Merge pull request #124 from nf-core/dev

Dev -> Master for 1.3.1 patch release

CHANGELOG.md

@@ -3,6 +3,13 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## 1.3.1 - 2023-06-05
+
+### `Fixed`
+
+- [#103](https://github.com/nf-core/demultiplex/issues/103) `-profile test` failing due to relative path in `flowcell_input.csv`
+- [#122](https://github.com/nf-core/demultiplex/pull/122) Fails gracefully if an error is encountered
+
 ## 1.3.0 - 2023-05-31
 
 ### `Added`

conf/test.config

@@ -20,7 +20,7 @@ params {
     max_time   = '6.h'
 
     // Input data
-    input = "${projectDir}/assets/inputs/flowcell_input.csv"
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/flowcell_input.csv'
     demultiplexer = 'bclconvert'
 
 }

conf/test_bases2fastq.config

@@ -20,6 +20,6 @@ params {
     max_time   = '6.h'
 
     // Input data
-    input = "${projectDir}/assets/inputs/b2fq-samplesheet.csv"
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/b2fq-samplesheet.csv'
     demultiplexer = 'bases2fastq'
 }

conf/test_bcl2fastq.config

@@ -20,7 +20,7 @@ params {
     max_time   = '6.h'
 
     // Input data
-    input = "${projectDir}/assets/inputs/flowcell_input.csv"
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/flowcell_input.csv'
     demultiplexer = 'bcl2fastq'
 
 }

conf/test_fqtk.config

@@ -20,6 +20,6 @@ params {
     max_time   = '1.h'
 
     // Input data
-    input = "${projectDir}/assets/inputs/fqtk-samplesheet.csv"
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/fqtk-samplesheet.csv'
     demultiplexer = 'fqtk'
 }

conf/test_full.config

@@ -15,6 +15,6 @@ cleanup = true
 params {
     config_profile_name        = 'Full test profile'
     config_profile_description = 'Full test dataset to check pipeline function'
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.1.0/samplesheet.csv'
-    demultiplexer = "bcl2fastq"
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/samplesheet_full.csv'
+    demultiplexer = 'bcl2fastq'
 }

conf/test_sgdemux.config

@@ -20,6 +20,6 @@ params {
     max_time   = '1.h'
 
     // Input data
-    input = "${projectDir}/assets/inputs/sgdemux-samplesheet.csv"
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/sgdemux-samplesheet.csv'
     demultiplexer = 'sgdemux'
 }

docs/usage.md

@@ -33,7 +33,7 @@ DDMMYY_SERIAL_NUMBER_FC3,/path/to/SampleSheet3.csv,3,/path/to/sequencer/output3
 | `lane`        | Optional lane number. When a lane number is provided, only the given lane will be demultiplexed                   |
 | `run_dir`     | Full path to the Illumina sequencer output directory or a `tar.gz` file containing the contents of said directory |
 
-An [example samplesheet](../assets/inputs/flowcell_input.csv) has been provided with the pipeline.
+An [example samplesheet](https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/flowcell_input.csv) has been provided with the pipeline.
 
 Note `run_dir` must lead to a `tar.gz` for compatability with the demultiplexers sgdemux and fqtk
 

nextflow.config

@@ -227,7 +227,7 @@ manifest {
     description     = """Demultiplexing pipeline for Illumina sequencing data"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '1.3.0'
+    version         = '1.3.1'
     doi             = '10.5281/zenodo.7153103'
 }
 

tests/functions/demultiplex.nf.test

@@ -12,7 +12,7 @@ nextflow_function {
         when {
             function {
                 """
-                input[0] = 'https://raw.githubusercontent.com/nf-core/demultiplex/master/assets/inputs/flowcell_input.csv'
+                input[0] = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/flowcell_input.csv'
                 """
             }
         }

tests/functions/demultiplex.nf.test.snap

@@ -0,0 +1,6 @@
+{
+    "Test Function extract_csv": {
+        "content": null,
+        "timestamp": "2023-06-05T10:39:32+0000"
+    }
+}

tests/pipeline/default/bases2fastq.nf.test

@@ -7,7 +7,7 @@ nextflow_pipeline {
 
         when {
             params {
-                input = "$baseDir/assets/inputs/b2fq-samplesheet.csv"
+                input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/b2fq-samplesheet.csv'
                 demultiplexer = 'bases2fastq'
                 outdir = "$outputDir"
             }

tests/pipeline/default/bcl2fastq.nf.test

@@ -8,7 +8,7 @@ nextflow_pipeline {
         when {
             params {
                 outdir = "$outputDir"
-                input = "${baseDir}/assets/inputs/flowcell_input.csv"
+                input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/flowcell_input.csv'
                 demultiplexer = 'bcl2fastq'
             }
         }

tests/pipeline/default/bclconvert.nf.test

@@ -7,7 +7,7 @@ nextflow_pipeline {
 
         when {
             params {
-                input = "$baseDir/assets/inputs/flowcell_input.csv"
+                input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/flowcell_input.csv'
                 demultiplexer = 'bclconvert'
                 outdir = "$outputDir"
             }

tests/pipeline/default/fqtk.nf.test

@@ -7,7 +7,7 @@ nextflow_pipeline {
 
         when {
             params {
-                input = "$baseDir/assets/inputs/fqtk-samplesheet.csv"
+                input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/fqtk-samplesheet.csv'
                 demultiplexer = 'fqtk'
                 outdir = "$outputDir"
             }

tests/pipeline/default/sgdemux.nf.test

@@ -7,7 +7,7 @@ nextflow_pipeline {
 
         when {
             params {
-                input = "$baseDir/assets/inputs/sgdemux-samplesheet.csv"
+                input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/sgdemux-samplesheet.csv'
                 demultiplexer = 'sgdemux'
                 outdir = "$outputDir"
             }

tests/pipeline/default/skip_tools.nf.test

@@ -8,7 +8,7 @@ nextflow_pipeline {
 
         when {
             params {
-                input = "$baseDir/assets/inputs/flowcell_input.csv"
+                input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/flowcell_input.csv'
                 demultiplexer = 'bclconvert'
                 trim_fastq  = false
                 outdir = "$outputDir"
@@ -33,7 +33,7 @@ nextflow_pipeline {
 
         when {
             params {
-                input = "$baseDir/assets/inputs/flowcell_input.csv"
+                input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/flowcell_input.csv'
                 demultiplexer = 'bclconvert'
                 skip_tools = "fastp"
                 outdir = "$outputDir"
@@ -58,7 +58,7 @@ nextflow_pipeline {
 
         when {
             params {
-                input = "$baseDir/assets/inputs/flowcell_input.csv"
+                input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/flowcell_input.csv'
                 demultiplexer = 'bclconvert'
                 skip_tools = "fastqc"
                 outdir = "$outputDir"
@@ -84,7 +84,7 @@ nextflow_pipeline {
 
         when {
             params {
-                input = "$baseDir/assets/inputs/flowcell_input.csv"
+                input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/flowcell_input.csv'
                 demultiplexer = 'bclconvert'
                 skip_tools = "fastp,fastqc"
                 outdir = "$outputDir"

workflows/demultiplex.nf

@@ -21,7 +21,7 @@ def checkPathParamList = [
 for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
 
 // Check mandatory parameters
-if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
+if (params.input) { ch_input = file(params.input) } else { Nextflow.error 'Input samplesheet not specified!' }
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     CONFIG FILES
@@ -84,7 +84,9 @@ workflow DEMULTIPLEX {
 
     // Sanitize inputs and separate input types
     // FQTK's input contains an extra column 'per_flowcell_manifest' so it is handled seperately
-    // For reference - assets/inputs/fqtk-samplesheet.csv vs assets/inputs/sgdemux-samplesheet
+    // For reference:
+    //      https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/fqtk-samplesheet.csv VS 
+    //      https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/sgdemux-samplesheet.csv
     if (demultiplexer == 'fqtk'){
         ch_inputs = extract_csv_fqtk(ch_input)
 
@@ -190,7 +192,7 @@ workflow DEMULTIPLEX {
             ch_versions = ch_versions.mix(SINGULAR_DEMULTIPLEX.out.versions)
             break
         default:
-            exit 1, "Unknown demultiplexer: ${demultiplexer}"
+            Nextflow.error "Unknown demultiplexer: ${demultiplexer}"
     }
     ch_raw_fastq.dump(tag: "DEMULTIPLEX::Demultiplexed Fastq",{FormattingService.prettyFormat(it)})
 
@@ -319,14 +321,14 @@ def extract_csv(input_csv, input_schema=null) {
                     diff in all_columns ? missing_columns.add(diff) : wrong_columns.add(diff)
                 }
                 if(missing_columns.size() > 0){
-                    exit 1, "[Samplesheet Error] The column(s) $missing_columns is/are not present. The header should look like: $all_columns"
+                    Nextflow.error "[Samplesheet Error] The column(s) $missing_columns is/are not present. The header should look like: $all_columns"
                 }
                 else {
-                    exit 1, "[Samplesheet Error] The column(s) $wrong_columns should not be in the header. The header should look like: $all_columns"
+                    Nextflow.error "[Samplesheet Error] The column(s) $wrong_columns should not be in the header. The header should look like: $all_columns"
                 }
             }
             else {
-                exit 1, "[Samplesheet Error] The columns $row are not in the right order. The header should look like: $all_columns"
+                Nextflow.error "[Samplesheet Error] The columns $row are not in the right order. The header should look like: $all_columns"
             }
 
         }
@@ -343,7 +345,7 @@ def extract_csv(input_csv, input_schema=null) {
             row[column] ?: missing_mandatory_columns.add(column)
         }
         if(missing_mandatory_columns.size > 0){
-            exit 1, "[Samplesheet Error] The mandatory column(s) $missing_mandatory_columns is/are empty on line $row_count"
+            Nextflow.error "[Samplesheet Error] The mandatory column(s) $missing_mandatory_columns is/are empty on line $row_count"
         }
 
         def output = []
@@ -353,7 +355,7 @@ def extract_csv(input_csv, input_schema=null) {
             content = row[key]
 
             if(!(content ==~ col.value['pattern']) && col.value['pattern'] != '' && content != '') {
-                exit 1, "[Samplesheet Error] The content of column '$key' on line $row_count does not match the pattern '${col.value['pattern']}'"
+                Nextflow.error "[Samplesheet Error] The content of column '$key' on line $row_count does not match the pattern '${col.value['pattern']}'"
             }
 
             if(col.value['content'] == 'path'){