Get the CWL workflow graph as a list of two data frames: a data frame of nodes and a data frame of edges.
get_graph(inputs, outputs, steps)
| inputs | Parsed inputs |
|---|---|
| outputs | Parsed outputs |
| steps | Parsed steps |
List of two data frames containing node and edge information
# sbg:draft2 flow <- system.file("cwl/sbg/workflow/gatk4-wgs.json", package = "tidycwl") %>% read_cwl_json() get_graph( flow %>% parse_inputs(), flow %>% parse_outputs(), flow %>% parse_steps() ) %>% str()#> List of 2 #> $ nodes:'data.frame': 36 obs. of 3 variables: #> ..$ id : chr [1:36] "intervals_file" "dbsnp" "mills" "fastq" ... #> ..$ label: chr [1:36] "Target BED" "dbsnp" "Mills" "Fastq" ... #> ..$ group: chr [1:36] "input" "input" "input" "input" ... #> $ edges:'data.frame': 43 obs. of 5 variables: #> ..$ from : chr [1:43] "SBG_FASTA_Indices" "Sambamba_Merge" "reference" "BWA_MEM_Bundle_0_7_17" ... #> ..$ to : chr [1:43] "SBG_Genome_Coverage" "SBG_Genome_Coverage" "SBG_Untar_fasta" "Sambamba_Merge" ... #> ..$ port_from: chr [1:43] "fasta_reference" "merged_bam" NA "aligned_reads" ... #> ..$ port_to : chr [1:43] "fasta" "bam" "input_tar_with_reference" "bams" ... #> ..$ type : chr [1:43] "step_to_step" "step_to_step" "input_to_step" "step_to_step" ...# v1.0 flow <- system.file("cwl/sbg/workflow/rnaseq-salmon.json", package = "tidycwl") %>% read_cwl_json() get_graph( flow %>% parse_inputs(), flow %>% parse_outputs(), flow %>% parse_steps() ) %>% str()#> List of 2 #> $ nodes:'data.frame': 62 obs. of 3 variables: #> ..$ id : chr [1:62] "transcriptome_fasta_or_salmon_index_archive" "reads" "gtf" "max_number_of_parallel_jobs" ... #> ..$ label: chr [1:62] "Transcriptome FASTA or Salmon index archive" "FASTQ Read Files" "Gene map or GTF file" "Maximum number of parallel jobs" ... #> ..$ group: chr [1:62] "input" "input" "input" "input" ... #> $ edges:'data.frame': 62 obs. of 5 variables: #> ..$ from : chr [1:62] "Salmon_Quant___Reads" "Salmon_Quant___Reads" "reads" "max_number_of_parallel_jobs" ... #> ..$ to : chr [1:62] "SBG_Create_Expression_Matrix___Transcripts" "SBG_Create_Expression_Matrix___Genes" "SBG_Pair_FASTQs_by_Metadata_1" "SBG_Pair_FASTQs_by_Metadata_1" ... #> ..$ port_from: chr [1:62] "quant_sf" "quant_genes_sf" NA NA ... #> ..$ port_to : chr [1:62] NA NA NA NA ... #> ..$ type : chr [1:62] "step_to_step" "step_to_step" "input_to_step" "input_to_step" ...