Explore Workflows

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Graph Name Retrieved From View
workflow graph FastQC - a quality control tool for high throughput sequence data

FastQC - a quality control tool for high throughput sequence data ===================================== FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. The main functions of FastQC are: - Import of data from FastQ files (any variant) - Providing a quick overview to tell you in which areas there may be problems - Summary graphs and tables to quickly assess your data - Export of results to an HTML based permanent report - Offline operation to allow automated generation of reports without running the interactive application

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

Path: workflows/fastqc.cwl

Branch/Commit ID: 10ce6e113f749c7bd725e426445220c3bdc5ddf1
workflow graph Cellranger Reanalyze

Cellranger Reanalyze ====================

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

Path: workflows/cellranger-reanalyze.cwl

Branch/Commit ID: ebbf23764ede324cabc064bd50647c1f643726fa
workflow graph exome alignment and somatic variant detection

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

Path: definitions/pipelines/somatic_exome.cwl

Branch/Commit ID: 051074fce4afd9732ef34db9dd43d3a1d8e979d6
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: c6bfa0de917efb536dd385624fc7702e6748e61d
workflow graph iwdr_with_nested_dirs.cwl

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

Path: cwltool/schemas/v1.0/v1.0/iwdr_with_nested_dirs.cwl

Branch/Commit ID: f207d168f4e7eb4dd2279840d4062ba75d9c79c3
workflow graph Unaligned to aligned BAM

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

Path: definitions/subworkflows/align.cwl

Branch/Commit ID: 7b4b489474473c3d2d992a838b89632c2b97dc2c
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: 5c7799a145595323d0a8628be1fe0e24985e793a

Packed ID: main
workflow graph kfdrc_bwamem_subwf.cwl

https://github.com/kids-first/kf-alignment-workflow.git

Path: dev/ultra-opt/kfdrc_bwamem_subwf.cwl

Branch/Commit ID: 4b8dc1e00d3dd082ee31629afdeda6103f75dc3a
workflow graph kmer_cache_retrieve

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

Path: task_types/tt_kmer_cache_retrieve.cwl

Branch/Commit ID: a7fced3ed8c839272c8f3a8db9da7bc8cd50271f
workflow graph trnascan_wnode and gpx_qdump combined

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

Path: bacterial_trna/wf_scan_and_dump.cwl

Branch/Commit ID: 551493f5c24b757a46cd22821a05e6ac6dcceb7f