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nf-core · Aug 15, 2024 · 452e918 · 452e918
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commit 452e918
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Showing 2 changed files with 22 additions and 62 deletions.
diff --git a/modules.json b/modules.json
@@ -8,107 +8,77 @@
                     "bases2fastq": {
                         "branch": "master",
                         "git_sha": "c651992bf8425fecefe14085ff486f42172cba77",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bcl2fastq": {
                         "branch": "master",
                         "git_sha": "22261833fced91665b986c6833e91a4a5cccb0a9",
-                        "installed_by": [
-                            "bcl_demultiplex"
-                        ]
+                        "installed_by": ["bcl_demultiplex"]
                     },
                     "bclconvert": {
                         "branch": "master",
                         "git_sha": "22261833fced91665b986c6833e91a4a5cccb0a9",
-                        "installed_by": [
-                            "bcl_demultiplex"
-                        ]
+                        "installed_by": ["bcl_demultiplex"]
                     },
                     "cellranger/mkfastq": {
                         "branch": "master",
                         "git_sha": "61123e49c6034920eb6f312ad71e4815a7853257",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "checkqc": {
                         "branch": "master",
                         "git_sha": "337bc962d03c2e08a728c9bf731a2148e323e731",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "falco": {
                         "branch": "master",
                         "git_sha": "a236d2c2ec9e68db9b8501105d804acb359552b5",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "fastp": {
                         "branch": "master",
                         "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "fqtk": {
                         "branch": "master",
                         "git_sha": "c60c14b285b89bdd0607e371417dadb80385ad6e",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "kraken2/kraken2": {
                         "branch": "master",
                         "git_sha": "a13d5d945742a60bbef6e5c177e81cda540f75dc",
-                        "installed_by": [
-                            "fastq_contam_seqtk_kraken"
-                        ]
+                        "installed_by": ["fastq_contam_seqtk_kraken"]
                     },
                     "md5sum": {
                         "branch": "master",
                         "git_sha": "1164836d4d3922ab937865b17086485f0f472748",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "seqtk/sample": {
                         "branch": "master",
                         "git_sha": "730f3aee80d5f8d0b5fc532202ac59361414d006",
-                        "installed_by": [
-                            "fastq_contam_seqtk_kraken"
-                        ]
+                        "installed_by": ["fastq_contam_seqtk_kraken"]
                     },
                     "sgdemux": {
                         "branch": "master",
                         "git_sha": "574074e6ea2497b53df1f226473a8c71524af0d0",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "untar": {
                         "branch": "master",
                         "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     }
                 }
             },
@@ -117,40 +87,30 @@
                     "bcl_demultiplex": {
                         "branch": "master",
                         "git_sha": "22261833fced91665b986c6833e91a4a5cccb0a9",
-                        "installed_by": [
-                            "subworkflows"
-                        ]
+                        "installed_by": ["subworkflows"]
                     },
                     "fastq_contam_seqtk_kraken": {
                         "branch": "master",
                         "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
-                        "installed_by": [
-                            "subworkflows"
-                        ]
+                        "installed_by": ["subworkflows"]
                     },
                     "utils_nextflow_pipeline": {
                         "branch": "master",
                         "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
-                        "installed_by": [
-                            "subworkflows"
-                        ]
+                        "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
                         "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
-                        "installed_by": [
-                            "subworkflows"
-                        ]
+                        "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {
                         "branch": "master",
                         "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
-                        "installed_by": [
-                            "subworkflows"
-                        ]
+                        "installed_by": ["subworkflows"]
                     }
                 }
             }
         }
     }
-}
+}
diff --git a/tests/pipeline/mkfastq.nf.test b/tests/pipeline/mkfastq.nf.test
@@ -40,7 +40,7 @@ nextflow_pipeline {
                     path("${outputDir}/cellranger-tiny-bcl-simple/L001/undetermined/Undetermined_S0_L001_R1_001.fastq.gz"),
                     path("${outputDir}/cellranger-tiny-bcl-simple/L001/undetermined/Undetermined_S0_L001_R2_001.fastq.gz"),
                     path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.html").exists(),
-                    path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001.fastp.html").exists(),                    
+                    path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001.fastp.html").exists(),
                     path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001.fastp.json"),
                     path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.json"),
                     path("${outputDir}/cellranger-tiny-bcl-simple/InterOp/IndexMetricsOut.bin")