Explore Workflows

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Graph Name Retrieved From View
workflow graph Trim Galore RNA-Seq pipeline single-read

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.cwl

Branch/Commit ID: 664de58d95728edbf7d369d894f9037ebe2475fa
workflow graph workflow.cwl

https://gitlab.ebrains.eu/sofiakar/yre-standardised-workflows.git

Path: Workflows/PSD_workflow_smr_2/workflow.cwl

Branch/Commit ID: 320a96321dcbc39afb8e82cec797726733eb70f7
workflow graph checkm_wnode

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

Path: task_types/tt_checkm_wnode.cwl

Branch/Commit ID: c009eeba7379efbbd37b8d5013a83f161f06939b
workflow graph sum-wf-noET.cwl

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/sum-wf-noET.cwl

Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733
workflow graph preprocessing for metagenomic short reads

https://github.com/EBI-Metagenomics/CWL-assembly.git

Path: src/workflows/metagenome_qc.cwl

Branch/Commit ID: 39efebc161b7022163094e5a73a51a08a968e9c7
workflow graph gp_makeblastdb

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

Path: progs/gp_makeblastdb.cwl

Branch/Commit ID: c7c674b873b9925b28ffbd602974eec4bfe78cf9
workflow graph worldpopulation-htcondorcern.cwl

https://github.com/reanahub/reana-demo-worldpopulation.git

Path: workflow/cwl/worldpopulation-htcondorcern.cwl

Branch/Commit ID: 7d08708a8deff739a2b9bc0a7b2d4e50105f21d8
workflow graph gridss-germline.cwl

https://github.com/biosciencedbc/jga-analysis.git

Path: per-sample/Workflows/gridss-germline.cwl

Branch/Commit ID: main
workflow graph bwa_index

Modified from https://github.com/kids-first/kf-somatic-workflow/blob/master/sub_workflows/prepare_reference.cwl

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

Path: structuralvariants/cwl/subworkflows/bwa_index.cwl

Branch/Commit ID: f4c51a054b1ec51d07d89c6a8218e610653675f3
workflow graph Detect Variants workflow

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

Path: definitions/pipelines/detect_variants_nonhuman.cwl

Branch/Commit ID: 8da2b1cd6fa379b2c22baf9dad762d39630e6f46