Now emitting trimmed reads

nf-core · Jun 21, 2024 · f7c9361 · f7c9361
1 parent 5cab379
commit f7c9361
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Showing 2 changed files with 56 additions and 12 deletions.
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf
@@ -12,9 +12,9 @@ include { FASTP                 } from '../../../modules/nf-core/fastp/main'
 //
 import groovy.json.JsonSlurper
 
-def getFastpReadsAfterFiltering(json_file) {
+def getFastpReadsAfterFiltering(json_file, min_num_reads) {
 
-    if ( workflow.stubRun ) { return 0 }
+    if ( workflow.stubRun ) { return min_num_reads }
 
     def Map json = (Map) new JsonSlurper().parseText(json_file.text).get('summary')
     return json['after_filtering']['total_reads'].toLong()
@@ -115,7 +115,7 @@ workflow FASTQ_FASTQC_UMITOOLS_FASTP {
             .out
             .reads
             .join(trim_json)
-            .map { meta, reads, json -> [ meta, reads, getFastpReadsAfterFiltering(json) ] }
+            .map { meta, reads, json -> [ meta, reads, getFastpReadsAfterFiltering(json, min_trimmed_reads.toLong()) ] }
             .set { ch_num_trimmed_reads }
 
         ch_num_trimmed_reads

diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test.snap
@@ -550,7 +550,16 @@
         "content": [
             {
                 "0": [
-
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
                 ],
                 "1": [
                     [
@@ -567,17 +576,30 @@
                             "id": "test",
                             "single_end": false
                         },
-                        0
+                        1
                     ]
                 ],
                 "11": [
-
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "12": [
-
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "13": [
                     "versions.yml:md5,85bd0117e5778fff18e3920972a296ad",
+                    "versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0",
                     "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e"
                 ],
                 "2": [
@@ -662,13 +684,34 @@
                     ]
                 ],
                 "fastqc_trim_html": [
-
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "fastqc_trim_zip": [
-
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "reads": [
-
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
                 ],
                 "trim_html": [
                     [
@@ -703,7 +746,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        0
+                        1
                     ]
                 ],
                 "trim_reads_fail": [
@@ -717,6 +760,7 @@
                 ],
                 "versions": [
                     "versions.yml:md5,85bd0117e5778fff18e3920972a296ad",
+                    "versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0",
                     "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e"
                 ]
             }
@@ -725,6 +769,6 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-21T12:21:48.845872"
+        "timestamp": "2024-06-21T14:46:58.329605"
     }
 }