Explore Workflows

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

Graph Name Retrieved From View
workflow graph 02-trim-se.cwl

ChIP-seq 02 trimming - reads: SE

 https://github.com/Duke-GCB/GGR-cwl.git

Path: v1.0/ChIP-seq_pipeline/02-trim-se.cwl

Branch/Commit ID: master
workflow graph gcaccess_from_list

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

Path: task_types/tt_gcaccess_from_list.cwl

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

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

Path: tools/SSU-from-tablehits.cwl

Branch/Commit ID: 8515542
workflow graph wf_get_peaks_nostats_se.cwl

https://github.com/YeoLab/eclip.git

Path: cwl/wf_get_peaks_nostats_se.cwl

Branch/Commit ID: master
workflow graph exome alignment and germline variant detection, with optitype for HLA typing

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

Path: definitions/pipelines/germline_exome_hla_typing.cwl

Branch/Commit ID: master
workflow graph kfdrc_cram_reheader_wf.cwl

https://github.com/cr-ste-justine/chujs-alignment-workflow.git

Path: workflows/kfdrc_cram_reheader_wf.cwl

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

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

Path: definitions/subworkflows/pindel_cat.cwl

Branch/Commit ID: downsample_and_recall
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: master
workflow graph rhapsody_wta_1.8.cwl#UncompressDatatables.cwl

https://github.com/longbow0/cwl.git

Path: v1.8/rhapsody_wta_1.8.cwl

Branch/Commit ID: master

Packed ID: UncompressDatatables.cwl
workflow graph workflow.cwl

https://github.com/FarahZKhan/scalability-reproducibility-chapter.git

Path: CWL/workflow.cwl

Branch/Commit ID: ProvCaptureDemo