Explore Workflows

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

Graph Name Retrieved From View
workflow graph functional analysis prediction with InterProScan

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

Path: workflows/functional_analysis.cwl

Branch/Commit ID: 25129f55226dee595ef941edc24d3c44414e0523
workflow graph tRNA_selection.cwl

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

Path: tools/tRNA_selection.cwl

Branch/Commit ID: 25129f55226dee595ef941edc24d3c44414e0523
workflow graph 02-trim-pe.cwl

ChIP-seq 02 trimming - reads: PE

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

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

Branch/Commit ID: 6da8cef69f3a585fc3e2f4f2f730d361cbe2e978
workflow graph Trim Galore RNA-Seq pipeline paired-end

The 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.cwl

Branch/Commit ID: 00ea05e22788029370898fd4c17798b11edf0e57
workflow graph varscan_remap_test.cwl

https://github.com/ding-lab/TinDaisy.git

Path: cwl/workflows/varscan_remap_test.cwl

Branch/Commit ID: 41d27deba0ca34b0cc3f3a7eefcd44d0cb7baffa
workflow graph tindaisy-420.cwl

https://github.com/ding-lab/TinDaisy.git

Path: cwl/workflows/tindaisy-420.cwl

Branch/Commit ID: 41d27deba0ca34b0cc3f3a7eefcd44d0cb7baffa
workflow graph revsort-single-no-docker.cwl

Reverse the lines in a document, then sort those lines.

 https://github.com/Duke-GCB/calrissian.git

Path: input-data/revsort-single-no-docker.cwl

Branch/Commit ID: 367e35ceabf68ab49e8097075abb0471d84a7fde
workflow graph restart-tindaisy-hotspot.cwl

https://github.com/ding-lab/TinDaisy.git

Path: cwl/workflows/restart-tindaisy-hotspot.cwl

Branch/Commit ID: 41d27deba0ca34b0cc3f3a7eefcd44d0cb7baffa
workflow graph exomeseq-gatk4-02-variantdiscovery.cwl

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

Path: subworkflows/exomeseq-gatk4-02-variantdiscovery.cwl

Branch/Commit ID: e82f3a71183048dd6700ec6725ee526ac1a95238
workflow graph QIIME2 Step 1 paired end sequences

QIIME2 Import and Demux Step 1 paired end sequences

https://github.com/duke-gcb/bespin-cwl.git

Path: packed/qiime2-step1-import-demux-paired.cwl

Branch/Commit ID: e2dc95d4f12210359360d814382e7201d836dfcf

Packed ID: main