Explore Workflows

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

Graph Name Retrieved From View
workflow graph Exome QC workflow

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

Path: definitions/subworkflows/qc_exome_no_verify_bam.cwl

Branch/Commit ID: 479c9b3e3fa32ec9c7cd4073cfbccc675fd254d9
workflow graph EMG QC workflow, (paired end version). Benchmarking with MG-RAST expt.

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

Path: workflows/emg-qc-paired.cwl

Branch/Commit ID: 7bb76f33bf40b5cd2604001cac46f967a209c47f
workflow graph Trim Galore RNA-Seq pipeline paired-end strand specific

Modified 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-dutp.cwl

Branch/Commit ID: b1a5dabeeeb9079b30b2871edd9c9034a1e00c1c
workflow graph QuantSeq 3' FWD, FWD-UMI or REV for single-read mRNA-Seq data

### Devel version of QuantSeq 3' FWD, FWD-UMI or REV for single-read mRNA-Seq data

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

Path: workflows/trim-quantseq-mrnaseq-se-strand-specific.cwl

Branch/Commit ID: 9e3c3e65c19873cd1ed3cf7cc3b94ebc75ae0cc5
workflow graph SV filtering workflow

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

Path: definitions/subworkflows/filter_sv_vcf.cwl

Branch/Commit ID: 869b331cfeb9dbd5907498e3eccdebc7c28283e5
workflow graph merge and annotate svs with population allele freq and vep

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

Path: definitions/subworkflows/merge_svs.cwl

Branch/Commit ID: 869b331cfeb9dbd5907498e3eccdebc7c28283e5
workflow graph rRNA_selection.cwl

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

Path: tools/rRNA_selection.cwl

Branch/Commit ID: 583307878ab83c5845c897f03db920ae8e1929e2
workflow graph cram_to_bam workflow

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

Path: cram_to_bam/workflow.cwl

Branch/Commit ID: d1ee6a2a323cee7e4af00c7e0b926c2192038e1d
workflow graph Downsample and HaplotypeCaller

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

Path: definitions/pipelines/downsample_and_recall.cwl

Branch/Commit ID: fbeea265295ae596d5a3ba563e766be0c4fc26e8
workflow graph Create Genomic Collection for Bacterial Pipeline, ASN.1 input

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

Path: genomic_source/wf_genomic_source_asn.cwl

Branch/Commit ID: 4b73bfeb967ee9f57a0410276f7c39e784f0846f