Explore Workflows

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

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

Path: workflows/trim-rnaseq-pe-dutp.cwl

Branch/Commit ID: cf678db8304ffaa20c1d6c854364db5ed41803c2

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

Path: workflows/16S_taxonomic_analysis.cwl

Branch/Commit ID: 0746e12

Differential abundance testing with ANCOM from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/

https://github.com/duke-gcb/bespin-cwl.git

Path: packed/qiime2-step2-dada2.cwl

Branch/Commit ID: qiime2-workflow

Packed ID: qiime2-09-ancom.cwl

# H3ABioNet GATK Germline Workflow # Overview A [GATK best-practices](https://software.broadinstitute.org/gatk/best-practices/bp_3step.php?case=GermShortWGS) germline workflow designed to work with GATK 3.5 (Van der Auwera et al., 2013). For more information see our [GitHub](https://github.com/h3abionet/h3agatk) site. # Workflow Summary  # Workflow Tool Details ## FastQC FastQC is used as an initial QC step where the input files are checked for usual metrics such as: - Read length - Reads distribution - GC content - ... ## Trimmomatic Trimmomatic is the entry point of the pipeline, it is used to cleanup the reads in the input fastq files from any sequencing adaptors. ## BWA [BWA](http://bio-bwa.sourceforge.net) is used to align the reads from the the input fastq files -paired-ends- (Li, 2013). We use specifically `bwa mem` as recommended by the [GATK best-practices](https://software.broadinstitute.org/gatk/best-practices/bp_3step.php?case=GermShortWGS). BWA produces a SAM file containing the aligned reads against the human reference genome (hg19, GATK bundle build 2.8). As GATK tools downstream requires properly formatted Read Group information. We add by default 'toy' Read Group information while processing the alignment to the output SAM file. we specifically use the flag `-R '@RG\tID:foo\tSM:bar\tLB:library1'`. ## SAMtools [SAMtools](http://www.htslib.org) (Li et al., 2009) are used few times in the pipeline: 1. Convert BWA's output from a SAM format to a BAM format 2. Sort the reads in the generated BAM file in step 1 (above) 3. Indexing the BAM file for the following tools to use ## Picard [Picard tools](https://broadinstitute.github.io/picard/) are used to mark duplicated reads in the aligned and sorted BAM file, making thus the files lighter and less prone to errors in the downstream steps of the pipeline. ## GATK [Genome Analysis Tool Kit](https://software.broadinstitute.org/gatk) refered to as GATK (DePristo et al., 2011) is used to process the data throught multiple steps as described by the [GATK best-practices](https://software.broadinstitute.org/gatk/best-practices/bp_3step.php?case=GermShortWGS) (i.e. figure bellow).  The GATK steps are the following: 1. Indel Realignment: 1. [Realign Target Creator](https://software.broadinstitute.org/gatk/documentation/tooldocs/org_broadinstitute_gatk_tools_walkers_indels_RealignerTargetCreator.php) 2. [Indel Realigner](https://software.broadinstitute.org/gatk/documentation/tooldocs/org_broadinstitute_gatk_tools_walkers_indels_IndelRealigner.php) 2. Mark Duplicates (a picard step) 3. Base Quality Score Recalibration (BQSR): 1. [Base Recalibrator](https://software.broadinstitute.org/gatk/documentation/tooldocs/org_broadinstitute_gatk_tools_walkers_bqsr_BaseRecalibrator.php) 2. [Print Reads](https://software.broadinstitute.org/gatk/documentation/tooldocs/org_broadinstitute_gatk_tools_walkers_readutils_PrintReads.php) 4. [Haplotype Caller](https://software.broadinstitute.org/gatk/documentation/tooldocs/) 5. Variant Quality Score Recalibration (VQSR): 1. [Variant Recalibrator](https://software.broadinstitute.org/gatk/documentation/tooldocs/org_broadinstitute_gatk_tools_walkers_variantrecalibration_VariantRecalibrator.php) 2. [Apply Recalibration](https://software.broadinstitute.org/gatk/documentation/tooldocs/org_broadinstitute_gatk_tools_walkers_variantrecalibration_ApplyRecalibration.php) ## SnpEff SNPEff is used in this pipeline to annotate the variant calls (Cingolani et al., 2012). The annotation is extensive and uses multi-database approach to provide the user with as much information about the called variants as possible. ## BAMStat [BAMStats](http://bamstats.sourceforge.net), is a simple software tool built on the Picard Java API (2), which can calculate and graphically display various metrics derived from SAM/BAM files of value in QC assessments.

https://github.com/mr-c/h3agatk.git

Path: workflows/GATK/GATK-complete-WES-Workflow-h3abionet.cwl

Branch/Commit ID: cwl_v1_0

DNase-seq 01 mapping - reads: SE

https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/DNase-seq_pipeline/01-map-se.cwl

Branch/Commit ID: master

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/io-int-default-wf.cwl

Branch/Commit ID: main

Generate a tree for phylogenetic diversity analyses from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/

https://github.com/duke-gcb/bespin-cwl.git

Path: packed/qiime2-step2-dada2.cwl

Branch/Commit ID: qiime2-workflow

Packed ID: qiime2-05-phylogeny.cwl

This is a very simple workflow of two steps. It will zip an input VCF file and then index it. The zipped file and the index file will be in the workflow output.

https://github.com/svonworl/OxoG-Dockstore-Tools.git

Path: zip_and_index_vcf.cwl

Branch/Commit ID: develop

https://github.com/hubmapconsortium/salmon-rnaseq.git

Path: bulk-pipeline.cwl

Branch/Commit ID: 72cf42a

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

Path: tools/SSU-from-tablehits.cwl

Branch/Commit ID: 5e82174