Explore Workflows

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

Graph Name Retrieved From View
workflow graph count-lines6-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines6-wf.cwl

Branch/Commit ID: 8010fd2bf1e7090ba6df6ca8c84bbb96e2272d32
workflow graph AltAnalyze ICGS

AltAnalyze ICGS ===============

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

Path: workflows/altanalyze-icgs.cwl

Branch/Commit ID: 36fd18f11e939d3908b1eca8d2939402f7a99b0f
workflow graph Report generation workflow

https://github.com/arvados/arvados-tutorial.git

Path: WGS-processing/cwl/helper/report-wf.cwl

Branch/Commit ID: e4d896f5f94a9cf7b157cf87d5042e416649d87b
workflow graph gcaccess_from_list

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

Path: task_types/tt_gcaccess_from_list.cwl

Branch/Commit ID: 7b21dc40840852f3942c31b9c472346ea3f9a3ca
workflow graph extract_gencoll_ids

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

Path: task_types/tt_extract_gencoll_ids.cwl

Branch/Commit ID: 664e99a23a3ed4ba36c08323ac597c4fbcd88df1
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: 4dcc405133f22c63478b6091fb5f591b6be8950f
workflow graph Detect Variants workflow for WGS pipeline

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

Path: definitions/pipelines/detect_variants_wgs.cwl

Branch/Commit ID: cc3e7f1ccfdc7101c22bf88792608504eea7d53a
workflow graph tt_blastn_wnode

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

Path: task_types/tt_blastn_wnode.cwl

Branch/Commit ID: 16d1198871195e2229fd44dd0ad94a4ed6a87caf
workflow graph format_rrnas_from_seq_entry

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

Path: task_types/tt_format_rrnas_from_seq_entry.cwl

Branch/Commit ID: e668f9c4047f1971ae53040a5af3eccc4bfc3c53
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: 7bb76f33bf40b5cd2604001cac46f967a209c47f