Merge pull request #365 from drpatelh/sync

Create new folder on test-datasets for all samplesheets

Author: drpatelh

conf/test.config

@@ -20,7 +20,7 @@ params {
     max_time   = '6.h'
 
     // Input data to test amplicon analysis
-    input              = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
+    input              = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/v2.6/samplesheet_test_amplicon_illumina.csv'
     platform           = 'illumina'
     protocol           = 'amplicon'
     primer_set         = 'artic'

conf/test_full.config

@@ -15,7 +15,7 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full test of amplicon analysis
-    input              = 's3://ngi-igenomes/test-data/viralrecon/210212_K00102_0557_AHKN3LBBXY/samplesheet.csv'
+    input              = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/v2.6/samplesheet_full_amplicon_illumina.csv'
     platform           = 'illumina'
     protocol           = 'amplicon'
     primer_set         = 'artic'

conf/test_full_nanopore.config

@@ -16,7 +16,7 @@ params {
 
     // Input data for full test of amplicon analysis
     platform           = 'nanopore'
-    input              = 's3://ngi-igenomes/test-data/viralrecon/20210205_1526_X4_FAP51364_21fa8135/samplesheet.csv'
+    input              = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/v2.6/samplesheet_full_amplicon_nanopore.csv'
     fastq_dir          = 's3://ngi-igenomes/test-data/viralrecon/20210205_1526_X4_FAP51364_21fa8135/fastq_pass/'
     fast5_dir          = 's3://ngi-igenomes/test-data/viralrecon/20210205_1526_X4_FAP51364_21fa8135/fast5_pass/'
     sequencing_summary = 's3://ngi-igenomes/test-data/viralrecon/20210205_1526_X4_FAP51364_21fa8135/sequencing_summary.txt'

conf/test_full_sispa.config

@@ -15,7 +15,7 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full test of SISPA/metagenomics analysis
-    input    = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_full_illumina_sispa.csv'
+    input    = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/v2.6/samplesheet_full_metagenomic_illumina.csv'
     platform = 'illumina'
     protocol = 'metagenomic'
 

conf/test_nanopore.config

@@ -21,7 +21,7 @@ params {
 
     // Input data to test nanopore analysis
     platform           = 'nanopore'
-    input              = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_nanopore.csv'
+    input              = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/v2.6/samplesheet_test_amplicon_nanopore.csv'
     fastq_dir          = 's3://ngi-igenomes/test-data/viralrecon/minion_test/fastq_pass/'
     fast5_dir          = 's3://ngi-igenomes/test-data/viralrecon/minion_test/fast5_pass/'
     sequencing_summary = 's3://ngi-igenomes/test-data/viralrecon/minion_test/sequencing_summary.txt'

conf/test_sispa.config

@@ -20,7 +20,7 @@ params {
     max_time   = '6.h'
 
     // Input data to test SISPA/metagenomics analysis
-    input    = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_sispa.csv'
+    input    = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/v2.6/samplesheet_test_metagenomic_illumina.csv'
     platform = 'illumina'
     protocol = 'metagenomic'
 

nextflow.config

@@ -51,7 +51,7 @@ params {
     skip_multiqc               = false
 
     // Illumina QC, read trimming and filtering options
-    kraken2_db                 = 's3://nf-core-awsmegatests/viralrecon/input_data/kraken2_human.tar.gz'
+    kraken2_db                 = 's3://ngi-igenomes/test-data/viralrecon/kraken2_human.tar.gz'
     kraken2_db_name            = 'human'
     kraken2_variants_host_filter = false
     kraken2_assembly_host_filter = true