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new "stable" schema.org stable RDF URL (#145)
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‎CONTRIBUTING.md

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‎bamtools/bamtools_stats.cwl

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$schemas:
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- https://schema.org/version/latest/schemaorg-current-https.rdf
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s:name: "bamtools_stats"
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s:license: http://www.apache.org/licenses/LICENSE-2.0

‎bash/custom_bash.cwl

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- https://schema.org/version/latest/schemaorg-current-https.rdf
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s:name: "custom_bash"
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s:downloadUrl: https://raw.githubusercontent.com/common-workflow-library/bio-cwl-tools/release/tools/bash/custom_bash.cwl

‎bash/extract_fastq.cwl

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- https://schema.org/version/latest/schemaorg-current-https.rdf
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s:name: "extract_fastq"
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s:downloadUrl: https://raw.githubusercontent.com/common-workflow-library/bio-cwl-tools/release/tools/bash/extract_fastq.cwl

‎bedtools/bedtools_bamtobed_2.cwl

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s:name: "bedtools_bamtobed_2"
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‎bedtools/bedtools_genomecov.cwl

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s:name: "bedtools_genomecov"
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‎bedtools/bedtools_getfasta.cwl

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s:name: "bedtools_getfasta"
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‎bedtools/bedtools_intersect.cwl

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‎bedtools/bedtools_merge.cwl

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s:name: "bedtools_merge"
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‎bismark/bismark_align.cwl

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‎bismark/bismark_extract_methylation.cwl

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s:name: "bismark_extract_methylation"
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s:license: http://www.apache.org/licenses/LICENSE-2.0

‎bismark/bismark_prepare_genome.cwl

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s:name: "bismark_prepare_genome"
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‎bismark/bismark_report.cwl

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‎bowtie/bowtie_align.cwl

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‎bowtie/bowtie_build.cwl

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‎bowtie2/bowtie2_align.cwl

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‎bowtie2/bowtie2_build.cwl

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‎bzip2/bzip2_compress.cwl

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‎cellranger/cellranger-aggr.cwl

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label: "Cellranger aggr - aggregates data from multiple Cellranger runs"
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s:alternateName: "Cellranger aggr takes a list of cellranger count output files and produces a single feature-barcode matrix containing all the data"

‎cellranger/cellranger-arc-aggr.cwl

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label: "Cellranger ARC aggr - aggregates data from multiple Cellranger ARC runs"
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s:alternateName: "Cellranger ARC aggr takes a list of cellranger ARC count output files and produces a single feature-barcode matrix containing all the data"

‎cellranger/cellranger-arc-count.cwl

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label: "Cell Ranger ARC count - generates single cell feature counts for a single multiome library"
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s:alternateName: "Counts ATAC and gene expression reads from a single 10x Genomics Cell Ranger Multiome ATAC + Gene Expression library"

‎cellranger/cellranger-arc-mkref.cwl

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label: "Cell Ranger ARC mkref - builds compatible with Cell Ranger ARC indices"
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s:alternateName: "Builds compatible with Cell Ranger ARC reference folder from user-supplied genome FASTA and gene GTF files"

‎cellranger/cellranger-count.cwl

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label: "Cellranger count - generates single cell feature counts for a single library"
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‎cellranger/cellranger-mkref.cwl

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‎cellranger/cellranger-reanalyze.cwl

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‎crossmap/crossmap.cwl

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‎deeptools/deeptools_alignmentsieve.cwl

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‎deseq/deseq_advanced.cwl

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‎fastqc/fastqc_2.cwl

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‎fastx_toolkit/fastx_quality_stats.cwl

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‎gat/gat-run.cwl

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‎gffread/gffread.cwl

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‎gsea/gseapy.cwl

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‎hal/halliftover.cwl

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‎haltools/halliftover.cwl

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‎homer/homer-annotate-peaks-hist.cwl

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‎homer/homer-make-metagene-profile.cwl

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‎homer/homer-make-tag-directory.cwl

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‎hopach/hopach.cwl

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‎intervene/intervene.cwl

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‎kraken2/kraken2.cwl

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‎mafft/mafft.cwl

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- class: s:Person

‎manorm/manorm.cwl

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@@ -231,7 +231,7 @@ $namespaces:
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s: http://schema.org/
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$schemas:
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- https://github.com/schemaorg/schemaorg/raw/main/data/releases/11.01/schemaorg-current-http.rdf
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- https://schema.org/version/latest/schemaorg-current-https.rdf
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s:name: "manorm"
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s:license: http://www.apache.org/licenses/LICENSE-2.0

‎mashmap/MashMap.cwl

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@@ -121,7 +121,7 @@ $namespaces:
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edam: http://edamontology.org/
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$schemas:
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- https://github.com/schemaorg/schemaorg/raw/main/data/releases/11.01/schemaorg-current-http.rdf
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- https://schema.org/version/latest/schemaorg-current-https.rdf
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- https://edamontology.org/EDAM_1.20.owl
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