cwlVersion: v1.0 class: Workflow label: EMG pipeline v4.0 (single end version) requirements: - class: SubworkflowFeatureRequirement - class: SchemaDefRequirement types: - $import: ../tools/FragGeneScan-model.yaml - $import: ../tools/InterProScan-apps.yaml - $import: ../tools/InterProScan-protein_formats.yaml - $import: ../tools/esl-reformat-replace.yaml - $import: ../tools/biom-convert-table.yaml inputs: reads: type: File format: edam:format_1930 # FASTQ fraggenescan_model: ../tools/FragGeneScan-model.yaml#model #Rfam modelts for ribosomal subunits and other ubiquitous ncRNAs #For each there is an assoicated clan file. ncRNA_ribosomal_models: File[] ncRNA_ribosomal_model_clans: File ncRNA_other_models: File[] ncRNA_other_model_clans: File #Input files for mapseq mapseq_ref: type: File format: edam:format_1929 # FASTA secondaryFiles: .mscluster mapseq_taxonomy: File mapseq_taxonomy_otu_table: File sequencing_run_id: string #Go summary file for slimming go_summary_config: File outputs: # processed_nucleotide_reads: type: File outputSource: trim_and_reformat_reads/trimmed_and_reformatted_reads #The idenditied SSU rRNA and their classification SSU_sequences: type: File outputSource: unified_processing/SSU_sequences ssu_classifications: type: File outputSource: unified_processing/ssu_classifications LSU_sequences: type: File outputSource: unified_processing/LSU_sequences 5S_sequences: type: File outputSource: unified_processing/5S_sequences #Keep all of the protein stuff here predicted_CDS: type: File outputSource: unified_processing/predicted_CDS functional_annotations: type: File outputSource: unified_processing/functional_annotations go_summary: type: File outputSource: unified_processing/go_summary go_summary_slim: type: File outputSource: unified_processing/go_summary_slim #Other non-coding RNA hits other_ncRNAs: type: File outputSource: unified_processing/other_ncRNAs #All of the sequence file QC stats qc_stats_summary: type: File outputSource: unified_processing/qc_stats_summary qc_stats_seq_len_pbcbin: type: File outputSource: unified_processing/qc_stats_seq_len_pcbin qc_stats_seq_len_bin: type: File outputSource: unified_processing/qc_stats_seq_len_bin qc_stats_seq_len: type: File outputSource: unified_processing/qc_stats_seq_len qc_stats_nuc_dist: type: File outputSource: unified_processing/qc_stats_nuc_dist qc_stats_gc_pcbin: type: File outputSource: unified_processing/qc_stats_gc_pcbin qc_stats_gc_bin: type: File outputSource: unified_processing/qc_stats_gc_bin qc_stats_gc: type: File outputSource: unified_processing/qc_stats_gc #TODO - # Add a step to extract ncRNAs # Sequence categoriastion outputs # Summary files match_count: type: int outputSource: unified_processing/match_count CDS_with_match_count: type: int outputSource: unified_processing/CDS_with_match_count reads_with_match_count: type: int outputSource: unified_processing/reads_with_match_count stats_reads: type: File outputSource: unified_processing/stats_reads numberReadsWithOrf: type: int outputSource: unified_processing/numberReadsWithOrf numberOrfs: type: int outputSource: unified_processing/numberOrfs readsWithOrf: type: File outputSource: unified_processing/readsWithOrf interproscan: type: File outputSource: unified_processing/interproscan no_functions_seqs: type: File outputSource: unified_processing/no_functions_seqs pCDS_seqs: type: File outputSource: unified_processing/pCDS_seqs steps: trim_and_reformat_reads: run: trim_and_reformat_reads.cwl in: reads: reads out: [ trimmed_and_reformatted_reads ] unified_processing: label: continue with the main workflow run: emg-core-analysis-v4.cwl in: mapseq_ref: mapseq_ref mapseq_taxonomy: mapseq_taxonomy sequencing_run_id: sequencing_run_id input_sequences: trim_and_reformat_reads/trimmed_and_reformatted_reads fraggenescan_model: fraggenescan_model ncRNA_ribosomal_models: ncRNA_ribosomal_models ncRNA_ribosomal_model_clans: ncRNA_ribosomal_model_clans ncRNA_other_models: ncRNA_other_models ncRNA_other_model_clans: ncRNA_other_model_clans go_summary_config: go_summary_config out: - other_ncRNAs - SSU_sequences - LSU_sequences - 5S_sequences - ssu_classifications - predicted_CDS - functional_annotations - go_summary - go_summary_slim - qc_stats_summary - qc_stats_seq_len_pcbin - qc_stats_seq_len_bin - qc_stats_seq_len - qc_stats_nuc_dist - qc_stats_gc_pcbin - qc_stats_gc_bin - qc_stats_gc - match_count - CDS_with_match_count - reads_with_match_count - stats_reads - numberReadsWithOrf - numberOrfs - readsWithOrf - interproscan - no_functions_seqs - pCDS_seqs #- otu_table_summary #TODO - checkouts and rationalise file names between v3 and v4 #- tree #- biom_json $namespaces: edam: http://edamontology.org/ s: http://schema.org/ $schemas: - http://edamontology.org/EDAM_1.16.owl - https://schema.org/docs/schema_org_rdfa.html s:license: "https://www.apache.org/licenses/LICENSE-2.0" s:copyrightHolder: "EMBL - European Bioinformatics Institute"