Explore Workflows
View already parsed workflows here or click here to add your own
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gp_makeblastdb
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https://github.com/ncbi/pgap.git
Path: progs/gp_makeblastdb.cwl Branch/Commit ID: c00944bae1a9d0f726f271786dae5454aa36f6e1 |
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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: d6ec0dee61ef65a110e10141bde1a79332a64ab0 |
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waltz_workflow_all_bams.cwl
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https://github.com/mskcc/Innovation-Pipeline.git
Path: workflows/waltz/waltz_workflow_all_bams.cwl Branch/Commit ID: 476f3dcda929ee9eb67391bbc819573d75751b7c |
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Generate genome indices for Bismark
Copy input fasta file to the folder and 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 fasta file basename without extension. |
https://github.com/datirium/workflows.git
Path: workflows/bismark-indices.cwl Branch/Commit ID: bfa3843bcf36125ff258d6314f64b41336f06e6b |
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hmmsearch_wnode and gpx_qdump combined workflow to apply scatter/gather
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https://github.com/ncbi/pgap.git
Path: task_types/tt_hmmsearch_wnode_plus_qdump.cwl Branch/Commit ID: a3affd1b9e3e16f0644a25fee1a7b87b99df57b0 |
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wf_trim_partial_and_map_se_scatter.cwl
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https://github.com/YeoLab/eclip.git
Path: cwl/wf_trim_partial_and_map_se_scatter.cwl Branch/Commit ID: c0fffc4979a92371dc0667a03e3d957bf7f77600 |
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forome_vcf_upload_archive.cwl
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https://github.com/ForomePlatform/vcf-upload-cwl-pipeline.git
Path: forome_vcf_upload_archive.cwl Branch/Commit ID: 30114fc1643733f5a3cc8ca6ee956e33290c6022 |
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Cell Ranger Count Gene Expression
Cell Ranger Count Gene Expression ================================= |
https://github.com/datirium/workflows.git
Path: workflows/single-cell-preprocess-cellranger.cwl Branch/Commit ID: 7ae3b75bbe614e59cdeaba06047234a6c40c0fe9 |
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Sort and merge input bed file and generate a .sorted.merged.bed file
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https://github.com/swamyuma/cwl-tools.git
Path: sort_merge.cwl Branch/Commit ID: 14be112d65ebb76f0368747099b5778f35d0387f |
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waltz_workflow_all_bams.cwl
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https://github.com/mskcc/ACCESS-Pipeline.git
Path: workflows/waltz/waltz_workflow_all_bams.cwl Branch/Commit ID: 9998da2da694af2edad7c2135f6995e2282794a3 |
