Explore Workflows

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

Path: cwltool/schemas/v1.0/v1.0/count-lines7-wf.cwl

Branch/Commit ID: 216fbe57afcf67d81c99b49c1aa3aee0844f0a6a

ChIP-seq 03 mapping - reads: PE

https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/ChIP-seq_pipeline/03-map-pe.cwl

Branch/Commit ID: e019c548a0bc2f17b13365abd213259887069978

https://github.com/curoverse/l7g.git

Path: cwl-version/experimental/l7g-tile-assembly/tile-assembly-human_g1k_v37/l7g-build-human_g1k_v37-tile-assembly.cwl

Branch/Commit ID: 720b557e4a822da8c6139a1143e2c8ceaf2102ff

1. Convert input SRA file into pair of upsrtream and downstream FASTQ files (run fastq-dump) 2. Analyze quality of FASTQ files (run fastqc with each of the FASTQ files) 3. If any of the following fields in fastqc generated report is marked as failed for at least one of input FASTQ files: \"Per base sequence quality\", \"Per sequence quality scores\", \"Overrepresented sequences\", \"Adapter Content\", - trim adapters (run trimmomatic) 4. Align original or trimmed FASTQ files to reference genome, calculate genes and isoforms expression (run RSEM) 5. Count mapped reads number in sorted BAM file (run bamtools stats) 6. Generate genome coverage BED file (run bedtools genomecov) 7. Sort genearted BED file (run sort) 8. Generate genome coverage bigWig file from BED file (run bedGraphToBigWig)

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

Path: workflows/xenbase-rnaseq-se.cwl

Branch/Commit ID: 2b8146f76595f0c4d8bf692de78b21280162b1d0

https://github.com/kids-first/kf-alignment-workflow.git

Path: workflows/kf_alignment_fq_input_wf.cwl

Branch/Commit ID: c4771ebcfc43309e9abe4719f1c567c95bf47234

https://github.com/pitagora-network/pitagora-cwl.git

Path: workflows/tophat2-cufflinks/single_end/tophat2-cufflinks_wf_se.cwl

Branch/Commit ID: e2528f4d7e4ba5664fc171f9a25fc1490ae27c91

ChIP-seq 02 trimming - reads: SE

https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/ChIP-seq_pipeline/02-trim-se.cwl

Branch/Commit ID: e019c548a0bc2f17b13365abd213259887069978

abundace profiles from annotated files, for protein and/or rna

https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/abundance-clca.workflow.cwl

Branch/Commit ID: 2addcde0f4c1c8547f7f3906c2523cded23e9869

https://github.com/pitagora-network/pitagora-cwl.git

Path: workflows/tophat2-cufflinks/paired_end/tophat2-cufflinks_wf_pe.cwl

Branch/Commit ID: e2528f4d7e4ba5664fc171f9a25fc1490ae27c91

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

Path: protein_alignment/wf_protein_alignment.cwl

Branch/Commit ID: f5c11df465aaadf712c38ba4933679fe1cbe03ca