Changes test data

conf/cloud-region/ap_southeast_1.config

@@ -0,0 +1,3 @@
+params {
+    reference_data_bucket = "s3://ap-southeast-1-lb-featured-datasets"
+}

conf/tests/full/test_full.config

@@ -1,9 +1,9 @@
 params {
     input           = "${params.reference_data_bucket}/pipelines/parabricks/germline/output/HG001-NA12878-pFDA_S1_L001_20k.vcf"
-    // input = 'https://lifebit-featured-datasets.s3-eu-west-1.amazonaws.com/pipelines/parabricks/germline/output/HG001-NA12878-pFDA_S1_L001_20k.vcf'
-    sample_name     = 'HG001_NA12878'
+    // input = "https://lifebit-featured-datasets.s3-eu-west-1.amazonaws.com/pipelines/parabricks/germline/output/HG001-NA12878-pFDA_S1_L001_20k.vcf"
+    sample_name     = "HG001_NA12878"
     hpo_terms_file  = "${params.reference_data_bucket}/pipelines/exomiser-nf/hpo_terms_file.txt"
-    prioritisers    = 'hiPhivePrioritiser'
-    exomiser_profile_files = 'full'
+    prioritisers    = "hiPhivePrioritiser"
+    exomiser_profile_files = "full"
     application_properties = "${params.reference_data_bucket}/pipelines/exomiser-nf/application.properties"
 }

conf/tests/full/test_full_family.config

@@ -1,7 +1,7 @@
 params {
-    families_file     = 's3://lifebit-featured-datasets/pipelines/exomiser-nf/fam_file.tsv'
-    prioritisers    = 'hiPhivePrioritiser'
-    exomiser_profile_files = 'full'
-    application_properties = 's3://lifebit-featured-datasets/pipelines/exomiser-nf/application.properties'
-    auto_config_yml = 's3://lifebit-featured-datasets/pipelines/exomiser-nf/auto_config.yml'
+    families_file     = "${params.reference_data_bucket}/pipelines/exomiser-nf/fam_file.tsv"
+    prioritisers    = "hiPhivePrioritiser"
+    exomiser_profile_files = "full"
+    application_properties = "${params.reference_data_bucket}/pipelines/exomiser-nf/application.properties"
+    auto_config_yml = "${params.reference_data_bucket}/pipelines/exomiser-nf/auto_config.yml"
 }

conf/tests/full/test_full_multi_hpo.config

@@ -1,7 +1,7 @@
 params {
-    families_file     = 's3://lifebit-featured-datasets/pipelines/exomiser-nf/fam_file_multi_hpo.tsv'
-    prioritisers    = 'hiPhivePrioritiser'
-    exomiser_profile_files = 'full'
-    application_properties = 's3://lifebit-featured-datasets/pipelines/exomiser-nf/application.properties'
-    auto_config_yml = 's3://lifebit-featured-datasets/pipelines/exomiser-nf/auto_config.yml'
+    families_file     = "${params.reference_data_bucket}/pipelines/exomiser-nf/fam_file_multi_hpo.tsv"
+    prioritisers    = "hiPhivePrioritiser"
+    exomiser_profile_files = "full"
+    application_properties = "${params.reference_data_bucket}/pipelines/exomiser-nf/application.properties"
+    auto_config_yml = "${params.reference_data_bucket}/pipelines/exomiser-nf/auto_config.yml"
 }

conf/tests/full/test_full_single_vcf.config

@@ -1,8 +1,8 @@
 params {
-    families_file     = 's3://lifebit-featured-datasets/pipelines/exomiser-nf/single_vcf.tsv'
-    hpo_terms_file  = 's3://lifebit-featured-datasets/pipelines/exomiser-nf/hpo_terms_file.txt'
-    prioritisers    = 'hiPhivePrioritiser'
-    exomiser_profile_files = 'full'
-    application_properties = 's3://lifebit-featured-datasets/pipelines/exomiser-nf/application.properties'
-    auto_config_yml = 's3://lifebit-featured-datasets/pipelines/exomiser-nf/auto_config.yml'
+    families_file     = "${params.reference_data_bucket}/pipelines/exomiser-nf/single_vcf.tsv"
+    hpo_terms_file  = "${params.reference_data_bucket}/pipelines/exomiser-nf/hpo_terms_file.txt"
+    prioritisers    = "hiPhivePrioritiser"
+    exomiser_profile_files = "full"
+    application_properties = "${params.reference_data_bucket}/pipelines/exomiser-nf/application.properties"
+    auto_config_yml = "${params.reference_data_bucket}/pipelines/exomiser-nf/auto_config.yml"
 }

main.nf

@@ -45,6 +45,16 @@ log.info ""
 //   Check input parameters
 // ---------------------------------------------------*/
 
+def replaceBucket(file, bucket="${params.reference_data_bucket}", pattern="${params.bucket_pattern}") {
+    reg_exp = ~/(s3:\/\/[a-zA-Z0-9\-]*$pattern)/
+    file = file.toString()
+    if (file =~ reg_exp) {
+         replace_bucket = (file =~ reg_exp)[0]
+         file = file.replaceAll(replace_bucket[0], bucket)
+    }
+    return file
+}
+
 if(params.families_file) {
   Channel
       .fromPath( "${params.families_file}")
@@ -60,7 +70,7 @@ Channel
     .fromPath(params.families_file)
     .ifEmpty { exit 1, "Cannot find input file : ${params.families_file}" }
     .splitCsv(header:true, sep:'\t', strip: true)
-    .map {row -> [ row.proband_id, file(row.vcf_path), file(row.vcf_index_path)] }
+    .map {row -> [ row.proband_id, file(replaceBucket(row.vcf_path)), file(replaceBucket(row.vcf_index_path))] }
     .into {ch_vcf_paths; ch_vcf_paths2}
 
 // Conditional creation of channels, custom if provided else default from bin/

nextflow.config

@@ -82,6 +82,7 @@ profiles {
    awsbatch { includeConfig 'conf/executors/awsbatch.config' }
    eu_west_1 { includeConfig 'conf/cloud-region/eu_west_1.config' }
    eu_west_2 { includeConfig 'conf/cloud-region/eu_west_2.config' }
+   ap_southeast_1 { includeConfig 'conf/cloud-region/ap_southeast_1.config' } 
    test_full { includeConfig "conf/tests/full/test_full.config" }
    test_full_family { includeConfig 'conf/tests/full/test_full_family.config' }
    test_full_single_vcf { includeConfig 'conf/tests/full/test_full_single_vcf.config' }