path "versions.yml"                                                               , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}_nanoq"
+    def prefix = task.ext.prefix ?: "${meta.id}_filtered"
     """
     nanoq -i $ontreads \\
+        ${args} \\
         -r ${prefix}.stats \\
         -o ${prefix}.$output_format
 
@@ -35,7 +36,7 @@ process NANOQ {
 
     stub:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}_nanoq"
+    def prefix = task.ext.prefix ?: "${meta.id}_filtered"
     """
     echo "" | gzip > ${prefix}.$output_format
     touch ${prefix}.stats

diff --git a/modules/nf-core/nanoq/meta.yml b/modules/nf-core/nanoq/meta.yml
@@ -42,7 +42,7 @@ output:
   - stats:
       type: file
       description: Summary report of reads statistics.
-      pattern: "*.stats"
+      pattern: "*.{stats,json}"
 
   - reads:
       type: file

diff --git a/modules/nf-core/nanoq/tests/main.nf.test.snap b/modules/nf-core/nanoq/tests/main.nf.test.snap
@@ -8,7 +8,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                        "test_filtered.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
                     ]
                 ],
                 "1": [
@@ -17,7 +17,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.fastq.gz:md5,7567d853ada6ac142332619d0b541d76"
+                        "test_filtered.fastq.gz:md5,7567d853ada6ac142332619d0b541d76"
                     ]
                 ],
                 "2": [
@@ -29,7 +29,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.fastq.gz:md5,7567d853ada6ac142332619d0b541d76"
+                        "test_filtered.fastq.gz:md5,7567d853ada6ac142332619d0b541d76"
                     ]
                 ],
                 "stats": [
@@ -38,7 +38,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                        "test_filtered.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
                     ]
                 ],
                 "versions": [
@@ -50,7 +50,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.1"
         },
-        "timestamp": "2024-07-02T10:00:12.328317"
+        "timestamp": "2024-07-11T11:39:32.117229"
     },
     "sarscov2 - nanopore_compressed_gz - stub": {
         "content": [
@@ -61,7 +61,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_filtered.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
@@ -70,7 +70,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        "test_filtered.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "2": [
@@ -82,7 +82,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        "test_filtered.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "stats": [
@@ -91,7 +91,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_filtered.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
@@ -103,7 +103,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.1"
         },
-        "timestamp": "2024-07-02T10:00:24.873908"
+        "timestamp": "2024-07-11T11:42:06.039307"
     },
     "sarscov2 - nanopore_compressed_bz2": {
         "content": [
@@ -114,7 +114,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                        "test_filtered.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
                     ]
                 ],
                 "1": [
@@ -123,7 +123,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.fastq.bz2:md5,b53cf14fd4eb5b16c459c41f03cc8a4b"
+                        "test_filtered.fastq.bz2:md5,b53cf14fd4eb5b16c459c41f03cc8a4b"
                     ]
                 ],
                 "2": [
@@ -135,7 +135,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.fastq.bz2:md5,b53cf14fd4eb5b16c459c41f03cc8a4b"
+                        "test_filtered.fastq.bz2:md5,b53cf14fd4eb5b16c459c41f03cc8a4b"
                     ]
                 ],
                 "stats": [
@@ -144,7 +144,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                        "test_filtered.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
                     ]
                 ],
                 "versions": [
@@ -156,7 +156,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.1"
         },
-        "timestamp": "2024-07-02T10:00:16.460467"
+        "timestamp": "2024-07-11T11:39:36.674647"
     },
     "sarscov2 - nanopore_compressed_lzma": {
         "content": [
@@ -167,7 +167,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                        "test_filtered.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
                     ]
                 ],
                 "1": [
@@ -176,7 +176,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.fastq.lzma:md5,65dda701689f913734dc245b68c89e07"
+                        "test_filtered.fastq.lzma:md5,65dda701689f913734dc245b68c89e07"
                     ]
                 ],
                 "2": [
@@ -188,7 +188,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.fastq.lzma:md5,65dda701689f913734dc245b68c89e07"
+                        "test_filtered.fastq.lzma:md5,65dda701689f913734dc245b68c89e07"
                     ]
                 ],
                 "stats": [
@@ -197,7 +197,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                        "test_filtered.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
                     ]
                 ],
                 "versions": [
@@ -209,7 +209,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.1"
         },
-        "timestamp": "2024-07-02T10:00:20.825269"
+        "timestamp": "2024-07-11T11:39:41.51344"
     },
     "sarscov2 - nanopore_uncompressed": {
         "content": [
@@ -220,7 +220,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                        "test_filtered.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
                     ]
                 ],
                 "1": [
@@ -229,7 +229,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.fastq:md5,7567d853ada6ac142332619d0b541d76"
+                        "test_filtered.fastq:md5,7567d853ada6ac142332619d0b541d76"
                     ]
                 ],
                 "2": [
@@ -241,7 +241,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.fastq:md5,7567d853ada6ac142332619d0b541d76"
+                        "test_filtered.fastq:md5,7567d853ada6ac142332619d0b541d76"
                     ]
                 ],
                 "stats": [
@@ -250,7 +250,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                        "test_filtered.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
                     ]
                 ],
                 "versions": [
@@ -262,6 +262,6 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.1"
         },
-        "timestamp": "2024-07-02T10:00:07.8772"
+        "timestamp": "2024-07-11T11:39:26.868897"
     }
 }