Code review

.github/workflows/ci.yml

@@ -45,7 +45,17 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        config: ["test", "test_cram", "test_chr", "test_no_bai", "test_no_crai"]
+        config:
+          [
+            "test",
+            "test_cram",
+            "test_chr",
+            "test_no_bai",
+            "test_no_crai",
+            "test_no_stats",
+            "test_no_qc",
+            "test_collate_fast",
+          ]
         # Nextflow versions
         include:
           # Test pipeline minimum Nextflow version

CHANGELOG.md

@@ -3,7 +3,7 @@
 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).
 
-## v2.0.0dev - [date]
+## v2.0.0 - Annie Easley
 
 Initial release of nf-core/bamtofastq, created with the [nf-core](https://nf-co.re/) template.
 

conf/test.config

@@ -17,7 +17,7 @@ params {
     // Limit resources so that this can run on GitHub Actions
     max_cpus = 2
     max_memory = '6.GB'
-    max_time = '48.h'
+    max_time = '6.h'
 
     // Input data
     input = "https://raw.githubusercontent.com/nf-core/test-datasets/bamtofastq/samplesheet/test_bam_samplesheet.csv"

conf/test_chr.config

@@ -15,7 +15,7 @@ params {
     // Limit resources so that this can run on GitHub Actions
     max_cpus = 2
     max_memory = '6.GB'
-    max_time = '48.h'
+    max_time = '6.h'
 
     // Input data
     input = "https://raw.githubusercontent.com/nf-core/test-datasets/bamtofastq/samplesheet/test_chr_samplesheet.csv"

conf/test_collate_fast.config

@@ -17,7 +17,7 @@ params {
     // Limit resources so that this can run on GitHub Actions
     max_cpus = 2
     max_memory = '6.GB'
-    max_time = '48.h'
+    max_time = '6.h'
 
     // Input data
     input = "https://raw.githubusercontent.com/nf-core/test-datasets/bamtofastq/samplesheet/test_bam_samplesheet.csv"

conf/test_cram.config

@@ -15,7 +15,7 @@ params {
     // Limit resources so that this can run on GitHub Actions
     max_cpus = 2
     max_memory = '6.GB'
-    max_time = '48.h'
+    max_time = '6.h'
 
     // Input data
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/bamtofastq/samplesheet/test_cram_samplesheet.csv'

conf/test_no_bai.config

@@ -18,7 +18,7 @@ params {
     // Limit resources so that this can run on GitHub Actions
     max_cpus = 2
     max_memory = '6.GB'
-    max_time = '48.h'
+    max_time = '6.h'
 
     // Input data
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/bamtofastq/samplesheet/test_bam_samplesheet_no_bai.csv'

conf/test_no_crai.config

@@ -19,7 +19,7 @@ params {
     // Limit resources so that this can run on GitHub Actions
     max_cpus = 2
     max_memory = '6.GB'
-    max_time = '48.h'
+    max_time = '6.h'
 
     // Input data
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/bamtofastq/samplesheet/test_cram_samplesheet_no_crai.csv'

conf/test_no_qc.config

@@ -17,7 +17,7 @@ params {
     // Limit resources so that this can run on GitHub Actions
     max_cpus = 2
     max_memory = '6.GB'
-    max_time = '48.h'
+    max_time = '6.h'
 
     // Input data
     input = "https://raw.githubusercontent.com/nf-core/test-datasets/bamtofastq/samplesheet/test_bam_samplesheet.csv"

conf/test_no_stats.config

@@ -17,7 +17,7 @@ params {
     // Limit resources so that this can run on GitHub Actions
     max_cpus = 2
     max_memory = '6.GB'
-    max_time = '48.h'
+    max_time = '6.h'
 
     // Input data
     input = "https://raw.githubusercontent.com/nf-core/test-datasets/bamtofastq/samplesheet/test_bam_samplesheet.csv"

nextflow.config

@@ -34,7 +34,7 @@ params {
     multiqc_methods_description = null
 
     // Boilerplate options
-    outdir                     = 'results'
+    outdir                     = null
     tracedir                   = "${params.outdir}/pipeline_info"
     publish_dir_mode           = 'copy'
     email                      = null
@@ -183,6 +183,7 @@ profiles {
     test_no_crai      { includeConfig 'conf/test_no_crai.config' }
     test_no_stats     { includeConfig 'conf/test_no_stats.config' }
     test_no_qc        { includeConfig 'conf/test_no_qc.config' }
+    test_collate_fast { includeConfig 'conf/test_collate_fast.config' }
 }
 
 // Load igenomes.config if required
@@ -232,7 +233,7 @@ manifest {
     description     = """Workflow converts one or multiple bam/cram files to fastq format"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version = '2.0'
+    version         = '2.0.0'
     doi             = ''
 }