Explore Workflows
View already parsed workflows here or click here to add your own
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RNA-Seq pipeline paired-end stranded mitochondrial
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 pair-end** 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 the pair-end 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-pe-dutp-mitochondrial.cwl Branch/Commit ID: 44214a9d02e6d85b03eb708552ed812ae3d4a733 |
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Sentinel-3 SLSTR Level-2 reprojection and tiling
This service takes as input a Sentinel-3 SLSTR Level 2 (SL_2_LST____) product on DESCENDING pass and does the reprojection and tiling |
https://github.com/EOEPCA/proc-ades.git
Path: docs/examples/slstr-tiling.cwl Branch/Commit ID: bf81f3c1ca2f7fdd638f6eb1cabbc02b6f5450b2 Packed ID: slstr-tiling |
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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. |
https://github.com/datirium/workflows.git
Path: tools/heatmap-prepare.cwl Branch/Commit ID: 12e5256de1b680c551c87fd5db6f3bc65428af67 |
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CNV_pipeline
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https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/cwl/workflow.cwl Branch/Commit ID: 93fbc4e51770d953fc44104a7b09436f75719470 |
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CNV_pipeline
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https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/cwl/abstract_workflow/abstract_workflow.cwl Branch/Commit ID: f4c51a054b1ec51d07d89c6a8218e610653675f3 |
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protein annotation
Proteins - predict, cluster, identify, annotate |
https://github.com/MG-RAST/pipeline.git
Path: CWL/Workflows/protein-annotation.workflow.cwl Branch/Commit ID: f5839797da8209a9d3e441023f88130219751020 |
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kmer_cache_store
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https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_cache_store.cwl Branch/Commit ID: 909f26beaf96c2cdfe208f87ecd1e9c3de20b81c |
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gcaccess_from_list
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https://github.com/ncbi/pgap.git
Path: task_types/tt_gcaccess_from_list.cwl Branch/Commit ID: 7f857f7f2d7c080d27c775b67a6d6f7d94bce31f |
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exome alignment and germline variant detection
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/germline_exome.cwl Branch/Commit ID: c711498c04d6b8ddf92ddceb6219f074765f7993 |
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bam-bedgraph-bigwig.cwl
Workflow converts input BAM file into bigWig and bedGraph files. Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step). If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs. `scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`. `bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided. All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow. |
https://github.com/datirium/workflows.git
Path: tools/bam-bedgraph-bigwig.cwl Branch/Commit ID: 12e5256de1b680c551c87fd5db6f3bc65428af67 |
