Explore Workflows

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Graph Name Retrieved From View
workflow graph processing.cwl

https://github.com/hubmapconsortium/spatial-transcriptomics-pipeline.git

Path: steps/processing.cwl

Branch/Commit ID: 5b866e480fb557cf53d619a22068c73548e337d5
workflow graph abundance

abundace profiles from annotated files, for protein and/or rna

 https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/abundance-clca.workflow.cwl

Branch/Commit ID: 932da3abed7166bd5a962871386ba2c31d47b85c
workflow graph heatmap-prepare.cwl

Workflow runs homer-make-tag-directory.cwl tool using scatter for the following inputs - bam_file - fragment_size - total_reads `dotproduct` is used as a `scatterMethod`, so one element will be taken from each array to construct each job: 1) bam_file[0] fragment_size[0] total_reads[0] 2) bam_file[1] fragment_size[1] total_reads[1] ... N) bam_file[N] fragment_size[N] total_reads[N] `bam_file`, `fragment_size` and `total_reads` arrays should have the identical order.

https://github.com/datirium/workflows.git

Path: subworkflows/heatmap-prepare.cwl

Branch/Commit ID: 09c08f858e91c4cfd387067f07445722ac7e18aa
workflow graph Trim Galore RNA-Seq pipeline single-read strand specific

Note: should be updated The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **single-end** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the single-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ file 2. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 4. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 5. Generate BigWig file on the base of sorted BAM file 6. Map input FASTQ file to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 7. Calculate isoform expression level for the sorted BAM file and GTF/TAB annotation file using GEEP reads-counting utility; export results to file

 https://github.com/datirium/workflows.git

Path: workflows/trim-rnaseq-se-dutp.cwl

Branch/Commit ID: cbefc215d8286447620664fb47076ba5d81aa47f
workflow graph Nested workflow example

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/nested.cwl

Branch/Commit ID: 691dea280b40ac177b4a38b33375139ca0ce7e81
workflow graph conflict-wf.cwl#collision

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/conflict-wf.cwl

Branch/Commit ID: 3e90671b25f7840ef2926ad2bacbf447772dda94

Packed ID: collision
workflow graph trnascan_wnode and gpx_qdump combined

https://github.com/ncbi/pgap.git

Path: bacterial_trna/wf_scan_and_dump.cwl

Branch/Commit ID: 424a01693259a75641dc249d553235aa38a6ce23
workflow graph count-lines11-wf.cwl

https://github.com/common-workflow-language/cwltool.git

Path: cwltool/schemas/v1.0/v1.0/count-lines11-wf.cwl

Branch/Commit ID: aaaece1c097c3f06afa21f7ecddcc85519e2bb2b
workflow graph mut2.cwl

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/mut2.cwl

Branch/Commit ID: 691dea280b40ac177b4a38b33375139ca0ce7e81
workflow graph kmer_top_n

https://github.com/ncbi/pgap.git

Path: task_types/tt_kmer_top_n.cwl

Branch/Commit ID: 807fe40bca1fbd18ede6250851b9f71de98da69b