Explore Workflows

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

Graph Name Retrieved From View
workflow graph indexing_bed

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/subworkflows/indexing_bed.cwl

Branch/Commit ID: c494fa4f60d9215842c4d2c75ed7d89757435b0f
workflow graph step-valuefrom2-wf.cwl

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

Path: tests/step-valuefrom2-wf.cwl

Branch/Commit ID: 31ec48a8d81ef7c1b2c5e9c0a19e7623efe4a1e2
workflow graph Running cellranger count and lineage inference

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/single_cell_rnaseq.cwl

Branch/Commit ID: 4bc0a4577d626b65a4b44683e5a1ab2f7d7faf4c
workflow graph record-output-wf_v1_0.cwl

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

Path: testdata/record-output-wf_v1_0.cwl

Branch/Commit ID: 6a46105708870aa3cf97c8ba91884272b2857975
workflow graph Trim Galore SMARTer RNA-Seq pipeline paired-end strand specific

https://chipster.csc.fi/manual/library-type-summary.html 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-smarter-dutp.cwl

Branch/Commit ID: 00ea05e22788029370898fd4c17798b11edf0e57
workflow graph bam to trimmed fastqs and biscuit alignments

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl

Branch/Commit ID: d2c2f2eb846ae2e9cdcab46e3bb88e42126cb3f5
workflow graph ValidatePedestalEvents

Compare simulated and measured pedestal events (exposed to night-sky background light and with closed camera lid).

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

Path: workflows/ValidatePedestalEvents.cwl

Branch/Commit ID: 789752af87eb190387ff2acb4c95c7a5cdb961e7
workflow graph scatter-valuefrom-wf4.cwl#main

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

Path: tests/scatter-valuefrom-wf4.cwl

Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3

Packed ID: main
workflow graph io-file-default-wf.cwl

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

Path: tests/io-file-default-wf.cwl

Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3
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: 77669d4dd1d1ebd2bdd9810f911608146d9b8e51