Bump bases2fastq (#3558)

* chore: Bump bases2fastq from 1.1.0 to 1.4.0 * fix: Move bases2fastq to dockerhub This way it's just reliant on Element * chore: Bump snapshot * chore: Bump bases2fastq to 1.8.0 * test(bases2fastq): Add versions * style: Fix indention
nf-core · Jun 8, 2024 · c651992 · c651992
1 parent 5890d9e
commit c651992
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Showing 3 changed files with 30 additions and 22 deletions.
diff --git a/modules/nf-core/bases2fastq/main.nf b/modules/nf-core/bases2fastq/main.nf
@@ -2,20 +2,20 @@ process BASES2FASTQ {
     tag "$meta.id"
     label 'process_high'
 
-    container "nf-core/bases2fastq:1.1.0"
+    container "docker.io/elembio/bases2fastq:1.8.0"
 
     input:
     tuple val(meta), path(run_manifest), path(run_dir)
 
     output:
-    tuple val(meta), path('output/Samples/*/*_R*.fastq.gz'), emit: sample_fastq
-    tuple val(meta), path('output/Samples/*/*.json')       , emit: sample_json
-    tuple val(meta), path('output/*.html')                 , emit: qc_report
-    tuple val(meta), path('output/RunStats.json')          , emit: run_stats
-    tuple val(meta), path('output/RunManifest.json')       , emit: generated_run_manifest
-    tuple val(meta), path('output/Metrics.csv')            , emit: metrics
-    tuple val(meta), path('output/UnassignedSequences.csv'), emit: unassigned
-    path "versions.yml"                             , emit: versions
+    tuple val(meta), path('output/Samples/**/*_R*.fastq.gz'), emit: sample_fastq
+    tuple val(meta), path('output/Samples/**/*_stats.json') , emit: sample_json
+    tuple val(meta), path('output/*.html')                  , emit: qc_report
+    tuple val(meta), path('output/RunStats.json')           , emit: run_stats
+    tuple val(meta), path('output/RunManifest.json')        , emit: generated_run_manifest
+    tuple val(meta), path('output/Metrics.csv')             , emit: metrics
+    tuple val(meta), path('output/UnassignedSequences.csv') , emit: unassigned
+    path "versions.yml"                                     , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/modules/nf-core/bases2fastq/tests/main.nf.test b/modules/nf-core/bases2fastq/tests/main.nf.test
@@ -38,10 +38,11 @@ nextflow_process {
                     process.out.generated_run_manifest,
                     process.out.unassigned,
                     process.out.sample_fastq,
+                    process.out.versions,
                     file(process.out.qc_report[0][1]).name,
                     file(process.out.run_stats[0][1]).name,
-                    file(process.out.sample_json[0][1]).name
-                    ).match() 
+                    file(process.out.sample_json[0][1]).name,
+                ).match()
                 }
             )
         }
@@ -67,10 +68,11 @@ nextflow_process {
                     process.out.generated_run_manifest,
                     process.out.unassigned,
                     process.out.sample_fastq,
+                    process.out.versions,
                     file(process.out.qc_report[0][1]).name,
                     file(process.out.run_stats[0][1]).name,
-                    file(process.out.sample_json[0][1]).name
-                    ).match() 
+                    file(process.out.sample_json[0][1]).name,
+                ).match()
                 }
             )
         }

diff --git a/modules/nf-core/bases2fastq/tests/main.nf.test.snap b/modules/nf-core/bases2fastq/tests/main.nf.test.snap
@@ -40,15 +40,18 @@
                     ]
                 ]
             ],
+            [
+                "versions.yml:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
             "Bases2Fastq-Sim_QC.html",
             "RunStats.json",
             "DefaultSample_stats.json"
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-03-19T16:28:23.376144712"
+        "timestamp": "2024-06-08T13:22:53.536627298"
     },
     "sim-data.tar.gz - bcl": {
         "content": [
@@ -58,7 +61,7 @@
                         "id": "sim-data",
                         "samplesheet": "/nf-core/test-datasets/demultiplex/testdata/sim-data/RunManifest.csv"
                     },
-                    "Metrics.csv:md5,a8094b308b5653071ac029a27733e4a6"
+                    "Metrics.csv:md5,1db1769b9b5917b8353e05bf8fd699c7"
                 ]
             ],
             [
@@ -67,7 +70,7 @@
                         "id": "sim-data",
                         "samplesheet": "/nf-core/test-datasets/demultiplex/testdata/sim-data/RunManifest.csv"
                     },
-                    "RunManifest.json:md5,a07dce8ee25c2a6f9355b677c26b53e2"
+                    "RunManifest.json:md5,d584cdf00f577937a6cb691bb5331fe8"
                 ]
             ],
             [
@@ -86,19 +89,22 @@
                         "samplesheet": "/nf-core/test-datasets/demultiplex/testdata/sim-data/RunManifest.csv"
                     },
                     [
-                        "DefaultSample_R1.fastq.gz:md5,eeec01b3de76c2b849b0f08b18081a2d",
-                        "DefaultSample_R2.fastq.gz:md5,ccbd16b893d2a069b91d5e4284109868"
+                        "DefaultSample_R1.fastq.gz:md5,44ff0899ad4568a5cab7ccb7df9928e8",
+                        "DefaultSample_R2.fastq.gz:md5,f57acd0136bac5780d1592a5de7005ef"
                     ]
                 ]
             ],
-            "Bases2Fastq-Sim_QC.html",
+            [
+                "versions.yml:md5,018cd865ddeaf6d03a2cabf6da664ec8"
+            ],
+            "20230404-Bases2Fastq-Sim_QC.html",
             "RunStats.json",
             "DefaultSample_stats.json"
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-03-19T16:20:46.509235687"
+        "timestamp": "2024-06-08T13:22:38.54589349"
     }
 }