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Graph Name Retrieved From View
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: ad948b2691ef7f0f34de38f0102c3cd6f5182b29
workflow graph scatter-wf4.cwl#main

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

Path: tests/wf/scatter-wf4.cwl

Branch/Commit ID: 07ebbea2bdf97955060c1dd563580b386388519b

Packed ID: main
workflow graph allele-vcf-alignreads-se-pe.cwl

Workflow maps FASTQ files from `fastq_files` input into reference genome `reference_star_indices_folder` and insilico generated `insilico_star_indices_folder` genome (concatenated genome for both `strain1` and `strain2` strains). For both genomes STAR is run with `outFilterMultimapNmax` parameter set to 1 to discard all of the multimapped reads. For insilico genome SAM file is generated. Then it's splitted into two SAM files based on strain names and then sorted by coordinates into the BAM format. For reference genome output BAM file from STAR slignment is also coordinate sorted.

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

Path: subworkflows/allele-vcf-alignreads-se-pe.cwl

Branch/Commit ID: 9bf0aa495735f8081bb5870cb32fc898b9e6eb22
workflow graph Single-Cell Preprocessing Pipeline

Devel version of Single-Cell Preprocessing Pipeline ===================================================

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

Path: workflows/single-cell-preprocess.cwl

Branch/Commit ID: 4ab9399a4777610a579ea2c259b9356f27641dcc
workflow graph Functional analyis of sequences that match the 16S SSU

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

Path: workflows/16S_functional_analysis.cwl

Branch/Commit ID: caea457b17388fdc5cb088364c194504ae736bdd
workflow graph Motif Finding with HOMER with random background regions

Motif Finding with HOMER with random background regions --------------------------------------------------- HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. Here is how we generate background for Motifs Analysis ------------------------------------- 1. Take input file with regions in a form of “chr\" “start\" “end\" 2. Sort and remove duplicates from this regions file 3. Extend each region in 20Kb into both directions 4. Merge all overlapped extended regions 5. Subtract not extended regions from the extended ones 6. Randomly distribute not extended regions within the regions that we got as a result of the previous step 7. Get fasta file from these randomly distributed regions (from the previous step). Use it as background For more information please refer to: ------------------------------------- [Official documentation](http://homer.ucsd.edu/homer/motif/)

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

Path: workflows/homer-motif-analysis.cwl

Branch/Commit ID: 935a78f1aff757f977de4e3672aefead3b23606b
workflow graph VIRTUS.SE.singlevirus.cwl

https://github.com/yyoshiaki/VIRTUS.git

Path: workflow/VIRTUS.SE.singlevirus.cwl

Branch/Commit ID: 49faf55f97c8f3084b426d2db6640519d6f2ce71
workflow graph rnaseq-pe-dutp.cwl

Runs RNA-Seq BioWardrobe basic analysis with strand specific pair-end data file.

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

Path: workflows/rnaseq-pe-dutp.cwl

Branch/Commit ID: 12edfc2207507e53c6b5bb21e50decb5535a12f7
workflow graph Filter differentially expressed genes from DESeq for Tag Density Profile Analyses

Filters differentially expressed genes from DESeq for Tag Density Profile Analyses ================================================================================== Tool filters output from DESeq pipeline run for genes to create a file with regions of interest for Tag Density Profile Analyses.

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

Path: workflows/filter-deseq-for-heatmap.cwl

Branch/Commit ID: 935a78f1aff757f977de4e3672aefead3b23606b
workflow graph Nanopore assembly workflow

**Workflow for sequencing with ONT Nanopore data, from basecalled reads to (meta)assembly and binning**<br> - Workflow Nanopore Quality - Kraken2 taxonomic classification of FASTQ reads - Flye (de-novo assembly) - Medaka (assembly polishing) - metaQUAST (assembly quality reports) **When Illumina reads are provided:** - Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1 - Assembly polishing with Pilon<br> - Workflow binnning https://workflowhub.eu/workflows/64?version=11 - Metabat2 - CheckM - BUSCO - GTDB-Tk **All tool CWL files and other workflows can be found here:**<br> Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl<br> Workflows: https://git.wur.nl/unlock/cwl/-/tree/master/cwl/workflows<br> The dependencies are either accessible from https://unlock-icat.irods.surfsara.nl (anonymous,anonymous)<br> and/or<br> By using the conda / pip environments as shown in https://git.wur.nl/unlock/docker/-/blob/master/kubernetes/scripts/setup.sh<br>

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

Path: cwl/workflows/workflow_nanopore_assembly.cwl

Branch/Commit ID: b9097b82e6ab6f2c9496013ce4dd6877092956a0