Explore Workflows

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

Graph Name Retrieved From View
workflow graph Trim Galore RNA-Seq pipeline single-read

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.cwl

Branch/Commit ID: 87f213456b3f966b773d396cce1fe5a272dad858
workflow graph cgpRna_workflow.cwl

https://github.com/cancerit/cgpRna.git

Path: cwls/cgpRna_workflow.cwl

Branch/Commit ID: 48345a737f47e6067c161814b16413c0e2f1d48b
workflow graph mut3.cwl

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

Path: tests/wf/mut3.cwl

Branch/Commit ID: bbe20f54deea92d9c9cd38cb1f23c4423133d3de
workflow graph linc_calibrator.cwl

https://git.astron.nl/RD/LINC.git

Path: workflows/linc_calibrator.cwl

Branch/Commit ID: a94862bb3d50860cd348a5d5d1aa76fa0cde332a
workflow graph cond-wf-005.1.cwl

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

Path: testdata/cond-wf-005.1.cwl

Branch/Commit ID: 77669d4dd1d1ebd2bdd9810f911608146d9b8e51
workflow graph kmer_cache_store

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: 16e3915d2a357e2a861b30911c832e5ddc0c1784
workflow graph Filter Protein Alignments I

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

Path: protein_alignment/wf_align_filter.cwl

Branch/Commit ID: 62464fecfe319398affdec50d46054a97466f61a
workflow graph cache_asnb_entries

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

Path: task_types/tt_cache_asnb_entries.cwl

Branch/Commit ID: cd97086739ae5988bab09b05e9259675c4b6bce6
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: a23f42ef49c10a588fd35a3afaad5de03e253533
workflow graph exome alignment and somatic variant detection for cle purpose

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

Path: definitions/pipelines/somatic_exome_cle.cwl

Branch/Commit ID: 40097e1ed094c5b42b68f3db2ff2cbe78c182479