Explore Workflows

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf1.cwl

Branch/Commit ID: 665141f319e6b23bd9924b14844f2e979f141944

https://github.com/sapojnik/av_screen_x.git

Path: progs/workflow.cwl

Branch/Commit ID: 2f464b439b914c05b2a3e3b2f9fcab3657f33ca2

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/harmonization/alignment_bwa_mem.cwl

Branch/Commit ID: 13c106834d6c9031de08496faeff521740a0c95f

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/utils/download_fastq.cwl

Branch/Commit ID: 13c106834d6c9031de08496faeff521740a0c95f

Copy fasta_file file to the folder and run run bismark_genome_preparation script to prepare indices for Bismark Methylation Analysis. Bowtie2 aligner is used by default. The name of the output indices folder is equal to the genome input.

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

Path: workflows/bismark-index.cwl

Branch/Commit ID: 1a46cb0e8f973481fe5ae3ae6188a41622c8532e

Reverse the lines in a document, then sort those lines.

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

Path: cwltool/schemas/v1.0/v1.0/revsort.cwl

Branch/Commit ID: 1e3f5404b7d5af02e3dec0faea31352111ad7cd8

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

Path: tests/conflict-wf.cwl

Branch/Commit ID: 0e37d46e793e72b7c16b5ec03e22cb3ce1f55ba3

Packed ID: collision

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: cb5e5b8563be4977e9f2babc14fe084faa234847

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

Path: cwltool/schemas/v1.0/v1.0/count-lines12-wf.cwl

Branch/Commit ID: 4fd5ca5a927594c361a9320d5331b326d06cecd3

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

Path: v1.0/v1.0/basename-fields-test.cwl

Branch/Commit ID: f02557902989c749c9c2187c7045e340e2d76bfc