diff --git a/assets/test_oncoflow.config b/assets/test_oncoflow.config new file mode 100644 index 0000000..32aa5e4 --- /dev/null +++ b/assets/test_oncoflow.config @@ -0,0 +1,93 @@ +// +// Oncoanalyser configuration +// + +// TODO + +// +// Oncorefiner configuration +// + +// TODO +params { + // Parameters and options for tools + extra_args_cadd_annotate = '--columns Chrom,Pos,Ref,Alt,-,CADD' + extra_args_snv_clinical_filter = "--include '(INFO/GNOMADAF_grpmax <= 0.001 || INFO/GNOMADAF_grpmax == \".\")'" + extra_args_snv_research_filter = "--include '(INFO/GNOMADAF_grpmax <= 0.001 || INFO/GNOMADAF_grpmax == \".\")'" + extra_args_snv_vep = '' + extra_args_sv_vep = '' + + // Pipeline resource files + // VEP + vep_cache_version = 115 + vep_plugin_files = params.oncoflow_resources_dir + 'vep_plugin.csv' + vep_cache = params.oncoflow_resources_dir + 'VEP' + + // Vcfanno + vcfanno_toml = params.oncoflow_resources_dir + 'grch38_vcfanno_config.toml' + vcfanno_resources = params.oncoflow_resources_dir + 'grch38_vcfanno_resources.txt' + vcfanno_lua = null + + // SVDB + svdb_query_dbs = params.oncoflow_resources_dir + 'grch38_svdb_query_dbs.csv' + + // Reference + fasta = params.oncoflow_resources_dir + 'GRCh38_masked_exclusions_alts_hlas.fasta' + fai = params.oncoflow_resources_dir + 'GRCh38_masked_exclusions_alts_hlas.fasta.fai' +} + + +process { + + withName: '.*:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE' { + errorStrategy = 'ignore' + } + + withName:'.*PROCESS_SNVS:BCFTOOLS_VIEW_RESEARCH' { + ext.args = { [ + "${params.extra_args_snv_research_filter}", + "--output-type z", + "--write-index=tbi", + ].join(' ') } + } + + withName: '.*PROCESS_SNVS:ENSEMBLVEP_VEP' { + maxForks = 8 + memory = { 10.GB * task.attempt } + cpus = { 2 * task.attempt } + time = { 4.h * task.attempt } + } + + + withName: '.*PROCESS_SVS:ENSEMBLVEP_VEP' { + maxForks = 8 + memory = { 10.GB * task.attempt } + cpus = { 2 * task.attempt } + time = { 4.h * task.attempt } + } + + withName: '.*ANNOTATE_CADD:CADD' { + memory = { 30.GB * task.attempt } + cpus = { 1 * task.attempt } + time = { 1.h * task.attempt } + } + + withName: '.*ANNOTATE_CADD:RENAME_CHR_CADD' { + memory = { 1.GB * task.attempt } + cpus = { 1 * task.attempt } + time = { 1.h * task.attempt } + } + + withName: '.*ANNOTATE_CADD:ANNOTATE_INDELS' { + memory = { 1.GB * task.attempt } + cpus = { 1 * task.attempt } + time = { 1.h * task.attempt } + } + + withName: '.*ANNOTATE_CADD:BCFTOOLS_VIEW' { + memory = { 1.GB * task.attempt } + cpus = { 1 * task.attempt } + time = { 1.h * task.attempt } + } + +} diff --git a/assets/test_oncoflow_params.yaml b/assets/test_oncoflow_params.yaml new file mode 100644 index 0000000..714e076 --- /dev/null +++ b/assets/test_oncoflow_params.yaml @@ -0,0 +1,8 @@ +case_id: "test_case_id" +sample_id_tumor: "test_sample_id_tumor" +sample_id_normal: "test_sample_id_normal" +sex: "female" + +oncoanalyser_create_stub_placeholders: true +oncoanalyser_genome: "GRCh38_hmf" +oncoanalyser_mode: "wgts"