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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,9 @@ | ||
| version: 1.2 | ||
| workflows: | ||
| - subclass: WDL | ||
| name: PharmCAT-Pipeline | ||
| primaryDescriptorPath: /pipeline/PharmCAT_Pipeline.wdl | ||
| readMePath: /pipeline/README.md | ||
| filters: | ||
| tags: | ||
| - /v\d+.*/ |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,127 +1,152 @@ | ||
| version 1.0 | ||
|
|
||
| # It is a single task that runs the PharmCAT pipeline on a VCF file | ||
| # as a single task the workflow is just a wrapper for the task and get the same name | ||
| # The output is an array of files that are the results of the pipeline save in the plataform where the workflow is running | ||
| task pharmcat_pipeline { | ||
| input { | ||
| File vcf_file | ||
| String sample_ids = "" | ||
| File? sample_file | ||
| Boolean missing_to_ref = false | ||
| Boolean no_gvcf_check = false | ||
| Boolean retain_specific_regions = false | ||
| File? reference_regions | ||
| Boolean run_matcher = false | ||
| Boolean matcher_all_results = false | ||
| Boolean matcher_save_html = false | ||
| String research_mode = "" | ||
| Boolean run_phenotyper = false | ||
| Boolean run_reporter = false | ||
| String reporter_sources = "" | ||
| Boolean reporter_extended = false | ||
| Boolean reporter_save_json = false | ||
| String base_filename = "" | ||
| Boolean delete_intermediate_files = false | ||
| Int max_concurrent_processes = 1 | ||
| String max_memory = "4G" | ||
| } | ||
|
|
||
| command <<< | ||
| set -x -e -o pipefail | ||
| mkdir -p data | ||
| cp ~{vcf_file} data/ | ||
|
|
||
| pharmcat_pipeline data/$(basename ~{vcf_file}) \ | ||
| ~{if sample_ids != "" then '-s ' + sample_ids else ''} \ | ||
| ~{if defined(sample_file) then '-S ' + sample_file else ''} \ | ||
| ~{if missing_to_ref then '-0' else ''} \ | ||
| ~{if no_gvcf_check then '-G' else ''} \ | ||
| ~{if retain_specific_regions then '-R' else ''} \ | ||
| ~{if defined(reference_regions) then '-refRegion ' + reference_regions else ''} \ | ||
| ~{if run_matcher then '-matcher' else ''} \ | ||
| ~{if matcher_all_results then '-ma' else ''} \ | ||
| ~{if matcher_save_html then '-matcherHtml' else ''} \ | ||
| ~{if research_mode != "" then '-research ' + research_mode else ''} \ | ||
| ~{if run_phenotyper then '-phenotyper' else ''} \ | ||
| ~{if run_reporter then '-reporter' else ''} \ | ||
| ~{if reporter_sources != "" then '-rs ' + reporter_sources else ''} \ | ||
| ~{if reporter_extended then '-re' else ''} \ | ||
| ~{if reporter_save_json then '-reporterJson' else ''} \ | ||
| ~{if base_filename != "" then '-bf ' + base_filename else ''} \ | ||
| ~{if delete_intermediate_files then '-del' else ''} \ | ||
| -cp ~{max_concurrent_processes} -cm ~{max_memory} | ||
| >>> | ||
|
|
||
| output { | ||
| Array[File] results = glob("data/*") | ||
| } | ||
|
|
||
| runtime { | ||
| docker: "pgkb/pharmcat:2.15.2" | ||
| memory: max_memory | ||
| cpu: max_concurrent_processes | ||
| } | ||
|
|
||
| meta { | ||
| author: "PharmGKB" | ||
| email: "[email protected]" | ||
| description: "Workflow to run the PharmCAT pipeline on a VCF file" | ||
| } | ||
| workflow pharmcat_pipeline { | ||
| meta { | ||
| author: "ClinPGx" | ||
| email: "[email protected]" | ||
| description: "This workflow runs a VCF file through the PharmCAT pipeline." | ||
| } | ||
|
|
||
| parameter_meta { | ||
| # description for this is intentionally different from pipeline script because it's hard to | ||
| # support a file of files on cloud services and directories aren't supported | ||
| vcf_file: "A VCF file (can be gzipped or bgzipped)." | ||
| sample_ids: "A comma-separated list of sample IDs. Only applicable if you have multiple samples and only want to work on specific ones." | ||
| sample_file: "A file containing a list of sample IDs, one sample ID per line. Only applicable if you have multiple samples and only want to work on specific ones." | ||
|
|
||
| missing_to_ref: "Assume genotypes at missing PGx sites are 0/0. DANGEROUS!" | ||
| no_gvcf_check: "Bypass check if VCF file is in gVCF format." | ||
| # not including retain_specific_regions and reference_regions | ||
| run_matcher: "Run named allele matcher independently." | ||
| matcher_all_results: "Return all possible diplotypes, not just top hits." | ||
| matcher_save_html: "Save named allele matcher results as HTML.'" | ||
| research_mode: "Comma-separated list of research features to enable: [cyp2d6, combinations]" | ||
|
|
||
| run_phenotyper: "Run phenotyper independently." | ||
|
|
||
| run_reporter: "Run reporter independently." | ||
| reporter_sources: "Comma-separated list of sources to limit recommendations to: [CPIC, DPWG, FDA]" | ||
| reporter_extended: "Write an extended report (includes all possible genes and drugs, even if no data is available)" | ||
| reporter_save_json: "Save reporter results as JSON." | ||
|
|
||
| base_filename: "Prefix for output files. Defaults to the same base name as the input." | ||
| delete_intermediate_files: "Delete intermediate PharmCAT files. Defaults to saving all files." | ||
|
|
||
| max_concurrent_processes: "The maximum number of processes to use when concurrent mode is enabled." | ||
| max_memory: "The maximum memory PharmCAT should use (e.g. '64G')." | ||
| } | ||
|
|
||
|
|
||
| input { | ||
| File vcf_file | ||
| String sample_ids = "" | ||
| File? sample_file | ||
| Boolean missing_to_ref = false | ||
| Boolean no_gvcf_check = false | ||
| Boolean run_matcher = false | ||
| Boolean matcher_all_results = false | ||
| Boolean matcher_save_html = false | ||
| String research_mode = "" | ||
| Boolean run_phenotyper = false | ||
| Boolean run_reporter = false | ||
| String reporter_sources = "" | ||
| Boolean reporter_extended = false | ||
| Boolean reporter_save_json = false | ||
| String base_filename = "" | ||
| Boolean delete_intermediate_files = false | ||
| Int max_concurrent_processes = 1 | ||
| String max_memory = "4G" | ||
| } | ||
|
|
||
| call pharmcat_pipeline_task { | ||
| input: | ||
| vcf_file = vcf_file, | ||
| sample_ids = sample_ids, | ||
| sample_file = sample_file, | ||
| missing_to_ref = missing_to_ref, | ||
| no_gvcf_check = no_gvcf_check, | ||
| run_matcher = run_matcher, | ||
| matcher_all_results = matcher_all_results, | ||
| matcher_save_html = matcher_save_html, | ||
| research_mode = research_mode, | ||
| run_phenotyper = run_phenotyper, | ||
| run_reporter = run_reporter, | ||
| reporter_sources = reporter_sources, | ||
| reporter_extended = reporter_extended, | ||
| reporter_save_json = reporter_save_json, | ||
| base_filename = base_filename, | ||
| delete_intermediate_files = delete_intermediate_files, | ||
| max_concurrent_processes = max_concurrent_processes, | ||
| max_memory = max_memory | ||
| } | ||
|
|
||
| output { | ||
| Array[File] results = pharmcat_pipeline_task.results | ||
| } | ||
| } | ||
|
|
||
| workflow pharmcat_pipeline { | ||
| input { | ||
| File vcf_file | ||
| String sample_ids = "" | ||
| File? sample_file | ||
| Boolean missing_to_ref = false | ||
| Boolean no_gvcf_check = false | ||
| Boolean retain_specific_regions = false | ||
| File? reference_regions | ||
| Boolean run_matcher = false | ||
| Boolean matcher_all_results = false | ||
| Boolean matcher_save_html = false | ||
| String research_mode = "" | ||
| Boolean run_phenotyper = false | ||
| Boolean run_reporter = false | ||
| String reporter_sources = "" | ||
| Boolean reporter_extended = false | ||
| Boolean reporter_save_json = false | ||
| String base_filename = "" | ||
| Boolean delete_intermediate_files = false | ||
| Int max_concurrent_processes = 1 | ||
| String max_memory = "4G" | ||
| } | ||
|
|
||
| call pharmcat_pipeline { | ||
| input: | ||
| vcf_file = vcf_file, | ||
| sample_ids = sample_ids, | ||
| sample_file = sample_file, | ||
| missing_to_ref = missing_to_ref, | ||
| no_gvcf_check = no_gvcf_check, | ||
| retain_specific_regions = retain_specific_regions, | ||
| reference_regions = reference_regions, | ||
| run_matcher = run_matcher, | ||
| matcher_all_results = matcher_all_results, | ||
| matcher_save_html = matcher_save_html, | ||
| research_mode = research_mode, | ||
| run_phenotyper = run_phenotyper, | ||
| run_reporter = run_reporter, | ||
| reporter_sources = reporter_sources, | ||
| reporter_extended = reporter_extended, | ||
| reporter_save_json = reporter_save_json, | ||
| base_filename = base_filename, | ||
| delete_intermediate_files = delete_intermediate_files, | ||
| max_concurrent_processes = max_concurrent_processes, | ||
| max_memory = max_memory | ||
| } | ||
|
|
||
| output { | ||
| Array[File] results_all = pharmcat_pipeline.results | ||
| } | ||
|
|
||
| task pharmcat_pipeline_task { | ||
| meta { | ||
| author: "ClinPGx" | ||
| email: "[email protected]" | ||
| description: "This task run a VCF file through the PharmCAT pipeline." | ||
| } | ||
|
|
||
| input { | ||
| File vcf_file | ||
| String sample_ids = "" | ||
| File? sample_file | ||
| Boolean missing_to_ref = false | ||
| Boolean no_gvcf_check = false | ||
| Boolean run_matcher = false | ||
| Boolean matcher_all_results = false | ||
| Boolean matcher_save_html = false | ||
| String research_mode = "" | ||
| Boolean run_phenotyper = false | ||
| Boolean run_reporter = false | ||
| String reporter_sources = "" | ||
| Boolean reporter_extended = false | ||
| Boolean reporter_save_json = false | ||
| String base_filename = "" | ||
| Boolean delete_intermediate_files = false | ||
| Int max_concurrent_processes = 1 | ||
| String max_memory = "4G" | ||
| } | ||
|
|
||
| command <<< | ||
| set -x -e -o pipefail | ||
| mkdir -p data | ||
| cp ~{vcf_file} data/ | ||
|
|
||
| pharmcat_pipeline data/$(basename ~{vcf_file}) \ | ||
| ~{if sample_ids != "" then '-s ' + sample_ids else ''} \ | ||
| ~{if defined(sample_file) then '-S ' + sample_file else ''} \ | ||
| ~{if missing_to_ref then '-0' else ''} \ | ||
| ~{if no_gvcf_check then '-G' else ''} \ | ||
| ~{if run_matcher then '-matcher' else ''} \ | ||
| ~{if matcher_all_results then '-ma' else ''} \ | ||
| ~{if matcher_save_html then '-matcherHtml' else ''} \ | ||
| ~{if research_mode != "" then '-research ' + research_mode else ''} \ | ||
| ~{if run_phenotyper then '-phenotyper' else ''} \ | ||
| ~{if run_reporter then '-reporter' else ''} \ | ||
| ~{if reporter_sources != "" then '-rs ' + reporter_sources else ''} \ | ||
| ~{if reporter_extended then '-re' else ''} \ | ||
| ~{if reporter_save_json then '-reporterJson' else ''} \ | ||
| ~{if base_filename != "" then '-bf ' + base_filename else ''} \ | ||
| ~{if delete_intermediate_files then '-del' else ''} \ | ||
| -cp ~{max_concurrent_processes} -cm ~{max_memory} | ||
| >>> | ||
|
|
||
| output { | ||
| Array[File] results = glob("data/*") | ||
| } | ||
|
|
||
| runtime { | ||
| docker: "pgkb/pharmcat:2.13.0" | ||
| memory: max_memory | ||
| cpu: max_concurrent_processes | ||
| } | ||
| } | ||
|
|
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