version 1.0 import "../tasks/task_phoenix.wdl" as phoenix_nf workflow phoenix_workflow { meta { description: "A WDL wrapper around the qc, assembly, AR gene calls components of phoenix." } input { File? read1 File? read2 File? input_assembly String samplename String kraken2db String mode Int? coverage String? scaffold_ext Boolean? create_ncbi_sheet Boolean? centar } call phoenix_nf.phoenix { input: read1 = read1, read2 = read2, input_assembly = input_assembly, samplename = samplename, kraken2db = kraken2db, mode = mode, coverage = coverage, scaffold_ext = scaffold_ext, create_ncbi_sheet = create_ncbi_sheet, centar = centar } output { #phoenix summary output values File? work_files = phoenix.work_files String project_dir = phoenix.project_dir String phoenix_version = phoenix.phoenix_version String phoenix_docker = phoenix.phoenix_docker String analysis_date = phoenix.analysis_date String qc_outcome = phoenix.qc_outcome String warnings = phoenix.warnings String warning_count = phoenix.warning_count String alerts = phoenix.alerts String estimated_coverage = phoenix.estimated_coverage #make ing for cases where it's "unknown" String genome_length = phoenix.genome_length #make string for cases where it's "unknown" String n50 = phoenix.N50 String assembly_ratio = phoenix.assembly_ratio String assembly_ratio_stdev = phoenix.assembly_ratio_stdev #make string for cases where it's "unknown" String scaffold_count = phoenix.scaffold_count #make string for cases where it's "unknown" String gc_percent = phoenix.gc_percent #make string for cases where it's "unknown" String final_taxa_id = phoenix.final_taxa_id String taxa_source = phoenix.taxa_source String busco = phoenix.busco String busco_db = phoenix.busco_db String kraken2_trimmed = phoenix.kraken2_trimmed String kraken2_weighted = phoenix.kraken2_weighted String shigapass_taxa = phoenix.shigapass_taxa String fastani_taxa = phoenix.fastani_taxa String fastani_confidence = phoenix.fastani_confidence String fastani_coverage = phoenix.fastani_coverage String mlst_scheme_1 = phoenix.mlst_scheme_1 String mlst_1 = phoenix.mlst_1 String mlst1_ncbi = phoenix.mlst1_ncbi String mlst_scheme_2 = phoenix.mlst_scheme_2 String mlst_2 = phoenix.mlst_2 String mlst2_ncbi = phoenix.mlst2_ncbi String gamma_beta_lactam_genes = phoenix.gamma_beta_lactam_genes String gamma_other_ar_genes = phoenix.gamma_other_ar_genes String amrfinder_point_mutations = phoenix.amrfinder_point_mutations String amrfinder_amr_classes = phoenix.amrfinder_amr_classes String amrfinder_amr_subclasses = phoenix.amrfinder_amr_subclasses String amrfinder_core_genes = phoenix.amrfinder_core_genes String amrfinder_plus_genes = phoenix.amrfinder_plus_genes String amrfinder_stress_genes = phoenix.amrfinder_stress_genes String amrfinder_virulence_genes = phoenix.amrfinder_virulence_genes String amrfinder_beta_lactam_genes = phoenix.amrfinder_beta_lactam_genes String hypervirulence_genes = phoenix.hypervirulence_genes String plasmid_incompatibility_replicons = phoenix.plasmid_incompatibility_replicons String qc_issues = phoenix.qc_issues #summary files File full_results = phoenix.full_results File griphin_excel_summary = phoenix.griphin_excel_summary File griphin_tsv_summary = phoenix.griphin_tsv_summary File phoenix_tsv_summary = phoenix.phoenix_tsv_summary #phoenix fastqc - optional for SCAFFOLDS and CDC_SCAFFOLDS entries File? raw_read1_html = phoenix.raw_read1_html # fastqc.html File? raw_read1_zip = phoenix.raw_read1_zip # fastqc.zip File? raw_read2_html = phoenix.raw_read2_html # fastqc.html File? raw_read2_zip = phoenix.raw_read2_zip # fastqc.zip #phoenix trimmed kraken/krona - optional for SCAFFOLDS and CDC_SCAFFOLDS entries File? kraken_trimd_summary = phoenix.kraken_trimd_summary # kraken2_trimd.summary.txt File? kraken_trimd_top_taxa = phoenix.kraken_trimd_top_taxa # trimd_top_taxa.txt File? trimd_html = phoenix.trimd_html # trimd.html File? trimd_krona = phoenix.trimd_krona # trimd.krona ## commented otu to save space, not really needed #File? classified_1 = phoenix.classified_1 # classified_1.fastq.gz #File? unclassified_1 = phoenix.unclassified_1 # unclassified_1.fastq.gz #File? classified_2 = phoenix.classified_2 # classified_2.fastq.gz #File? unclassified_2 = phoenix.unclassified_2 # unclassified_2.fastq.gz #phoenix QC - optional for SCAFFOLDS and CDC_SCAFFOLDS entries Array[File] file_integrity = phoenix.file_integrity # _summary.txt File? paired_fastp_html = phoenix.paired_fastp_html # fastp.html File? paired_fastp_json = phoenix.paired_fastp_json # fastp.json File? single_fastp_html = phoenix.single_fastp_html # singles.fastp.html File? single_fastp_json = phoenix.single_fastp_json # singles.fastp.json File? trimmed_singles = phoenix.trimmed_singles # singles.fastq.gz File? trimmed_read1 = phoenix.trimmed_read1 # read_1.trim.fastq.gz File? trimmed_read2 = phoenix.trimmed_read2 # read_2.trim.fastq.gz File? trimmed_read_counts = phoenix.trimmed_read_counts # trimmed_read_counts.txt File? raw_read_counts = phoenix.raw_read_counts # raw_read_counts.txt File? adapter_removal_log = phoenix.adapter_removal_log # bbduk.log #phoenix assembly - optional for SCAFFOLDS and CDC_SCAFFOLDS entries File? assembly_graph = phoenix.assembly_graph # gfa.gz File? filtered_scaffolds_log = phoenix.filtered_scaffolds_log # bbmap_filtered.log File? contigs = phoenix.contigs # contigs.fa.gz File? unzipped_contigs = phoenix.unzipped_contigs # contigs.fa File? filtered_scaffolds = phoenix.filtered_scaffolds # filtered.scaffolds.fa.gz File? unzipped_filtered_scaffolds = phoenix.unzipped_filtered_scaffolds # filtered.scaffolds.fa File? assembly_with_seq_names = phoenix.assembly_with_seq_names # renamed.scaffolds.fa.gz File? assembly = phoenix.assembly # scaffolds.fa.gz File? spades_log = phoenix.spades_log # spades.log #phoenix wtasmbld kraken/krona File? kraken_wtasmbld_summary = phoenix.kraken_wtasmbld_summary # kraken2_wtasmbld.summary.txt File? kraken_wtasmbld_top_taxa = phoenix.kraken_wtasmbld_top_taxa # wtasmbld_top_taxa.txt File? wtasmbld_html = phoenix.wtasmbld_html # wtasmbld.html File? wtasmbld_krona = phoenix.wtasmbld_krona # wtasmbld.krona File? kraken_asmbld_output = phoenix.kraken_asmbld_output # kraken2_asmbld.classifiedreads.txt File? kraken_asmbld_summary = phoenix.kraken_asmbld_summary # kraken2_asmbld.summary.txt File? kraken_asmbld_top_taxa = phoenix.kraken_asmbld_top_taxa # wtasmbld_top_taxa.txt File? asmbld_html = phoenix.asmbld_html # wtasmbld.html File? asmbld_krona = phoenix.asmbld_krona # wtasmbld.krona #phoenix ani File? fast_ani = phoenix.fast_ani # ani.txt File? reformated_fast_ani = phoenix.reformated_fast_ani # fastANI.txt File? top_20_taxa_matches = phoenix.top_20_taxa_matches # best_MASH_hits.txt File? mash_distance = phoenix.mash_distance # .txt #phoenix quast and mlst File? quast_summary = phoenix.quast_summary # _report.tsv File? mlst_tsv = phoenix.mlst_tsv # .tsv # cdc_phoenix busco and srst2 - optional for PHOENIX, SCAFFOLDS and SRA entries Array[File]? busco_generic = phoenix.busco_generic # short_summary.generic.*.filtered.scaffolds.fa.txt" Array[File]? busco_specific = phoenix.busco_specific # short_summary.specific.*.filtered.scaffolds.fa.txt" File? srst2 = phoenix.srst2 # __fullgenes__ResGANNCBI_20210507_srst2__results.txt" #phoenix gamma File? gamma_ar_calls = phoenix.gamma_ar_calls # ResGANNCBI_20210507_srst2.gamma File? blat_ar_calls = phoenix.blat_ar_calls # ResGANNCBI_20210507_srst2.psl File? gamma_hv_calls = phoenix.gamma_hv_calls # HyperVirulence_20220414.gamma File? blat_hv_calls = phoenix.blat_hv_calls # HyperVirulence_20220414.psl File? gamma_pf_calls = phoenix.gamma_pf_calls # PF-Replicons_20220414.gamma File? blat_pf_calls = phoenix.blat_pf_calls # PF-Replicons_20220414.psl #phoenix output File? assembly_ratio_file = phoenix.assembly_ratio_file # Assembly_ratio_20210819.txt File? gc_content_file = phoenix.gc_content_file # GC_content_20210819.txt File summary_line = phoenix.summary_line # summary_line.tsv File synopsis = phoenix.synopsis # synopsis File? best_taxa_id = phoenix.best_taxa_id # tax #phoenix AMRFinder File? amrfinder_mutations = phoenix.amrfinder_mutations # all_mutations.tsv File? amrfinder_taxa_match = phoenix.amrfinder_taxa_match # AMRFinder_Organism.csv File? amrfinder_hits = phoenix.amrfinder_hits # all_genes.tsv #species specific File? shigapass_summary = phoenix.shigapass_summary # *_ShigaPass_summary.csv File? centar_summary = phoenix.centar_summary # *_centar_output.tsv File? centar_ar_AA_gamma = phoenix.centar_ar_AA_gamma # *_centar_ar_db_wt_AA_20240910.gamma File? centar_ar_NT_gamma = phoenix.centar_ar_NT_gamma # *_centar_ar_db_wt_NT_20240910.gamma File? centar_tox_gamma = phoenix.centar_tox_gamma # *_Cdiff_toxins_srst2_20240909.gamma File? centar_clade = phoenix.centar_clade # *_cdifficile_clade.tsv #File? centar_plasmid = phoenix.centar_plasmid # *_plasmids.tsv # NCBI files - optional Array[File]? ncbi_biosample = phoenix.ncbi_biosample # BiosampleAttributes_Microbe.1.0.xlsx" Array[File]? ncbi_sra_metadata = phoenix.ncbi_sra_metadata # Sra_Microbe.1.0.xlsx" #run files - optional for SCAFFOLDS and CDC_SCAFFOLDS entries File versions_file = phoenix.versions_file # software_versions.yml" File? multiqc_output = phoenix.multiqc_output # multiqc_report.html" } }