Explore Workflows

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: e99e80a2c19682d59947bde04a892d7b6d90091c

Mark duplicates

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

Path: structuralvariants/cwl/abstract_operations/subworkflows/picard_markduplicates.cwl

Branch/Commit ID: 82e533a98a763a258bd841ed0032c79445478d56

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

Path: tests/wf/sec-wf.cwl

Branch/Commit ID: aec33fcfa3459a90cbba8c88ebb991be94d21429

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

Path: structuralvariants/cwl/abstract_operations/subworkflows/samtools_sort.cwl

Branch/Commit ID: 9ac2d150a57d1996210ed6a44dd0c0404dab383c

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

Path: workflows/16S_taxonomic_analysis.cwl

Branch/Commit ID: 5dc7c5ca618a248a99bd4bf5f3042cdb21947193

https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git

Path: workflows/emg-pipeline-v3.cwl

Branch/Commit ID: cac44f2cf14110fde9951161c663c4525772f616

Workflow runs homer-make-tag-directory.cwl tool using scatter for the following inputs - bam_file - fragment_size - total_reads `dotproduct` is used as a `scatterMethod`, so one element will be taken from each array to construct each job: 1) bam_file[0] fragment_size[0] total_reads[0] 2) bam_file[1] fragment_size[1] total_reads[1] ... N) bam_file[N] fragment_size[N] total_reads[N] `bam_file`, `fragment_size` and `total_reads` arrays should have the identical order.

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

Path: tools/heatmap-prepare.cwl

Branch/Commit ID: 8049a781ac4aae579fbd3036fa0bf654532f15be

https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git

Path: workflows/emg-assembly.cwl

Branch/Commit ID: 7bb76f33bf40b5cd2604001cac46f967a209c47f

**Workflow for nanopore read quality control and contamination filtering.** - FastQC before filtering (read quality control) - Kraken2 taxonomic read classification - Minimap2 read filtering based on given references - FastQC after filtering (read quality control) **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> WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default

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

Path: cwl/workflows/workflow_nanopore_quality.cwl

Branch/Commit ID: b9097b82e6ab6f2c9496013ce4dd6877092956a0

# ChIP-Seq basic analysis workflow for single-read data Reads are aligned to the reference genome with [Bowtie](http://bowtie-bio.sourceforge.net/index.shtml). Results are saved as coordinate sorted [BAM](http://samtools.github.io/hts-specs/SAMv1.pdf) alignment and index BAI files. Optionally, PCR duplicates can be removed. To obtain coverage in [bigWig](https://genome.ucsc.edu/goldenpath/help/bigWig.html) format, average fragment length is calculated by [MACS2](https://github.com/taoliu/MACS), and individual reads are extended to this length in the 3’ direction. Areas of enrichment identified by MACS2 are saved in ENCODE [narrow peak](http://genome.ucsc.edu/FAQ/FAQformat.html#format12) or [broad peak](https://genome.ucsc.edu/FAQ/FAQformat.html#format13) formats. Called peaks together with the nearest genes are saved in TSV format. In addition to basic statistics (number of total/mapped/multi-mapped/unmapped/duplicate reads), pipeline generates several quality control measures. Base frequency plots are used to estimate adapter contamination, a frequent occurrence in low-input ChIP-Seq experiments. Expected distinct reads count from [Preseq](http://smithlabresearch.org/software/preseq/) can be used to estimate read redundancy for a given sequencing depth. Average tag density profiles can be used to estimate ChIP enrichment for promoter proximal histone modifications. Use of different parameters for different antibodies (calling broad or narrow peaks) is possible. Additionally, users can elect to use BAM file from another experiment as control for MACS2 peak calling. ## Cite as *Kartashov AV, Barski A. BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data. Genome Biol. 2015;16(1):158. Published 2015 Aug 7. [doi:10.1186/s13059-015-0720-3](https://www.ncbi.nlm.nih.gov/pubmed/26248465)* ## Software versions - Bowtie 1.2.0 - Samtools 1.4 - Preseq 2.0 - MACS2 2.1.1.20160309 - Bedtools 2.26.0 - UCSC userApps v358 ## Inputs | ID | Label | Description | Required | Default | Upstream analyses | | ------------------------- | ---------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------- | :------: | ------- | ------------------------------- | | **fastq\_file** | FASTQ file | Single-read sequencing data in FASTQ format (fastq, fq, bzip2, gzip, zip) | + | | | | **indices\_folder** | Genome indices | Directory with the genome indices generated by Bowtie | + | | genome\_indices/bowtie\_indices | | **annotation\_file** | Genome annotation file | Genome annotation file in TSV format | + | | genome\_indices/annotation | | **genome\_size** | Effective genome size | The length of the mappable genome (hs, mm, ce, dm or number, for example 2.7e9) | + | | genome\_indices/genome\_size | | **chrom\_length** | Chromosome lengths file | Chromosome lengths file in TSV format | + | | genome\_indices/chrom\_length | | **broad\_peak** | Call broad peaks | Make MACS2 call broad peaks by linking nearby highly enriched regions | + | | | | **control\_file** | Control ChIP-Seq single-read experiment | Indexed BAM file from the ChIP-Seq single-read experiment to be used as a control for MACS2 peak calling | | Null | control\_file/bambai\_pair | | **exp\_fragment\_size** | Expected fragment size | Expected fragment size for read extenstion towards 3' end if *force\_fragment\_size* was set to True or if calculated by MACS2 fragment size was less that 80 bp | | 150 | | | **force\_fragment\_size** | Force peak calling with expected fragment size | Make MACS2 don't build the shifting model and use expected fragment size for read extenstion towards 3' end | | False | | | **clip\_3p\_end** | Clip from 3' end | Number of base pairs to clip from 3' end | | 0 | | | **clip\_5p\_end** | Clip from 5' end | Number of base pairs to clip from 5' end | | 0 | | | **remove\_duplicates** | Remove PCR duplicates | Remove PCR duplicates from sorted BAM file | | False | | | **threads** | Number of threads | Number of threads for those steps that support multithreading | | 2 | | ## Outputs | ID | Label | Description | Required | Visualization | | ------------------------ | ---------------------------------- | ------------------------------------------------------------------------------------ | :------: | ------------------------------------------------------------------ | | **fastx\_statistics** | FASTQ quality statistics | FASTQ quality statistics in TSV format | + | *Base Frequency* and *Quality Control* plots in *QC Plots* tab | | **bambai\_pair** | Aligned reads | Coordinate sorted BAM alignment and index BAI files | + | *Nucleotide Sequence Alignments* track in *IGV Genome Browser* tab | | **bigwig** | Genome coverage | Genome coverage in bigWig format | + | *Genome Coverage* track in *IGV Genome Browser* tab | | **iaintersect\_result** | Gene annotated peaks | MACS2 peak file annotated with nearby genes | + | *Peak Coordinates* table in *Peak Calling* tab | | **atdp\_result** | Average Tag Density Plot | Average Tag Density Plot file in TSV format | + | *Average Tag Density Plot* in *QC Plots* tab | | **macs2\_called\_peaks** | Called peaks | Called peaks file with 1-based coordinates in XLS format | + | | | **macs2\_narrow\_peaks** | Narrow peaks | Called peaks file in ENCODE narrow peak format | | *Narrow peaks* track in *IGV Genome Browser* tab | | **macs2\_broad\_peaks** | Broad peaks | Called peaks file in ENCODE broad peak format | | *Broad peaks* track in *IGV Genome Browser* tab | | **preseq\_estimates** | Expected Distinct Reads Count Plot | Expected distinct reads count file from Preseq in TSV format | | *Expected Distinct Reads Count Plot* in *QC Plots* tab | | **workflow\_statistics** | Workflow execution statistics | Overall workflow execution statistics from bowtie\_aligner and samtools\_rmdup steps | + | *Overview* tab and experiment's preview | | **bowtie\_log** | Read alignment log | Read alignment log file from Bowtie | + | |

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

Path: workflows/chipseq-se.cwl

Branch/Commit ID: b1a5dabeeeb9079b30b2871edd9c9034a1e00c1c