Explore Workflows

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

Graph Name Retrieved From View
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: d7cd45f7072960d264962ecc5a04d7c219f65c06
workflow graph workflow.cwl

https://github.com/nal-i5k/organism_onboarding.git

Path: flow_apollo2_data_processing/processing/workflow.cwl

Branch/Commit ID: add45db6f08de518e224bdc3c04094fd69cad2d2
workflow graph workflow.cwl

https://github.com/nal-i5k/organism_onboarding.git

Path: flow_md5checksums/workflow.cwl

Branch/Commit ID: add45db6f08de518e224bdc3c04094fd69cad2d2
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: 56dafa4dab5892c5afa35713563dddc78ec5a00d
workflow graph steplevel-resreq.cwl

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

Path: v1.0/v1.0/steplevel-resreq.cwl

Branch/Commit ID: 622134ebc48980676b7e53fe39405c428920c03e
workflow graph align_merge_sas

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

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: a3affd1b9e3e16f0644a25fee1a7b87b99df57b0
workflow graph gp_makeblastdb

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

Path: progs/gp_makeblastdb.cwl

Branch/Commit ID: 4def84df33963fc9ac9d5c5f804b911d01a0d9ad
workflow graph scatter-valuefrom-wf4.cwl#main

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf4.cwl

Branch/Commit ID: 665141f319e6b23bd9924b14844f2e979f141944

Packed ID: main
workflow graph chipseq-gen-bigwig.cwl

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

Path: subworkflows/chipseq-gen-bigwig.cwl

Branch/Commit ID: cb5e5b8563be4977e9f2babc14fe084faa234847
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: 4ab9399a4777610a579ea2c259b9356f27641dcc