Explore Workflows

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

Graph Name Retrieved From View
workflow graph allele-vcf-alignreads-se-pe.cwl

Workflow maps FASTQ files from `fastq_files` input into reference genome `reference_star_indices_folder` and insilico generated `insilico_star_indices_folder` genome (concatenated genome for both `strain1` and `strain2` strains). For both genomes STAR is run with `outFilterMultimapNmax` parameter set to 1 to discard all of the multimapped reads. For insilico genome SAM file is generated. Then it's splitted into two SAM files based on strain names and then sorted by coordinates into the BAM format. For reference genome output BAM file from STAR slignment is also coordinate sorted.

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

Path: subworkflows/allele-vcf-alignreads-se-pe.cwl

Branch/Commit ID: 09c08f858e91c4cfd387067f07445722ac7e18aa
workflow graph gcaccess_from_list

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

Path: task_types/tt_gcaccess_from_list.cwl

Branch/Commit ID: 6d8d29a2156b93a75f1d1c6952738bd63f6bd98e
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: 57863b6131d8262c5ce864adaf8e4038401e71a2
workflow graph chunking-subwf-IPS.cwl

https://github.com/EBI-Metagenomics/pipeline-v5.git

Path: workflows/subworkflows/chunking-subwf-IPS.cwl

Branch/Commit ID: 6ec8d032feb120eb0eebf9a0c01d48deabf42eea
workflow graph Pairwise genomic regions intersection

Pairwise genomic regions intersection ============================================= Overlaps peaks from two ChIP/ATAC experiments

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

Path: workflows/peak-intersect.cwl

Branch/Commit ID: 22880e0f41d0420a17d643e8a6e8ee18165bbfbf
workflow graph cache_asnb_entries

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

Path: task_types/tt_cache_asnb_entries.cwl

Branch/Commit ID: ac387721a55fd91df3dcdf16e199354618b136d1
workflow graph align_merge_sas

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

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: 6d8d29a2156b93a75f1d1c6952738bd63f6bd98e
workflow graph spurious_annot

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

Path: spurious_annot/wf_spurious_annot_pass1.cwl

Branch/Commit ID: cb15f907132fb90bc66b39bb0af3c211801feba1
workflow graph tt_hmmsearch_wnode.cwl

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

Path: task_types/tt_hmmsearch_wnode.cwl

Branch/Commit ID: cb15f907132fb90bc66b39bb0af3c211801feba1
workflow graph varscan somatic workflow

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

Path: definitions/subworkflows/varscan.cwl

Branch/Commit ID: 0c4f4e59c265eb22aed3d2d37b173cb5430773d2