Explore Workflows

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

Graph Name Retrieved From View
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: a59a803e1809a8fbfabca6b8962a8ad66dd01f1d

workflow graph qiime2 demux paired sequences

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

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

Branch/Commit ID: e2dc95d4f12210359360d814382e7201d836dfcf

Packed ID: qiime2-02-demux-emp-paired.cwl

workflow graph Functional analyis of sequences that match the 16S SSU

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

Path: workflows/16S_taxonomic_analysis.cwl

Branch/Commit ID: 7bb76f33bf40b5cd2604001cac46f967a209c47f

workflow graph EMG assembly for paired end Illumina

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

Path: workflows/emg-assembly.cwl

Branch/Commit ID: d3b8e458b7f9e52a12c0008aca645de9230e8bc9

workflow graph 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 **paired-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 paired-end RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 3. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 4. Generate BigWig file on the base of sorted BAM file 5. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 6. 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-pe.cwl

Branch/Commit ID: 581156366f91861bd4dbb5bcb59f67d468b32af3

workflow graph EMG pipeline v4.0 (single end version)

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

Path: workflows/emg-pipeline-v4-single.cwl

Branch/Commit ID: cac44f2cf14110fde9951161c663c4525772f616

workflow graph ani_top_n

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

Path: task_types/tt_ani_top_n.cwl

Branch/Commit ID: 4b73bfeb967ee9f57a0410276f7c39e784f0846f

workflow graph kmer_seq_entry_extract_wnode

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

Path: task_types/tt_kmer_seq_entry_extract_wnode.cwl

Branch/Commit ID: 4b73bfeb967ee9f57a0410276f7c39e784f0846f

workflow graph tt_kmer_compare_wnode

Pairwise comparison

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

Path: task_types/tt_kmer_compare_wnode.cwl

Branch/Commit ID: 4b73bfeb967ee9f57a0410276f7c39e784f0846f

workflow graph Cell Ranger Build Reference Indices

Cell Ranger Build Reference Indices ===================================

https://github.com/datirium/workflows.git

Path: workflows/cellranger-mkref.cwl

Branch/Commit ID: 581156366f91861bd4dbb5bcb59f67d468b32af3