Explore Workflows

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

Graph Name Retrieved From View
workflow graph Metagenomics workflow

Workflow for Metagenomics from raw reads to annotated bins. Steps: - workflow_illumina_quality.cwl: - FastQC (control) - fastp (quality trimming) - kraken2 (taxonomy) - bbmap contamination filter - SPAdes (Assembly) - QUAST (Assembly quality report) - BBmap (Read mapping to assembly) - Contig binning (OPTIONAL)

https://git.wur.nl/unlock/cwl.git

Path: cwl/workflows/workflow_metagenomics_assembly.cwl

Branch/Commit ID: b9097b82e6ab6f2c9496013ce4dd6877092956a0
workflow graph indexing_bed

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/cwl/subworkflows/indexing_bed.cwl

Branch/Commit ID: d2314468d2d2ec177d278899820de1cbfe8c8fb6
workflow graph EMG core analysis for Illumina

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

Path: workflows/emg-core-analysis-v4.cwl

Branch/Commit ID: 5dc7c5ca618a248a99bd4bf5f3042cdb21947193
workflow graph scatter-wf4.cwl#main

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

Path: tests/wf/scatter-wf4.cwl

Branch/Commit ID: 0e98de8f692bb7b9626ed44af835051750ac20cd

Packed ID: main
workflow graph Build STAR indices

Workflow runs [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) to build indices for reference genome provided in a single FASTA file as fasta_file input and GTF annotation file from annotation_gtf_file input. Generated indices are saved in a folder with the name that corresponds to the input genome.

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

Path: workflows/star-index.cwl

Branch/Commit ID: 8049a781ac4aae579fbd3036fa0bf654532f15be
workflow graph xenbase-sra-to-fastq-pe.cwl

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

Path: subworkflows/xenbase-sra-to-fastq-pe.cwl

Branch/Commit ID: 7a4593d2fa5b2fcbedc9219dc5687a4bc5aea66a
workflow graph SSU-from-tablehits.cwl

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

Path: tools/SSU-from-tablehits.cwl

Branch/Commit ID: 7bb76f33bf40b5cd2604001cac46f967a209c47f
workflow graph trimmed_fastq

Quality Control (raw data), Raw Data trimming and Quality Control (pre-processed)

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/cwl/subworkflows/trimmed_fastq.cwl

Branch/Commit ID: d2314468d2d2ec177d278899820de1cbfe8c8fb6
workflow graph LSU-from-tablehits.cwl

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

Path: tools/LSU-from-tablehits.cwl

Branch/Commit ID: 7bb76f33bf40b5cd2604001cac46f967a209c47f
workflow graph merge-bam-parallel

This workflow merge BAM files per condition in parallel

 https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/File-formats/merge-bam-parallel.cwl

Branch/Commit ID: 6eb7fec3bd018addf02bb3285cb56d9453319d5d