Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph 1st-workflow.cwl

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

Path: tests/wf/1st-workflow.cwl

Branch/Commit ID: 49cd284a8fc7884de763573075d3e1d6a4c1ffdd
workflow graph trim-rnaseq-pe-dutp.cwl

Runs RNA-Seq BioWardrobe basic analysis with strand specific pair-end data file.

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

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

Branch/Commit ID: 4b8bb1a1ec39056253ca8eee976078e51f4a954e
workflow graph workflow_input_format_expr_v1_2.cwl

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

Path: testdata/workflow_input_format_expr_v1_2.cwl

Branch/Commit ID: 0ab1d42d10f7311bb4032956c4a6f3d2730d9507
workflow graph pass-unconnected.cwl

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/pass-unconnected.cwl

Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733
workflow graph mut2.cwl

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

Path: tests/wf/mut2.cwl

Branch/Commit ID: d6000d32f6c8fbd26421a2d30d79b28901d58fb0
workflow graph taxonomy_check_16S

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

Path: task_types/tt_taxonomy_check_16S.cwl

Branch/Commit ID: be465ad19b07378f3f863f2c4e0019b420c859f2
workflow graph count-lines17-wf.cwl

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/count-lines17-wf.cwl

Branch/Commit ID: ea9f8634e41824ac3f81c3dde698d5f0eef54f1b
workflow graph kmer_seq_entry_extract_wnode

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

Path: task_types/tt_kmer_seq_entry_extract_wnode.cwl

Branch/Commit ID: 708e141d99f6e5f30d9402d9f890562606a0d97e
workflow graph align_sort_sa

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: 708e141d99f6e5f30d9402d9f890562606a0d97e
workflow graph Trim Galore RNA-Seq pipeline paired-end strand specific

Modified original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **pair-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 files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 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 files 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-pe-dutp.cwl

Branch/Commit ID: 4a80f5b8f86c83af39494ecc309b789aeda77964