Explore Workflows

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

Graph Name Retrieved From View
workflow graph sequence (bam or fastqs) to trimmed fastqs

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

Path: definitions/subworkflows/sequence_to_trimmed_fastq.cwl

Branch/Commit ID: 2f65fc96207a71b1cda4e246f808bed056608cd0
workflow graph kmer_cache_store

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: e2a6cbcc36212433d8fbc804919442787a5e2a49
workflow graph default-wf5.cwl

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

Path: tests/wf/default-wf5.cwl

Branch/Commit ID: a70a83fe14a100cd16e2402ec17b2904f5eeb17d
workflow graph Trim Galore SMARTer RNA-Seq pipeline paired-end strand specific

https://chipster.csc.fi/manual/library-type-summary.html Modified original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **pair-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 files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 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 files 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-pe-smarter-dutp.cwl

Branch/Commit ID: 36fd18f11e939d3908b1eca8d2939402f7a99b0f
workflow graph Filter Protein Alignments

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

Path: protein_alignment/wf_align_filter.cwl

Branch/Commit ID: cb15f907132fb90bc66b39bb0af3c211801feba1
workflow graph mini-ST610106.cwl

https://github.com/Marco-Salvi/dtc61.git

Path: mini-ST610106.cwl

Branch/Commit ID: 2072478962b3eb2b51a3e3afd046973517a55e11
workflow graph Feature expression merge - combines feature expression from several experiments

Feature expression merge - combines feature expression from several experiments ========================================================================= Workflows merges RPKM (by default) gene expression from several experiments based on the values from GeneId, Chrom, TxStart, TxEnd and Strand columns (by default). Reported unique columns are renamed based on the experiments names.

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

Path: workflows/feature-merge.cwl

Branch/Commit ID: 36fd18f11e939d3908b1eca8d2939402f7a99b0f
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: 807fe40bca1fbd18ede6250851b9f71de98da69b
workflow graph diffbind-parallel.cwl

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

Path: workflows/ChIP-Seq/diffbind-parallel.cwl

Branch/Commit ID: 7364aa3799fd3bd7584049228618301bda53a3af
workflow graph allele-process-strain.cwl

https://github.com/Barski-lab/workflows.git

Path: subworkflows/allele-process-strain.cwl

Branch/Commit ID: 69a15832fae36a128b6cbf74187dac0dd9cfae27