class: Workflow cwlVersion: v1.0 id: assembly_wf_virus label: assembly-wf-virus doc: "Virus genome assembly with Unicycler and spades, in parallel. visualisation with bandage" inputs: ##############unicycler - id: fastq_file_type type: type: enum symbols: [paired,single] doc: "Paired and single end data" - id: mode type: type: enum symbols: [conservative,normal,bold] doc: | Bridging mode, values: conservative (smaller contigs, lower misassembly) normal (moderate contig size and misassembly rate) bold (longest contigs, higher misassembly rate) - id: fastq1_type type: type: enum symbols: - fastqsanger - fastqsanger.gz doc: "Type of the First set of reads. Only when fastq_file_type = single or paired" default: fastqsanger - id: fastq1 type: File doc: "First set of reads with forward reads. Only when fastq_file_type = single or paired" - id: fastq2_type type: - "null" - type: enum symbols: - fastqsanger - fastqsanger.gz default: "null" doc: "Type of the Second set of reads. Only when fastq_file_type=paired" - id: fastq2 type: File? doc: "Second set of reads with reverse reads. Only when fastq_file_type=paired" ##############spades - id: libraries_metadata type: type: array items: type: record fields: - name: lib_index type: int? - name: orientation type: string? - name: lib_type type: string? doc: | reads library metadata related to libraries_fwd_rev and libraries_mono inputs lib_index(id) must match - id: libraries_fwd_rev type: type: array items: type: record fields: - name: lib_index type: int? - name: fwd_reads type: File? - name: rev_reads type: File? doc: | reads file orientation must be a value in ff, fr, rf K-mer choices can be chosen by SPAdes instead of being entered manually - id: libraries_mono type: type: array items: type: record fields: - name: lib_index type: int? - name: file_type type: string? - name: reads type: File? doc: | reads file file_type value must be in : interleaved, merged, unpaired - id: pacbio_reads type: - "null" - type: array items: File - id: nanopore_reads type: - "null" - type: array items: File - id: sanger_reads type: - "null" - type: array items: File - id: trusted_contigs type: - "null" - type: array items: File - id: untrusted_contigs type: - "null" - type: array items: File - id: auto_kmer_choice type: boolean default: true doc: | Automatically choose k-mer values. K-mer choices can be chosen by SPAdes instead of being entered manually - id: kmers type: string default: "21,33,55" doc: | K-mers to use, separated by commas. Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128, listed in ascending order, and smaller than the read length). The default value is 21,33,55 - id: cov_state type: - "null" - type: enum symbols: - off - value - auto doc: | Coverage cutoff ( 'auto', or 'off', or 'value'). auto if null when cov_state=value (User Specific) , cov_cutoff must be provided - id: cov_cutoff type: float? doc: | coverage cutoff value (a positive float number ) - id: iontorrent type: boolean default: false doc: | true if Libraries are IonTorrent reads. - id: sc type: boolean default: false doc: | This option is required for MDA. true if single-cell data. - id: onlyassembler type: boolean default: false doc: | Run only assembly if true (without read error correction) - id: careful type: boolean default: true doc: | Careful correction. Tries to reduce number of mismatches and short indels. Also runs MismatchCorrector, a post processing tool, which uses BWA tool (comes with SPAdes). outputs: - id: out_contigs_spades outputSource: - spades/out_contigs type: 'File' - id: out_scaffolds_spades outputSource: - spades/out_scaffolds type: 'File' - id: out_contig_stats_spades outputSource: - spades/out_contig_stats type: 'File' - id: out_scaffold_stats_spades outputSource: - spades/out_scaffold_stats type: 'File' - id: assembly_graph_spades outputSource: - spades/assembly_graph type: 'File' - id: assembly_graph_with_scaffolds_spades outputSource: - spades/assembly_graph_with_scaffolds type: 'File' - id: all_log_spades outputSource: - spades/all_log type: 'File[]' # - id: all_script # outputSource: # - spades/all_script # type: 'File[]' - id: assembly_image_spades outputSource: - bandage_image_spades/image type: File - id: assembly_info_spades outputSource: - bandage_info_spades/assembly_graph_info type: File - id: assembly_graph_unicycler outputSource: - unicycler/assembly_graph type: File - id: assembly_unicycler outputSource: - unicycler/assembly type: File # - id: exec_script2 # outputSource: # - unicycler/exec_script # type: File - id: assembly_image_unicycler outputSource: - bandage_image_unicycler/image type: File - id: assembly_info_unicycler outputSource: - bandage_info_unicycler/assembly_graph_info type: File steps: - id: unicycler in: - id: fastq1_type source: fastq1_type - id: fastq1 source: fastq1 - id: fastq2_type source: fastq2_type - id: fastq2 source: fastq2 - id: mode source: mode - id: fastq_file_type source: fastq_file_type out: # - id: exec_script - id: assembly_graph - id: assembly # run: ../../bio-cwl-tools/unicycler/unicycler.cwl run: ./tool/unicycler.cwl - id: spades in: - id: nanopore_reads source: nanopore_reads - id: pacbio_reads source: pacbio_reads - id: sanger_reads source: sanger_reads - id: libraries_metadata source: libraries_metadata - id: libraries_fwd_rev source: libraries_fwd_rev - id: libraries_mono source: libraries_mono - id: trusted_contigs source: trusted_contigs - id: untrusted_contigs source: untrusted_contigs - id: cov_state source: cov_state - id: cov_cutoff source: cov_cutoff - id: iontorrent source: iontorrent - id: sc source: sc - id: onlyassembler source: onlyassembler - id: careful source: careful - id: auto_kmer_choice source: auto_kmer_choice - id: kmers source: kmers out: - id: out_contigs - id: out_scaffolds - id: out_contig_stats - id: out_scaffold_stats - id: assembly_graph - id: assembly_graph_with_scaffolds - id: all_log # - id: all_script # run: ../../bio-cwl-tools/spades/spades.cwl run: ./tool/spades.cwl - id: bandage_image_unicycler in: - id: graph source: unicycler/assembly_graph out: - id: image # run: ../../bio-cwl-tools/bandage/bandage-image.cwl run: ./tool/bandage-image.cwl - id: bandage_info_unicycler in: - id: graph source: unicycler/assembly_graph out: - id: assembly_graph_info # run: ../../bio-cwl-tools/bandage/bandage-info.cwl run: ./tool/bandage-info.cwl - id: bandage_image_spades in: - id: graph source: spades/assembly_graph out: - id: image # run: ../../bio-cwl-tools/bandage/bandage-image.cwl run: ./tool/bandage-image.cwl - id: bandage_info_spades in: - id: graph source: spades/assembly_graph out: - id: assembly_graph_info # run: ../../bio-cwl-tools/bandage/bandage-info.cwl run: ./tool/bandage-info.cwl requirements: []