cwlVersion: v1.0 class: Workflow label: EMG pipeline v3.0 (paired end version) requirements: - class: SubworkflowFeatureRequirement - class: SchemaDefRequirement types: - $import: ../tools/FragGeneScan-model.yaml inputs: forward_reads: type: File format: edam:format_1930 # FASTQ reverse_reads: type: File format: edam:format_1930 # FASTQ run_id: string fraggenescan_model: ../tools/FragGeneScan-model.yaml#model 16S_model: type: File format: edam:format_1370 # HMMER 5S_model: type: File format: edam:format_1370 # HMMER 23S_model: type: File format: edam:format_1370 # HMMER tRNA_model: type: File format: edam:format_1370 # HMMER go_summary_config: File outputs: post_qc_read_count: type: int outputSource: unified_processing/post_qc_read_count processed_sequences: type: File outputSource: unified_processing/processed_sequences predicted_CDS_aa: type: File outputSource: unified_processing/predicted_CDS_aa 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 otu_table_summary: type: File outputSource: unified_processing/otu_table_summary tree: type: File outputSource: unified_processing/tree biom_json: type: File outputSource: unified_processing/biom_json biom_hdf5: type: File outputSource: unified_processing/biom_hdf5 biom_tsv: type: File outputSource: unified_processing/biom_tsv 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_pbcbin 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 ipr_match_count: type: int outputSource: unified_processing/ipr_match_count ipr_CDS_with_match_count: type: int outputSource: unified_processing/ipr_CDS_with_match_count ipr_reads_with_match_count: type: int outputSource: unified_processing/ipr_reads_with_match_count ipr_reads: type: File outputSource: unified_processing/ipr_reads ipr_summary: type: File outputSource: unified_processing/ipr_summary annotated_CDS_nuc: type: File outputSource: unified_processing/annotated_CDS_nuc annotated_CDS_aa: type: File outputSource: unified_processing/annotated_CDS_aa unannotated_CDS_nuc: type: File outputSource: unified_processing/unannotated_CDS_nuc unannotated_CDS_aa: type: File outputSource: unified_processing/unannotated_CDS_aa qiime_sequences-filtered_clusters: type: File outputSource: unified_processing/qiime_sequences-filtered_clusters qiime_sequences-filtered_otus: type: File outputSource: unified_processing/qiime_sequences-filtered_otus qiime_assigned_taxonomy: type: File outputSource: unified_processing/qiime_assigned_taxonomy krona_input: type: File outputSource: unified_processing/krona_input kingdom_counts: type: File outputSource: unified_processing/kingdom_counts otu_visualization: type: File outputSource: unified_processing/otu_visualization 16S_matches: type: File outputSource: unified_processing/16S_matches 23S_matches: type: File outputSource: unified_processing/23S_matches 5S_matches: type: File outputSource: unified_processing/5S_matches tRNA_matches: type: File outputSource: unified_processing/tRNA_matches interproscan_matches: type: File outputSource: unified_processing/interproscan_matches pCDS_seqs: type: File outputSource: unified_processing/pCDS_seqs no_functions_seqs: type: File outputSource: unified_processing/no_functions_seqs actual_run_id: type: string outputSource: run_id post_qc_reads: type: File outputSource: unified_processing/post_qc_reads summary: type: File outputSource: unified_processing/summary steps: overlap_reads: label: Paired-end overlapping reads are merged run: ../tools/seqprep.cwl in: forward_reads: forward_reads reverse_reads: reverse_reads out: [ merged_reads, forward_unmerged_reads, reverse_unmerged_reads ] combine_overlaped_and_unmerged_reads: run: ../tools/seqprep-merge.cwl in: merged_reads: overlap_reads/merged_reads forward_unmerged_reads: overlap_reads/forward_unmerged_reads reverse_unmerged_reads: overlap_reads/reverse_unmerged_reads out: [ merged_with_unmerged_reads ] unified_processing: label: continue with the main workflow run: emg-pipeline-v3.cwl in: reads: combine_overlaped_and_unmerged_reads/merged_with_unmerged_reads run_id: run_id fraggenescan_model: fraggenescan_model 16S_model: 16S_model 5S_model: 5S_model 23S_model: 23S_model tRNA_model: tRNA_model go_summary_config: go_summary_config out: - processed_sequences - predicted_CDS_aa - functional_annotations - go_summary - go_summary_slim - otu_table_summary - tree - biom_json - biom_hdf5 - biom_tsv - qc_stats_summary - qc_stats_seq_len_pbcbin - qc_stats_seq_len_bin - qc_stats_seq_len - qc_stats_nuc_dist - qc_stats_gc_pcbin - qc_stats_gc_bin - qc_stats_gc - ipr_match_count - ipr_CDS_with_match_count - ipr_reads_with_match_count - ipr_reads - ipr_summary - annotated_CDS_nuc - annotated_CDS_aa - unannotated_CDS_nuc - unannotated_CDS_aa - qiime_sequences-filtered_clusters - qiime_sequences-filtered_otus - qiime_assigned_taxonomy - tRNA_matches - 16S_matches - 23S_matches - 5S_matches - interproscan_matches - pCDS_seqs - no_functions_seqs - post_qc_reads - post_qc_read_count - summary - krona_input - kingdom_counts - otu_visualization $namespaces: edam: http://edamontology.org/ s: http://schema.org/ $schemas: - http://edamontology.org/EDAM_1.16.owl s:license: "https://www.apache.org/licenses/LICENSE-2.0" s:copyrightHolder: "EMBL - European Bioinformatics Institute"