Explore Workflows

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

Path: cwltool/schemas/v1.0/v1.0/conflict-wf.cwl

Branch/Commit ID: 886a6ac41c685f20d39e352f9c657e59f3312265

Packed ID: collision

https://github.com/Chi-CRL/cwl_check_workflow.git

Path: rhapsody_pipeline_2.0.cwl

Branch/Commit ID: 50ed14112f9db254034dd5530cf1a768e04eb7ff

Packed ID: VDJ_Preprocess_Reads.cwl

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

Path: tests/output-arrays-int-wf.cwl

Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733

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

Path: definitions/subworkflows/fp_filter.cwl

Branch/Commit ID: 641083e9ed933d388f36fa04c00c20a810599e94

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

Path: definitions/subworkflows/bgzip_and_index.cwl

Branch/Commit ID: 641083e9ed933d388f36fa04c00c20a810599e94

Workflow for Metagenomics from raw reads to annotated bins. Steps: - workflow_illumina_quality.cwl: - FastQC (control) - fastp (quality trimming) - kraken2 (taxonomy) - bbmap contamination filter - SPAdes (Assembly) - QUAST (Assembly quality report) - BBmap (Read mapping to assembly) - Contig binning (OPTIONAL)

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

Path: cwl/workflows/workflow_metagenomics_assembly.cwl

Branch/Commit ID: master

Slightly changed original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for **strand specific single-read** experiment. An additional steps were added to map data to mitochondrial chromosome only and then merge the output. Experiment files in [FASTQ](http://maq.sourceforge.net/fastq.shtml) format either compressed or not can be used. Current workflow should be used only with single-read strand specific RNA-Seq data. It performs the following steps: 1. `STAR` to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. `fastx_quality_stats` to analyze input FASTQ file and generate quality statistics file 3. `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/rnaseq-se-dutp-mitochondrial.cwl

Branch/Commit ID: 664de58d95728edbf7d369d894f9037ebe2475fa

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

Path: tests/scatter-wf4.cwl

Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733

Packed ID: main

Workflow for Metagenomics from raw reads to annotated bins.<br> Summary - MetaBAT2 (binning) - CheckM (bin completeness and contamination) - GTDB-Tk (bin taxonomic classification) - BUSCO (bin completeness) **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.wageningenur.nl/unlock/cwl.git

Path: cwl/workflows/workflow_metagenomics_binning.cwl

Branch/Commit ID: master

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

Path: task_types/tt_gcaccess_from_list.cwl

Branch/Commit ID: 69c0f25d08cfa02d8bfaa85ce5d70dd14cc52e3f