Updated samshee

CHANGELOG.md

@@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#216](https://github.com/nf-core/demultiplex/pull/216) List fastq reports for R1 and R2 separately in multiqc report.
 - [#219](https://github.com/nf-core/demultiplex/pull/219) Modified workflow to store samplesheet in results folder.
 - [#217](https://github.com/nf-core/demultiplex/pull/217) Update all nf-core modules and tests.
+- [#240](https://github.com/nf-core/demultiplex/pull/240) Updated samshee, stub script and error strategy
 
 ### `Fixed`
 

conf/modules.config

@@ -233,6 +233,10 @@ process {
             mode: params.publish_dir_mode
         ]
     }
+// Samshee should fail the entire pipeline immediately as it validated the illumina samplesheet to be valid before the pipeline runs. As such, it should not be running more than once & if it fails should stop the pipeline
+    withName: SAMSHEE {
+        errorStrategy = "terminate"
+    }
 
 }
 

modules/local/samshee/main.nf

@@ -45,90 +45,10 @@ process SAMSHEE {
 
     stub:
     """
-    #Generate minimal samplesheet
-    cat <<-END_SAMPLE_SHEET > minimal_samplesheet.csv
-    [Header]
-    FileFormatVersion,2
-    RunName,Run_001
-    Instrument Type,NextSeq 1000
-    InstrumentPlatform,NextSeq 1000
-
-    [Reads]
-    Read1Cycles,150
-    Read2Cycles,150
-    Index1Cycles,8
-    Index2Cycles,8
-
-    [Settings]
-
-    [Data]
-    Sample_ID,Sample_Name,Description,Sample_Project
-    Sample1,Sample1,,
-    END_SAMPLE_SHEET
-
-
-    #Generate minimal schema validator file
-    cat <<-END_SCHEMA > minimal_schema.json
-    {
-    "type": "object",
-    "properties": {
-        "Header": {
-        "type": "object",
-        "properties": {
-            "FileFormatVersion": { "type": "integer" },
-            "RunName": { "type": "string" },
-            "Instrument Type": { "type": "string" },
-            "InstrumentPlatform": { "type": "string" }
-        },
-        "required": ["FileFormatVersion", "RunName", "Instrument Type", "InstrumentPlatform"]
-        },
-        "Reads": {
-        "type": "object",
-        "properties": {
-            "Read1Cycles": { "type": "integer" },
-            "Read2Cycles": { "type": "integer" },
-            "Index1Cycles": { "type": "integer" },
-            "Index2Cycles": { "type": "integer" }
-        },
-        "required": ["Read1Cycles", "Read2Cycles", "Index1Cycles", "Index2Cycles"]
-        },
-        "Settings": {
-        "type": "object"
-        },
-        "Data": {
-        "type": "array",
-        "items": {
-            "type": "object",
-            "properties": {
-            "Sample_ID": { "type": "string" },
-            "Sample_Name": { "type": "string" },
-            "Description": { "type": "string" },
-            "Sample_Project": { "type": "string" }
-            },
-            "required": ["Sample_ID", "Sample_Name", "Description", "Sample_Project"]
-        }
-        }
-    },
-    "required": ["Header", "Reads", "Settings", "Data"]
-    }
-    END_SCHEMA
-
-    # Run validation command and capture output
-    output=\$(validate_samplesheet.py minimal_samplesheet.csv minimal_schema.json  2>&1)
-    status=\$?
-    # Check if validation failed
-    if echo "\$output" | grep -q "Validation failed:"; then
-        echo "\$output"  # Print output for debugging
-        exit 1  # Fail the process if validation failed
-    fi
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         samshee: \$( python -m pip show --version samshee | grep "Version" | sed -e "s/Version: //g" )
         python: \$( python --version | sed -e "s/Python //g" )
     END_VERSIONS
-
-    # If no validation errors, process exits with status 0
-    exit \$status
     """
 }

tests/pipeline/fqtk.nf.test.snap

@@ -4,7 +4,7 @@
             "demux-metrics.txt:md5,1d587fa959f9129155314cf531103347"
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "24.04.3"
         },
         "timestamp": "2023-10-17T08:06:53+0000"
@@ -14,7 +14,7 @@
             "{CSV2TSV={sed=4.8}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, FQTK={fqtk=0.2.1}, MD5SUM={md5sum=8.3}, UNTAR_FLOWCELL={untar=1.34}, Workflow={nf-core/demultiplex=v1.5.0dev}}"
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "23.10.0"
         },
         "timestamp": "2024-08-02T19:57:17.122084549"

tests/pipeline/kraken.nf.test.snap

@@ -15,7 +15,7 @@
                                     "laneBarcode.html:md5,2bbdae3ee57151eab520c966597d7438"
                                 ],
                                 [
-                                    
+
                                 ]
                             ]
                         ],
@@ -36,7 +36,7 @@
                                     "laneBarcode.html:md5,48842c23b9a2816aec540177df870968"
                                 ],
                                 [
-                                    
+
                                 ]
                             ]
                         ]
@@ -56,7 +56,7 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
         "timestamp": "2024-08-09T17:17:23.034777828"
@@ -66,7 +66,7 @@
             "{BCL2FASTQ={bcl2fastq=2.20.0.422}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, KRAKEN2={kraken2=2.1.3, pigz=2.8}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.0dev}}"
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
         "timestamp": "2024-08-09T17:17:22.999406989"
@@ -79,9 +79,9 @@
             "kraken-top-n-plot.txt:md5,84f10e652a1e2b98f96ffbe1a8ffe114"
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
         "timestamp": "2024-08-09T17:17:23.014483899"
     }
-}
+}

tests/pipeline/mkfastq.nf.test.snap

@@ -4,7 +4,7 @@
             "{CELLRANGER_MKFASTQ={cellranger=8.0.0}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, UNTAR_FLOWCELL={untar=1.34}, Workflow={nf-core/demultiplex=v1.5.0dev}}"
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "23.10.0"
         },
         "timestamp": "2024-08-02T20:09:53.707554042"
@@ -22,9 +22,9 @@
             "IndexMetricsOut.bin:md5,9e688c58a5487b8eaf69c9e1005ad0bf"
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "24.04.3"
         },
         "timestamp": "2024-07-23T23:50:42.910185053"
     }
-}
+}

tests/pipeline/sgdemux.nf.test.snap

@@ -4,7 +4,7 @@
             "{FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, SGDEMUX={sgdemux=1.1.1}, UNTAR_FLOWCELL={untar=1.34}, Workflow={nf-core/demultiplex=v1.5.0dev}}"
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "23.10.0"
         },
         "timestamp": "2024-08-02T19:58:24.75171605"
@@ -17,9 +17,9 @@
             "sample_barcode_hop_metrics.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "23.10.4"
         },
         "timestamp": "2023-10-17T08:01:14+0000"
     }
-}
+}

tests/pipeline/skip_tools.nf.test.snap

@@ -4,10 +4,10 @@
             "{BCLCONVERT={bclconvert=4.3.6}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.0dev}}"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-25T20:38:35.033660203"
+        "timestamp": "2024-08-12T17:21:22.50969783"
     },
     "skip_fastqc": {
         "content": [
@@ -31,9 +31,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-07T15:11:46.12688"
+        "timestamp": "2024-08-12T17:24:04.288349648"
     },
     "skip_fastp": {
         "content": [
@@ -57,9 +57,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-07T15:09:48.227109"
+        "timestamp": "2024-08-12T17:22:17.56007143"
     },
     "skip_multiqc": {
         "content": [
@@ -83,9 +83,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-07T15:14:47.991287"
+        "timestamp": "2024-08-12T17:27:14.471150173"
     },
     "skip_fastp_fastqc": {
         "content": [
@@ -109,49 +109,49 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-07T15:13:01.794999"
+        "timestamp": "2024-08-12T17:25:09.780834994"
     },
     "software_versions_skip_fastqc": {
         "content": [
             "{BCLCONVERT={bclconvert=4.3.6}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.0dev}}"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-25T20:40:12.591107775"
+        "timestamp": "2024-08-12T17:23:59.039256258"
     },
     "software_versions_skip_fastp_fastqc": {
         "content": [
             "{BCLCONVERT={bclconvert=4.3.6}, FALCO={falco=1.2.1}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.0dev}}"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-25T20:40:52.373539308"
+        "timestamp": "2024-08-12T17:25:01.70585844"
     },
     "software_versions_skip_multiqc": {
         "content": [
             "{BCLCONVERT={bclconvert=4.3.6}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.0dev}}"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-25T20:41:53.704450617"
+        "timestamp": "2024-08-12T17:27:03.685153368"
     },
     "software_versions_skip_fastp": {
         "content": [
             "{BCLCONVERT={bclconvert=4.3.6}, FALCO={falco=1.2.1}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.0dev}}"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-25T20:39:04.450501154"
+        "timestamp": "2024-08-12T17:22:14.728243247"
     },
     "skip_trimming": {
         "content": [
@@ -175,8 +175,8 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-07T15:08:34.10467"
+        "timestamp": "2024-08-12T17:21:22.530325808"
     }
-}
+}

tests/pipeline/test_pe.nf.test.snap

@@ -18,7 +18,7 @@
                                     "laneBarcode.html:md5,b5f0e5f5730d70513defa8024913b214"
                                 ],
                                 [
-                                    
+
                                 ]
                             ]
                         ],
@@ -39,7 +39,7 @@
                                     "laneBarcode.html:md5,eddae85d4b13d6fb5817df5fbfb756ff"
                                 ],
                                 [
-                                    
+
                                 ]
                             ]
                         ]
@@ -69,7 +69,7 @@
             "{BCL2FASTQ={bcl2fastq=2.20.0.422}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.0dev}}"
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "24.04.3"
         },
         "timestamp": "2024-07-31T13:03:01.047096473"
@@ -81,9 +81,9 @@
             "bcl2fastq_sample_counts.txt:md5,6454d154d69ffa563878f5b7fd3d9879"
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
         "timestamp": "2024-08-01T16:33:58.242361926"
     }
-}
+}