Explore Workflows
View already parsed workflows here or click here to add your own
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sec-wf-out.cwl
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![]() Path: tests/wf/sec-wf-out.cwl Branch/Commit ID: e6c2d955a448225f026a04130443d13661844440 |
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echo-wf-default.cwl
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![]() Path: cwltool/schemas/v1.0/v1.0/echo-wf-default.cwl Branch/Commit ID: 03af16c9df2ee77485d4ab092cd64ae096d2e71c |
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conditional_bamindex.cwl
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![]() Path: workflows/bamfastq_align/conditional_bamindex.cwl Branch/Commit ID: dd7f86b3cc10eb1cda07dc2fc279ba2529c8ad61 |
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heatmap-prepare.cwl
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. |
![]() Path: subworkflows/heatmap-prepare.cwl Branch/Commit ID: e627079d8431e4f1f1c7531af1ca2e7dcc684b90 |
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bwa_pe.cwl
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![]() Path: workflows/bamfastq_align/bwa_pe.cwl Branch/Commit ID: dd7f86b3cc10eb1cda07dc2fc279ba2529c8ad61 |
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EMG pipeline v4.0 (paired end version)
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![]() Path: workflows/emg-pipeline-v4-paired.cwl Branch/Commit ID: ecf044f3a5a7589cb2238487a19f22863c2bcdb1 |
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Transcriptome assembly workflow (paired-end version)
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![]() Path: workflows/TranscriptomeAssembly-wf.paired-end.cwl Branch/Commit ID: b837972f9d442f9fd1e0cbc8be83754032b2c0fe |
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mutect panel-of-normals workflow
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![]() Path: definitions/pipelines/panel_of_normals.cwl Branch/Commit ID: 9c9e6a6a48eb321804ce772a2c2c12b4f2f32529 |
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fastq_clean_pe.cwl
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![]() Path: workflows/bamfastq_align/fastq_clean_pe.cwl Branch/Commit ID: dd7f86b3cc10eb1cda07dc2fc279ba2529c8ad61 |
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allele-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. |
![]() Path: subworkflows/allele-alignreads-se-pe.cwl Branch/Commit ID: 7a4593d2fa5b2fcbedc9219dc5687a4bc5aea66a |