diff --git a/conf/test_full.config b/conf/test_full.config index 60a139c..d22b5ed 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -20,7 +20,7 @@ params { max_time = '8.h' // Input data - input = 'assets/samplesheet_full_small.csv' + input = "${projectDir}/assets/samplesheet_full_small.csv" outdir = 'results' // Genome references @@ -28,7 +28,7 @@ params { analysis = 'germline' variant_type = "small" method = 'happy,rtgtools' - preprocess = "normalization,deduplication,filter_contigs" + preprocess = "normalize,deduplicate,filter_contigs" truth_id = "HG002" truth_vcf = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/NISTv4.2.1/GRCh37/SupplementaryFiles/HG002_GRCh37_1_22_v4.2.1_highconf.vcf.gz" diff --git a/nextflow.config b/nextflow.config index 2badde6..82b5e24 100644 --- a/nextflow.config +++ b/nextflow.config @@ -186,15 +186,15 @@ profiles { executor.cpus = 4 executor.memory = 8.GB } - test { includeConfig 'conf/test.config' } - test_full { includeConfig 'conf/test_full.config' } - germline_small { includeConfig 'conf/tests/germline_small.config'} - germline_sv { includeConfig 'conf/tests/germline_sv.config' } - somatic_snv { includeConfig 'conf/tests/somatic_snv.config' } - somatic_indel { includeConfig 'conf/tests/somatic_indel.config' } - somatic_sv { includeConfig 'conf/tests/somatic_sv.config' } - liftover_test { includeConfig 'conf/tests/liftover_test.config' } - liftover_truth { includeConfig 'conf/tests/liftover_truth.config' } + test { includeConfig 'conf/test.config' } + test_full { includeConfig 'conf/test_full.config' } + germline_small { includeConfig 'conf/tests/germline_small.config'} + germline_structural { includeConfig 'conf/tests/germline_sv.config' } + somatic_snv { includeConfig 'conf/tests/somatic_snv.config' } + somatic_indel { includeConfig 'conf/tests/somatic_indel.config' } + somatic_structural { includeConfig 'conf/tests/somatic_sv.config' } + liftover_test { includeConfig 'conf/tests/liftover_test.config' } + liftover_truth { includeConfig 'conf/tests/liftover_truth.config' } }