Updated stub mkfastq (#6700)

nf-core · Sep 26, 2024 · a90a886 · a90a886
1 parent d1e0ec7
commit a90a886
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Showing 2 changed files with 16 additions and 25 deletions.
diff --git a/modules/nf-core/cellranger/mkfastq/main.nf b/modules/nf-core/cellranger/mkfastq/main.nf
@@ -48,34 +48,19 @@ process CELLRANGER_MKFASTQ {
     }
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    mkdir -p "${prefix}_outs/outs/fastq_path/sample/files/"
-    # data with something to avoid breaking nf-test java I/O stream, fastq
-    cat <<-FAKE_FQ > ${prefix}_outs/outs/fastq_path/fake_file.fastq
-    @SEQ_ID
-    GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
-    +
-    !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65
-    FAKE_FQ
-    gzip -n ${prefix}_outs/outs/fastq_path/fake_file.fastq
-
-    # data with something to avoid breaking nf-test java I/O stream, fastq_undetermined
-    cat <<-FAKE_FQ > ${prefix}_outs/outs/fastq_path/sample/files/fake_file.fastq
-    @SEQ_ID
-    GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
-    +
-    !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65
-    FAKE_FQ
-    gzip -n ${prefix}_outs/outs/fastq_path/sample/files/fake_file.fastq
-
     # data for reports output channel
     mkdir -p "${prefix}_outs/outs/fastq_path/Reports"
-
     # data for stats output channel
     mkdir -p "${prefix}_outs/outs/fastq_path/Stats"
-
     # data for interops output channel
     mkdir -p "${prefix}_outs/outs/interop_path/"
     touch "${prefix}_outs/outs/interop_path/IndexMetricsOut.bin"
+    # data for fastq channels
+    mkdir -p "${prefix}_outs/outs/fastq_path/sample/files/"
+    touch "${prefix}_outs/outs/fastq_path/Undetermined_fake_file.fastq"
+    touch "${prefix}_outs/outs/fastq_path/sample/files/fake_file.fastq"
+    gzip "${prefix}_outs/outs/fastq_path/Undetermined_fake_file.fastq"
+    gzip "${prefix}_outs/outs/fastq_path/sample/files/fake_file.fastq"
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/cellranger/mkfastq/tests/main.nf.test.snap b/modules/nf-core/cellranger/mkfastq/tests/main.nf.test.snap
@@ -54,11 +54,17 @@
                         "id": "test",
                         "lane": 1
                     },
-                    "fake_file.fastq.gz:md5,8e16c1f4a441cbb3b7de374d2c924da7"
+                    "fake_file.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ]
             ],
             [
-
+                [
+                    {
+                        "id": "test",
+                        "lane": 1
+                    },
+                    "Undetermined_fake_file.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
             ],
             [
                 [
@@ -75,9 +81,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-15T20:01:48.013075"
+        "timestamp": "2024-09-26T18:47:18.168033527"
     },
     "cellranger - tiny - illumina": {
         "content": [