Explore Workflows

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

Graph Name Retrieved From View
workflow graph tt_blastn_wnode

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

Path: task_types/tt_blastn_wnode.cwl

Branch/Commit ID: b0ee40d34d233f1611c2e2c66b6d22a3b7deec05
workflow graph gp_makeblastdb

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

Path: progs/gp_makeblastdb.cwl

Branch/Commit ID: b38b0070edf910984f29a4a495b5dfa525b8b305
workflow graph scatter-valuefrom-wf4.cwl#main

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf4.cwl

Branch/Commit ID: 26870e38cec81af880cd3e4789ae6cee8fc27020

Packed ID: main
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: 8049a781ac4aae579fbd3036fa0bf654532f15be
workflow graph scatter-valuefrom-wf3.cwl#main

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf3.cwl

Branch/Commit ID: 7bfd77118cdc80dd7150115dd7a1a7ee6046f6fe

Packed ID: main
workflow graph VIRTUS.PE.cwl

https://github.com/yyoshiaki/VIRTUS2.git

Path: workflow/VIRTUS.PE.cwl

Branch/Commit ID: 96ccb37e04af37474771526cf0d85d3ded2005f7
workflow graph createindex.cwl

https://github.com/yyoshiaki/VIRTUS2.git

Path: workflow/createindex.cwl

Branch/Commit ID: 96ccb37e04af37474771526cf0d85d3ded2005f7
workflow graph download_gtf.cwl

https://github.com/yyoshiaki/VIRTUS2.git

Path: workflow/download_gtf.cwl

Branch/Commit ID: 96ccb37e04af37474771526cf0d85d3ded2005f7
workflow graph wf_get_peaks_se.cwl

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

Path: cwl/wf_get_peaks_se.cwl

Branch/Commit ID: c0fffc4979a92371dc0667a03e3d957bf7f77600
workflow graph wf_get_peaks_scatter_se.cwl

The \"main\" workflow. Takes fastq files generated using the seCLIP protocol (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5991800/) and outputs candidate RBP binding regions (peaks). runs: wf_get_peaks_se.cwl through scatter across multiple samples.

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

Path: cwl/wf_get_peaks_scatter_se.cwl

Branch/Commit ID: c0fffc4979a92371dc0667a03e3d957bf7f77600