Explore Workflows

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

Graph Name Retrieved From View
workflow graph WF5201.cwl

https://github.com/Marco-Salvi/cwl-ro-crate.git

Path: WF5201.cwl

Branch/Commit ID: main
workflow graph SSU-from-tablehits.cwl

https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git

Path: tools/SSU-from-tablehits.cwl

Branch/Commit ID: 5833078
workflow graph workflow.cwl

https://github.com/mr-c/cwltests.git

Path: cwl/workflow.cwl

Branch/Commit ID: master
workflow graph RNA-Seq pipeline single-read stranded mitochondrial

Slightly changed original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for **strand specific single-read** experiment. An additional steps were added to map data to mitochondrial chromosome only and then merge the output. Experiment files in [FASTQ](http://maq.sourceforge.net/fastq.shtml) format either compressed or not can be used. Current workflow should be used only with single-read strand specific RNA-Seq data. It performs the following steps: 1. `STAR` to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. `fastx_quality_stats` to analyze input FASTQ file and generate quality statistics file 3. `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/rnaseq-se-dutp-mitochondrial.cwl

Branch/Commit ID: 7ced5a5259dbd8b3fc64456beaeffd44f4a24081
workflow graph bams2gvcf.wBQSR.multisamples.cwl

https://github.com/ddbj/human-reseq.git

Path: Workflows/bams2gvcf.wBQSR.multisamples.cwl

Branch/Commit ID: master
workflow graph kmer_ref_compare_wnode

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

Path: task_types/tt_kmer_ref_compare_wnode.cwl

Branch/Commit ID: cc7fb3e5c534036638921878527a610fd5e1c2ab
workflow graph Per-region pindel

https://github.com/apaul7/cancer-genomics-workflow.git

Path: definitions/subworkflows/pindel_cat.cwl

Branch/Commit ID: low-vaf
workflow graph Apply filters to VCF file

https://github.com/apaul7/cancer-genomics-workflow.git

Path: definitions/subworkflows/filter_vcf_nonhuman.cwl

Branch/Commit ID: low-vaf
workflow graph count-lines12-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines12-wf.cwl

Branch/Commit ID: 49cd284a8fc7884de763573075d3e1d6a4c1ffdd
workflow graph Functional analyis of sequences that match the 16S SSU

https://github.com/proteinswebteam/ebi-metagenomics-cwl.git

Path: workflows/16S_functional_analysis.cwl

Branch/Commit ID: caea457