├── .gitignore ├── LICENSE ├── README.md ├── test ├── bin │ ├── collect-steps.sh │ └── run-cwl ├── data │ ├── pe.test.id.list │ └── se.test.id.list ├── lib │ ├── get_UCSC_mrna_fasta │ ├── get_bowtie2_index_GRCh38 │ ├── get_gencode_gene_annotation │ ├── get_gencode_transcript_fasta │ ├── get_hisat2_index_GRCh38 │ ├── get_hisat2_index_refMrna │ ├── get_id_list │ ├── get_kallisto_index_GRCh38 │ ├── get_rsem_index_GRCh38 │ ├── get_sailfish_index │ ├── get_salmon_index │ └── get_star_index_GRCh38 └── reference │ ├── annotation │ └── gencode │ │ └── GRCh38 │ │ └── README.md │ ├── bowtie2_index │ └── GRCh38 │ │ └── README.md │ ├── hisat2_index │ └── GRCh38 │ │ └── README.md │ ├── kallisto_index │ └── GRCh38 │ │ └── README.md │ ├── salmon_index │ └── GRCh38 │ │ └── README.md │ └── star_index │ └── GRCh38 │ └── README.md ├── tools ├── annovar │ ├── annovar-version.cwl │ ├── annovar.cwl │ └── annovar.yml ├── bowtie │ ├── bowtie-pe.cwl │ ├── bowtie-se.cwl │ ├── bowtie-version.cwl │ ├── bowtie_index.cwl │ └── bowtie_index.yml ├── bowtie2 │ ├── bowtie2-pe.cwl │ ├── bowtie2-se.cwl │ ├── bowtie2-version.cwl │ ├── bowtie2_index.cwl │ └── bowtie2_index.yml ├── bwa │ ├── bwa-pe.cwl │ ├── bwa-se.cwl │ ├── bwa-version.cwl │ ├── bwa_index.cwl │ └── bwa_index.yml ├── cufflinks │ ├── cufflinks-version.cwl │ ├── cufflinks.cwl │ ├── cufflinks.yml │ └── test │ │ └── cufflinks.sh ├── download-sra │ ├── download-sra.cwl │ ├── download-sra.yml │ └── test │ │ ├── download-sra.sh │ │ └── id.list ├── eXpress │ ├── eXpress.cwl │ ├── eXpress.yml.sample │ ├── express-version.cwl │ └── test │ │ └── eXpress.sh ├── fasterq-dump │ ├── fasterq-dump.cwl │ └── fasterq-dump.yml.sample ├── fastq-dump │ ├── fastq-dump.cwl │ ├── fastq-dump.yml.sample │ └── test │ │ └── fastq-dump.sh ├── fastqc-util │ ├── fastqc-util-tsv.cwl │ ├── fastqc-util-ttl.cwl │ ├── fastqc-util.cwl │ └── fastqc-util.yml.sample ├── fastqc │ ├── fastqc.cwl │ └── fastqc.yml.sample ├── gatk │ ├── gatk-baserecalibrator.yml │ ├── gatk-haplotypecaller.yml │ ├── gatk-indelrealigner.yml │ ├── gatk-printreads.yml │ ├── gatk-realign.yml │ ├── gatk-version.cwl │ └── gatk.cwl ├── hisat2 │ ├── index │ │ ├── hisat2_index.cwl │ │ ├── hisat2_index.yml.sample │ │ └── test │ │ │ └── hisat2_index.sh │ └── mapping │ │ ├── paired_end │ │ ├── hisat2_mapping_pe.cwl │ │ ├── hisat2_mapping_pe.yml.sample │ │ └── test │ │ │ └── hisat2_pe.sh │ │ └── single_end │ │ ├── hisat2_mapping_se.cwl │ │ ├── hisat2_mapping_se.yml.sample │ │ └── test │ │ └── hisat2_se.sh ├── kallisto │ ├── index │ │ ├── kallisto_index.cwl │ │ ├── kallisto_index.yml │ │ └── test │ │ │ └── kallisto_index.sh │ └── quant │ │ ├── paired_end │ │ ├── kallisto_quant_pe.cwl │ │ ├── kallisto_quant_pe.yml.sample │ │ └── test │ │ │ └── kallisto_quanto_pe.sh │ │ └── single_end │ │ ├── kallisto_quant_se.cwl │ │ ├── kallisto_quant_se.yml.sample │ │ └── test │ │ └── kallisto_quant_se.sh ├── last │ ├── last-split.cwl │ ├── last-split.yml │ ├── last-version.cwl │ ├── last_index.cwl │ ├── last_index.yml │ ├── lastal.cwl │ ├── maf-convert.cwl │ └── maf-convert.yml ├── ngs-version │ ├── ngs-version.cwl │ └── ngs-version.yml ├── pfastq-dump │ ├── pfastq-dump-multi.cwl │ ├── pfastq-dump.cwl │ ├── pfastq-dump.yml.sample │ └── test │ │ └── pfastq-dump.sh ├── picard │ ├── picard-addorreplacereadgroups.cwl │ ├── picard-addorreplacereadgroups.yml │ ├── picard-fixmateinformation.cwl │ ├── picard-fixmateinformation.yml │ ├── picard-markduplicates.cwl │ ├── picard-markduplicates.yml │ ├── picard-reordersam.cwl │ ├── picard-reordersam.yml │ ├── picard-version.cwl │ ├── picard_index.cwl │ └── picard_index.yml ├── prefetch_pfastq-dump │ ├── prefetch_pfastq-dump.cwl │ └── prefetch_pfastq-dump.sh ├── rsem │ ├── calculate-expression │ │ ├── paired_end │ │ │ ├── rsem-calculate-expression_pe.cwl │ │ │ ├── rsem-calculate-expression_pe.yml.sample │ │ │ └── test │ │ │ │ └── rsem-calculate-expression_pe.sh │ │ └── single_end │ │ │ ├── rsem-calculate-expression_se.cwl │ │ │ ├── rsem-calculate-expression_se.yml.sample │ │ │ └── test │ │ │ └── rsem-calculate-expression_se.sh │ └── index │ │ ├── rsem_index.cwl │ │ ├── rsem_index.yml.sample │ │ └── test │ │ └── rsem_index.sh ├── rsubread │ ├── rsubread.cwl │ └── rsubread.yml ├── sailfish │ ├── index │ │ ├── sailfish_index.cwl │ │ ├── sailfish_index.yml.sample │ │ └── test │ │ │ └── sailfish_index.sh │ └── quant │ │ ├── paired_end │ │ ├── sailfish_quant_pe.cwl │ │ ├── sailfish_quant_pe.yml.sample │ │ └── test │ │ │ └── sailfish_quant_pe.sh │ │ └── single_end │ │ ├── sailfish_quant_se.cwl │ │ ├── sailfish_quant_se.yml.sample │ │ └── test │ │ └── sailfish_quant_se.sh ├── salmon │ ├── index │ │ ├── salmon_index.cwl │ │ ├── salmon_index.yml.sample │ │ └── test │ │ │ └── salmon_index.sh │ └── quant │ │ ├── paired_end │ │ ├── salmon_quant_pe.cwl │ │ ├── salmon_quant_pe.yml.sample │ │ └── test │ │ │ └── salmon_quant_pe.sh │ │ └── single_end │ │ ├── salmon_quant_se.cwl │ │ ├── salmon_quant_se.yml.sample │ │ └── test │ │ └── salmon_quant_se.sh ├── samtools │ ├── faidx │ │ ├── samtools_faidx.cwl │ │ ├── samtools_faidx.yml.sample │ │ └── test │ │ │ └── samtools_faidx.sh │ ├── index_bam │ │ ├── samtools_index_bam.cwl │ │ ├── samtools_index_bam.yml.sample │ │ └── test │ │ │ └── samtools_index_bam.sh │ ├── sam2bam │ │ ├── samtools_sam2bam.cwl │ │ ├── samtools_sam2bam.yml.sample │ │ └── test │ │ │ └── samtools_sam2bam.sh │ └── sort │ │ ├── samtools_sort.cwl │ │ ├── samtools_sort.yml.sample │ │ └── test │ │ └── samtools_sort.sh ├── star │ ├── index │ │ ├── star_index.cwl │ │ ├── star_index.yml.sample │ │ └── test │ │ │ └── star_index.sh │ ├── mapping │ │ ├── paired_end │ │ │ ├── star_mapping_pe.cwl │ │ │ ├── star_mapping_pe.yml.sample │ │ │ └── test │ │ │ │ └── star_mapping_pe.sh │ │ └── single_end │ │ │ ├── star_mapping_se.cwl │ │ │ ├── star_mapping_se.yml.sample │ │ │ └── test │ │ │ └── star_mapping_se.sh │ └── mapping_genomeLoad │ │ ├── star_load.cwl │ │ ├── star_load.yml.sample │ │ └── test │ │ └── star_load.sh ├── stringtie │ └── assemble │ │ ├── stringtie_assemble.cwl │ │ ├── stringtie_assemble.yml.sample │ │ └── test │ │ └── stringtie_assemble.sh ├── tophat2 │ └── mapping │ │ ├── paired_end │ │ ├── tophat2_mapping_pe.cwl │ │ └── tophat2_mapping_pe.yml.sample │ │ └── single_end │ │ ├── tophat2_mapping_se.cwl │ │ └── tophat2_mapping_se.yml.sample ├── trinity │ ├── trinity-pe.cwl │ ├── trinity-se.cwl │ └── trinity-version.cwl └── utils │ ├── grep.cwl │ └── grep.yml └── workflows ├── assembler ├── assembler-version.cwl ├── nucleotides.cwl ├── nucleotides.yml ├── nucleotides2.cwl ├── nucleotides2.yml ├── nucleotids.sh └── nucleotids2.sh ├── bowtie ├── BowtieWorkflow-pe-pfastq-ver.cwl ├── BowtieWorkflow-pe-pfastq-ver.yml ├── BowtieWorkflow-pe.cwl ├── BowtieWorkflow-pe.yml ├── BowtieWorkflow-se-pfastq-ver.cwl ├── BowtieWorkflow-se-pfastq-ver.yml ├── BowtieWorkflow-se.cwl └── BowtieWorkflow-se.yml ├── bowtie2 ├── Bowtie2Workflow-pe-pfastq-ver.cwl ├── Bowtie2Workflow-pe-pfastq-ver.yml ├── Bowtie2Workflow-pe.cwl ├── Bowtie2Workflow-pe.yml ├── Bowtie2Workflow-se-pfastq-ver.cwl ├── Bowtie2Workflow-se-pfastq-ver.yml ├── Bowtie2Workflow-se.cwl └── Bowtie2Workflow-se.yml ├── bwa ├── BwaWorkflow-pe-pfastq-ver.cwl ├── BwaWorkflow-pe-pfastq-ver.yml ├── BwaWorkflow-pe.cwl ├── BwaWorkflow-pe.yml ├── BwaWorkflow-se-pfastq-ver.cwl ├── BwaWorkflow-se-pfastq-ver.yml ├── BwaWorkflow-se.cwl └── BwaWorkflow-se.yml ├── download-fastq ├── README.md ├── download-fastq.cwl ├── download-fastq.packed.cwl ├── download-fastq.single.cwl ├── download-fastq.single.yml └── download-fastq.yml ├── fastqc ├── fastqc_wf.cwl └── fastqc_wf.yml.sample ├── hisat2-cufflinks ├── README.md ├── paired_end │ ├── hisat2-cufflinks_wf_pe.cwl │ ├── hisat2-cufflinks_wf_pe.yml.sample │ └── test │ │ ├── hisat2-cufflinks_wf_pe.sh │ │ └── hisat2-cufflinks_wf_pe_setup.sh └── single_end │ ├── hisat2-cufflinks_wf_se.cwl │ ├── hisat2-cufflinks_wf_se.yml.sample │ └── test │ ├── hisat2-cufflinks_wf_se.sh │ └── hisat2-cufflinks_wf_se_setup.sh ├── hisat2-eXpress ├── README.md ├── paired_end │ ├── hisat2-eXpress_wf_pe.cwl │ ├── hisat2-eXpress_wf_pe.yml.sample │ └── test │ │ ├── hisat2-eXpress_wf_pe.sh │ │ └── hisat2-eXpress_wf_pe_setup.sh └── single_end │ ├── hisat2-eXpress_wf_se.cwl │ ├── hisat2-eXpress_wf_se.yml.sample │ └── test │ ├── hisat2-eXpress_wf_se.sh │ └── hisat2-eXpress_wf_se_setup.sh ├── hisat2-stringtie ├── README.md ├── paired_end │ ├── hisat2-stringtie_wf_pe.cwl │ ├── hisat2-stringtie_wf_pe.yml.sample │ └── test │ │ ├── hisat2-stringtie_wf_pe.sh │ │ └── hisat2-stringtie_wf_pe_setup.sh └── single_end │ ├── hisat2-stringtie_wf_se.cwl │ ├── hisat2-stringtie_wf_se.yml.sample │ └── test │ ├── hisat2-stringtie_wf_se.sh │ └── hisat2-stringtie_wf_se_setup.sh ├── hisat2 ├── Hisat2Workflow-pe-pfastq-ver.cwl ├── Hisat2Workflow-pe-pfastq-ver.yml ├── Hisat2Workflow-pe.cwl ├── Hisat2Workflow-pe.yml ├── Hisat2Workflow-se-pfastq-ver.cwl ├── Hisat2Workflow-se-pfastq-ver.yml ├── Hisat2Workflow-se.cwl └── Hisat2Workflow-se.yml ├── kallisto ├── README.md ├── paired_end │ ├── kallisto_wf_pe.cwl │ ├── kallisto_wf_pe.yml.sample │ └── test │ │ ├── kallisto_wf_pe.sh │ │ └── kallisto_wf_pe_setup.sh └── single_end │ ├── kallisto_wf_se.cwl │ ├── kallisto_wf_se.yml.sample │ └── test │ ├── kallisto_wf_se.sh │ └── kallisto_wf_se_setup.sh ├── last ├── LastWorkflow-pe-pfastq-ver.cwl ├── LastWorkflow-pe-pfastq-ver.yml ├── LastWorkflow-pe.cwl ├── LastWorkflow-pe.yml ├── LastWorkflow-se-pfastq-ver.cwl ├── LastWorkflow-se-pfastq-ver.yml ├── LastWorkflow-se.cwl └── LastWorkflow-se.yml ├── sailfish ├── README.md ├── paired_end │ ├── sailfish_wf_pe.cwl │ ├── sailfish_wf_pe.yml.sample │ └── test │ │ ├── sailfish_wf_pe.sh │ │ └── sailfish_wf_pe_setup.sh └── single_end │ ├── sailfish_wf_se.cwl │ ├── sailfish_wf_se.yml.sample │ └── test │ ├── sailfish_wf_se.sh │ └── sailfish_wf_se_setup.sh ├── salmon ├── README.md ├── paired_end │ ├── salmon_wf_pe.cwl │ ├── salmon_wf_pe.yml.sample │ └── test │ │ ├── salmon_wf_pe.sh │ │ └── salmon_wf_pe_setup.sh └── single_end │ ├── salmon_wf_se.cwl │ ├── salmon_wf_se.yml.sample │ └── test │ ├── salmon_wf_se.sh │ └── salmon_wf_se_setup.sh ├── star-cufflinks ├── README.md ├── paired_end │ ├── star-cufflinks_wf_pe.cwl │ ├── star-cufflinks_wf_pe.yml.sample │ └── test │ │ ├── star-cufflinks_wf_pe.sh │ │ └── star-cufflinks_wf_pe_setup.sh └── single_end │ ├── star-cufflinks_wf_se.cwl │ ├── star-cufflinks_wf_se.yml.sample │ └── test │ ├── star-cufflinks_wf_se.sh │ └── star-cufflinks_wf_se_setup.sh ├── star-eXpress ├── README.md ├── paired_end │ ├── star-eXpress_wf_pe.cwl │ ├── star-eXpress_wf_pe.yml.sample │ └── test │ │ └── star-eXpress_wf_pe.sh └── single_end │ ├── star-eXpress_wf_se.cwl │ ├── star-eXpress_wf_se.yml.sample │ └── test │ └── star-eXpress_wf_se.sh ├── star-rsem ├── README.md ├── paired_end │ ├── star-rsem_wf_pe.cwl │ ├── star-rsem_wf_pe.yml.sample │ └── test │ │ ├── star-rsem_wf_pe.sh │ │ └── star-rsem_wf_pe_setup.sh └── single_end │ ├── star-rsem_wf_se.cwl │ ├── star-rsem_wf_se.yml.sample │ └── test │ ├── star-rsem_wf_se.sh │ └── star-rsem_wf_se_setup.sh ├── star-stringtie ├── README.md ├── paired_end │ ├── star-stringtie_wf_pe.cwl │ ├── star-stringtie_wf_pe.yml.sample │ └── test │ │ ├── star-stringtie_wf_pe.sh │ │ └── star-stringtie_wf_pe_setup.sh └── single_end │ ├── star-stringtie_wf_se.cwl │ ├── star-stringtie_wf_se.yml.sample │ └── test │ ├── star-stringtie_wf_se.sh │ └── star-stringtie_wf_se_setup.sh ├── star ├── StarWorkflow-pe-pfastq-ver.cwl ├── StarWorkflow-pe-pfastq-ver.yml ├── StarWorkflow-pe.cwl ├── StarWorkflow-pe.yml ├── StarWorkflow-se-pfastq-ver.cwl ├── StarWorkflow-se-pfastq-ver.yml ├── StarWorkflow-se.cwl └── StarWorkflow-se.yml ├── tophat2-cufflinks ├── README.md ├── paired_end │ ├── test │ │ ├── tophat2-cufflinks_wf_pe.sh │ │ └── tophat2-cufflinks_wf_pe_setup.sh │ ├── tophat2-cufflinks_wf_pe.cwl │ └── tophat2-cufflinks_wf_pe.yml.sample └── single_end │ ├── test │ ├── tophat2-cufflinks_wf_se.sh │ └── tophat2-cufflinks_wf_se_setup.sh │ ├── tophat2-cufflinks_wf_se.cwl │ └── tophat2-cufflinks_wf_se.yml.sample ├── tophat2 ├── Tophat2Workflow-pe-pfastq-ver.cwl ├── Tophat2Workflow-pe-pfastq-ver.yml ├── Tophat2Workflow-pe.cwl ├── Tophat2Workflow-pe.yml ├── Tophat2Workflow-se-pfastq-ver.cwl ├── Tophat2Workflow-se-pfastq-ver.yml ├── Tophat2Workflow-se.cwl └── Tophat2Workflow-se.yml └── trinity ├── TrinityWorkflow-pe-pfastq-ver.cwl ├── TrinityWorkflow-pe-pfastq-ver.yml ├── TrinityWorkflow-pe.cwl ├── TrinityWorkflow-pe.yml ├── TrinityWorkflow-se-pfastq-ver.cwl ├── TrinityWorkflow-se-pfastq-ver.yml ├── TrinityWorkflow-se.cwl └── TrinityWorkflow-se.yml /.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/README.md -------------------------------------------------------------------------------- /test/bin/collect-steps.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/test/bin/collect-steps.sh -------------------------------------------------------------------------------- /test/bin/run-cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/test/bin/run-cwl -------------------------------------------------------------------------------- /test/data/pe.test.id.list: -------------------------------------------------------------------------------- 1 | SRR1274306 2 | -------------------------------------------------------------------------------- /test/data/se.test.id.list: -------------------------------------------------------------------------------- 1 | SRR4058057 2 | -------------------------------------------------------------------------------- /test/lib/get_UCSC_mrna_fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/test/lib/get_UCSC_mrna_fasta -------------------------------------------------------------------------------- /test/lib/get_bowtie2_index_GRCh38: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/test/lib/get_bowtie2_index_GRCh38 -------------------------------------------------------------------------------- /test/lib/get_gencode_gene_annotation: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/test/lib/get_gencode_gene_annotation -------------------------------------------------------------------------------- /test/lib/get_gencode_transcript_fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/test/lib/get_gencode_transcript_fasta -------------------------------------------------------------------------------- /test/lib/get_hisat2_index_GRCh38: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/test/lib/get_hisat2_index_GRCh38 -------------------------------------------------------------------------------- /test/lib/get_hisat2_index_refMrna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/test/lib/get_hisat2_index_refMrna -------------------------------------------------------------------------------- /test/lib/get_id_list: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/test/lib/get_id_list -------------------------------------------------------------------------------- /test/lib/get_kallisto_index_GRCh38: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/test/lib/get_kallisto_index_GRCh38 -------------------------------------------------------------------------------- /test/lib/get_rsem_index_GRCh38: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/test/lib/get_rsem_index_GRCh38 -------------------------------------------------------------------------------- /test/lib/get_sailfish_index: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/test/lib/get_sailfish_index -------------------------------------------------------------------------------- /test/lib/get_salmon_index: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/test/lib/get_salmon_index -------------------------------------------------------------------------------- /test/lib/get_star_index_GRCh38: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/test/lib/get_star_index_GRCh38 -------------------------------------------------------------------------------- /test/reference/annotation/gencode/GRCh38/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/test/reference/annotation/gencode/GRCh38/README.md -------------------------------------------------------------------------------- /test/reference/bowtie2_index/GRCh38/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/test/reference/bowtie2_index/GRCh38/README.md -------------------------------------------------------------------------------- /test/reference/hisat2_index/GRCh38/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/test/reference/hisat2_index/GRCh38/README.md -------------------------------------------------------------------------------- /test/reference/kallisto_index/GRCh38/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/test/reference/kallisto_index/GRCh38/README.md -------------------------------------------------------------------------------- /test/reference/salmon_index/GRCh38/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/test/reference/salmon_index/GRCh38/README.md -------------------------------------------------------------------------------- /test/reference/star_index/GRCh38/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/test/reference/star_index/GRCh38/README.md -------------------------------------------------------------------------------- /tools/annovar/annovar-version.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/annovar/annovar-version.cwl -------------------------------------------------------------------------------- /tools/annovar/annovar.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/annovar/annovar.cwl -------------------------------------------------------------------------------- /tools/annovar/annovar.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/annovar/annovar.yml -------------------------------------------------------------------------------- /tools/bowtie/bowtie-pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/bowtie/bowtie-pe.cwl -------------------------------------------------------------------------------- /tools/bowtie/bowtie-se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/bowtie/bowtie-se.cwl -------------------------------------------------------------------------------- /tools/bowtie/bowtie-version.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/bowtie/bowtie-version.cwl -------------------------------------------------------------------------------- /tools/bowtie/bowtie_index.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/bowtie/bowtie_index.cwl -------------------------------------------------------------------------------- /tools/bowtie/bowtie_index.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/bowtie/bowtie_index.yml -------------------------------------------------------------------------------- /tools/bowtie2/bowtie2-pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/bowtie2/bowtie2-pe.cwl -------------------------------------------------------------------------------- /tools/bowtie2/bowtie2-se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/bowtie2/bowtie2-se.cwl -------------------------------------------------------------------------------- /tools/bowtie2/bowtie2-version.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/bowtie2/bowtie2-version.cwl -------------------------------------------------------------------------------- /tools/bowtie2/bowtie2_index.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/bowtie2/bowtie2_index.cwl -------------------------------------------------------------------------------- /tools/bowtie2/bowtie2_index.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/bowtie2/bowtie2_index.yml -------------------------------------------------------------------------------- /tools/bwa/bwa-pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/bwa/bwa-pe.cwl -------------------------------------------------------------------------------- /tools/bwa/bwa-se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/bwa/bwa-se.cwl -------------------------------------------------------------------------------- /tools/bwa/bwa-version.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/bwa/bwa-version.cwl -------------------------------------------------------------------------------- /tools/bwa/bwa_index.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/bwa/bwa_index.cwl -------------------------------------------------------------------------------- /tools/bwa/bwa_index.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/bwa/bwa_index.yml -------------------------------------------------------------------------------- /tools/cufflinks/cufflinks-version.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/cufflinks/cufflinks-version.cwl -------------------------------------------------------------------------------- /tools/cufflinks/cufflinks.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/cufflinks/cufflinks.cwl -------------------------------------------------------------------------------- /tools/cufflinks/cufflinks.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/cufflinks/cufflinks.yml -------------------------------------------------------------------------------- /tools/cufflinks/test/cufflinks.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/cufflinks/test/cufflinks.sh -------------------------------------------------------------------------------- /tools/download-sra/download-sra.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/download-sra/download-sra.cwl -------------------------------------------------------------------------------- /tools/download-sra/download-sra.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/download-sra/download-sra.yml -------------------------------------------------------------------------------- /tools/download-sra/test/download-sra.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/download-sra/test/download-sra.sh -------------------------------------------------------------------------------- /tools/download-sra/test/id.list: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/download-sra/test/id.list -------------------------------------------------------------------------------- /tools/eXpress/eXpress.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/eXpress/eXpress.cwl -------------------------------------------------------------------------------- /tools/eXpress/eXpress.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/eXpress/eXpress.yml.sample -------------------------------------------------------------------------------- /tools/eXpress/express-version.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/eXpress/express-version.cwl -------------------------------------------------------------------------------- /tools/eXpress/test/eXpress.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/eXpress/test/eXpress.sh -------------------------------------------------------------------------------- /tools/fasterq-dump/fasterq-dump.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/fasterq-dump/fasterq-dump.cwl -------------------------------------------------------------------------------- /tools/fasterq-dump/fasterq-dump.yml.sample: -------------------------------------------------------------------------------- 1 | srafile: _PATH_TO_SRAFILE_ 2 | -------------------------------------------------------------------------------- /tools/fastq-dump/fastq-dump.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/fastq-dump/fastq-dump.cwl -------------------------------------------------------------------------------- /tools/fastq-dump/fastq-dump.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/fastq-dump/fastq-dump.yml.sample -------------------------------------------------------------------------------- /tools/fastq-dump/test/fastq-dump.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/fastq-dump/test/fastq-dump.sh -------------------------------------------------------------------------------- /tools/fastqc-util/fastqc-util-tsv.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/fastqc-util/fastqc-util-tsv.cwl -------------------------------------------------------------------------------- /tools/fastqc-util/fastqc-util-ttl.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/fastqc-util/fastqc-util-ttl.cwl -------------------------------------------------------------------------------- /tools/fastqc-util/fastqc-util.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/fastqc-util/fastqc-util.cwl -------------------------------------------------------------------------------- /tools/fastqc-util/fastqc-util.yml.sample: -------------------------------------------------------------------------------- 1 | format: tsv 2 | fastqcResult: 3 | - class: File 4 | path: _PATH_TO_FASTQC_RESULT_ 5 | -------------------------------------------------------------------------------- /tools/fastqc/fastqc.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/fastqc/fastqc.cwl -------------------------------------------------------------------------------- /tools/fastqc/fastqc.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/fastqc/fastqc.yml.sample -------------------------------------------------------------------------------- /tools/gatk/gatk-baserecalibrator.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/gatk/gatk-baserecalibrator.yml -------------------------------------------------------------------------------- /tools/gatk/gatk-haplotypecaller.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/gatk/gatk-haplotypecaller.yml -------------------------------------------------------------------------------- /tools/gatk/gatk-indelrealigner.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/gatk/gatk-indelrealigner.yml -------------------------------------------------------------------------------- /tools/gatk/gatk-printreads.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/gatk/gatk-printreads.yml -------------------------------------------------------------------------------- /tools/gatk/gatk-realign.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/gatk/gatk-realign.yml -------------------------------------------------------------------------------- /tools/gatk/gatk-version.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/gatk/gatk-version.cwl -------------------------------------------------------------------------------- /tools/gatk/gatk.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/gatk/gatk.cwl -------------------------------------------------------------------------------- /tools/hisat2/index/hisat2_index.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/hisat2/index/hisat2_index.cwl -------------------------------------------------------------------------------- /tools/hisat2/index/hisat2_index.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/hisat2/index/hisat2_index.yml.sample -------------------------------------------------------------------------------- /tools/hisat2/index/test/hisat2_index.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/hisat2/index/test/hisat2_index.sh -------------------------------------------------------------------------------- /tools/hisat2/mapping/paired_end/hisat2_mapping_pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/hisat2/mapping/paired_end/hisat2_mapping_pe.cwl -------------------------------------------------------------------------------- /tools/hisat2/mapping/paired_end/hisat2_mapping_pe.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/hisat2/mapping/paired_end/hisat2_mapping_pe.yml.sample -------------------------------------------------------------------------------- /tools/hisat2/mapping/paired_end/test/hisat2_pe.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/hisat2/mapping/paired_end/test/hisat2_pe.sh -------------------------------------------------------------------------------- /tools/hisat2/mapping/single_end/hisat2_mapping_se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/hisat2/mapping/single_end/hisat2_mapping_se.cwl -------------------------------------------------------------------------------- /tools/hisat2/mapping/single_end/hisat2_mapping_se.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/hisat2/mapping/single_end/hisat2_mapping_se.yml.sample -------------------------------------------------------------------------------- /tools/hisat2/mapping/single_end/test/hisat2_se.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/hisat2/mapping/single_end/test/hisat2_se.sh -------------------------------------------------------------------------------- /tools/kallisto/index/kallisto_index.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/kallisto/index/kallisto_index.cwl -------------------------------------------------------------------------------- /tools/kallisto/index/kallisto_index.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/kallisto/index/kallisto_index.yml -------------------------------------------------------------------------------- /tools/kallisto/index/test/kallisto_index.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/kallisto/index/test/kallisto_index.sh -------------------------------------------------------------------------------- /tools/kallisto/quant/paired_end/kallisto_quant_pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/kallisto/quant/paired_end/kallisto_quant_pe.cwl -------------------------------------------------------------------------------- /tools/kallisto/quant/paired_end/kallisto_quant_pe.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/kallisto/quant/paired_end/kallisto_quant_pe.yml.sample -------------------------------------------------------------------------------- /tools/kallisto/quant/paired_end/test/kallisto_quanto_pe.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/kallisto/quant/paired_end/test/kallisto_quanto_pe.sh -------------------------------------------------------------------------------- /tools/kallisto/quant/single_end/kallisto_quant_se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/kallisto/quant/single_end/kallisto_quant_se.cwl -------------------------------------------------------------------------------- /tools/kallisto/quant/single_end/kallisto_quant_se.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/kallisto/quant/single_end/kallisto_quant_se.yml.sample -------------------------------------------------------------------------------- /tools/kallisto/quant/single_end/test/kallisto_quant_se.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/kallisto/quant/single_end/test/kallisto_quant_se.sh -------------------------------------------------------------------------------- /tools/last/last-split.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/last/last-split.cwl -------------------------------------------------------------------------------- /tools/last/last-split.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/last/last-split.yml -------------------------------------------------------------------------------- /tools/last/last-version.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/last/last-version.cwl -------------------------------------------------------------------------------- /tools/last/last_index.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/last/last_index.cwl -------------------------------------------------------------------------------- /tools/last/last_index.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/last/last_index.yml -------------------------------------------------------------------------------- /tools/last/lastal.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/last/lastal.cwl -------------------------------------------------------------------------------- /tools/last/maf-convert.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/last/maf-convert.cwl -------------------------------------------------------------------------------- /tools/last/maf-convert.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/last/maf-convert.yml -------------------------------------------------------------------------------- /tools/ngs-version/ngs-version.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/ngs-version/ngs-version.cwl -------------------------------------------------------------------------------- /tools/ngs-version/ngs-version.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/ngs-version/ngs-version.yml -------------------------------------------------------------------------------- /tools/pfastq-dump/pfastq-dump-multi.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/pfastq-dump/pfastq-dump-multi.cwl -------------------------------------------------------------------------------- /tools/pfastq-dump/pfastq-dump.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/pfastq-dump/pfastq-dump.cwl -------------------------------------------------------------------------------- /tools/pfastq-dump/pfastq-dump.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/pfastq-dump/pfastq-dump.yml.sample -------------------------------------------------------------------------------- /tools/pfastq-dump/test/pfastq-dump.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/pfastq-dump/test/pfastq-dump.sh -------------------------------------------------------------------------------- /tools/picard/picard-addorreplacereadgroups.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/picard/picard-addorreplacereadgroups.cwl -------------------------------------------------------------------------------- /tools/picard/picard-addorreplacereadgroups.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/picard/picard-addorreplacereadgroups.yml -------------------------------------------------------------------------------- /tools/picard/picard-fixmateinformation.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/picard/picard-fixmateinformation.cwl -------------------------------------------------------------------------------- /tools/picard/picard-fixmateinformation.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/picard/picard-fixmateinformation.yml -------------------------------------------------------------------------------- /tools/picard/picard-markduplicates.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/picard/picard-markduplicates.cwl -------------------------------------------------------------------------------- /tools/picard/picard-markduplicates.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/picard/picard-markduplicates.yml -------------------------------------------------------------------------------- /tools/picard/picard-reordersam.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/picard/picard-reordersam.cwl -------------------------------------------------------------------------------- /tools/picard/picard-reordersam.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/picard/picard-reordersam.yml -------------------------------------------------------------------------------- /tools/picard/picard-version.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/picard/picard-version.cwl -------------------------------------------------------------------------------- /tools/picard/picard_index.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/picard/picard_index.cwl -------------------------------------------------------------------------------- /tools/picard/picard_index.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/picard/picard_index.yml -------------------------------------------------------------------------------- /tools/prefetch_pfastq-dump/prefetch_pfastq-dump.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/prefetch_pfastq-dump/prefetch_pfastq-dump.cwl -------------------------------------------------------------------------------- /tools/prefetch_pfastq-dump/prefetch_pfastq-dump.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/prefetch_pfastq-dump/prefetch_pfastq-dump.sh -------------------------------------------------------------------------------- /tools/rsem/calculate-expression/paired_end/rsem-calculate-expression_pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/rsem/calculate-expression/paired_end/rsem-calculate-expression_pe.cwl -------------------------------------------------------------------------------- /tools/rsem/calculate-expression/paired_end/rsem-calculate-expression_pe.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/rsem/calculate-expression/paired_end/rsem-calculate-expression_pe.yml.sample -------------------------------------------------------------------------------- /tools/rsem/calculate-expression/paired_end/test/rsem-calculate-expression_pe.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/rsem/calculate-expression/paired_end/test/rsem-calculate-expression_pe.sh -------------------------------------------------------------------------------- /tools/rsem/calculate-expression/single_end/rsem-calculate-expression_se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/rsem/calculate-expression/single_end/rsem-calculate-expression_se.cwl -------------------------------------------------------------------------------- /tools/rsem/calculate-expression/single_end/rsem-calculate-expression_se.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/rsem/calculate-expression/single_end/rsem-calculate-expression_se.yml.sample -------------------------------------------------------------------------------- /tools/rsem/calculate-expression/single_end/test/rsem-calculate-expression_se.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/rsem/calculate-expression/single_end/test/rsem-calculate-expression_se.sh -------------------------------------------------------------------------------- /tools/rsem/index/rsem_index.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/rsem/index/rsem_index.cwl -------------------------------------------------------------------------------- /tools/rsem/index/rsem_index.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/rsem/index/rsem_index.yml.sample -------------------------------------------------------------------------------- /tools/rsem/index/test/rsem_index.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/rsem/index/test/rsem_index.sh -------------------------------------------------------------------------------- /tools/rsubread/rsubread.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/rsubread/rsubread.cwl -------------------------------------------------------------------------------- /tools/rsubread/rsubread.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/rsubread/rsubread.yml -------------------------------------------------------------------------------- /tools/sailfish/index/sailfish_index.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/sailfish/index/sailfish_index.cwl -------------------------------------------------------------------------------- /tools/sailfish/index/sailfish_index.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/sailfish/index/sailfish_index.yml.sample -------------------------------------------------------------------------------- /tools/sailfish/index/test/sailfish_index.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/sailfish/index/test/sailfish_index.sh -------------------------------------------------------------------------------- /tools/sailfish/quant/paired_end/sailfish_quant_pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/sailfish/quant/paired_end/sailfish_quant_pe.cwl -------------------------------------------------------------------------------- /tools/sailfish/quant/paired_end/sailfish_quant_pe.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/sailfish/quant/paired_end/sailfish_quant_pe.yml.sample -------------------------------------------------------------------------------- /tools/sailfish/quant/paired_end/test/sailfish_quant_pe.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/sailfish/quant/paired_end/test/sailfish_quant_pe.sh -------------------------------------------------------------------------------- /tools/sailfish/quant/single_end/sailfish_quant_se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/sailfish/quant/single_end/sailfish_quant_se.cwl -------------------------------------------------------------------------------- /tools/sailfish/quant/single_end/sailfish_quant_se.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/sailfish/quant/single_end/sailfish_quant_se.yml.sample -------------------------------------------------------------------------------- /tools/sailfish/quant/single_end/test/sailfish_quant_se.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/sailfish/quant/single_end/test/sailfish_quant_se.sh -------------------------------------------------------------------------------- /tools/salmon/index/salmon_index.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/salmon/index/salmon_index.cwl -------------------------------------------------------------------------------- /tools/salmon/index/salmon_index.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/salmon/index/salmon_index.yml.sample -------------------------------------------------------------------------------- /tools/salmon/index/test/salmon_index.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/salmon/index/test/salmon_index.sh -------------------------------------------------------------------------------- /tools/salmon/quant/paired_end/salmon_quant_pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/salmon/quant/paired_end/salmon_quant_pe.cwl -------------------------------------------------------------------------------- /tools/salmon/quant/paired_end/salmon_quant_pe.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/salmon/quant/paired_end/salmon_quant_pe.yml.sample -------------------------------------------------------------------------------- /tools/salmon/quant/paired_end/test/salmon_quant_pe.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/salmon/quant/paired_end/test/salmon_quant_pe.sh -------------------------------------------------------------------------------- /tools/salmon/quant/single_end/salmon_quant_se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/salmon/quant/single_end/salmon_quant_se.cwl -------------------------------------------------------------------------------- /tools/salmon/quant/single_end/salmon_quant_se.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/salmon/quant/single_end/salmon_quant_se.yml.sample -------------------------------------------------------------------------------- /tools/salmon/quant/single_end/test/salmon_quant_se.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/salmon/quant/single_end/test/salmon_quant_se.sh -------------------------------------------------------------------------------- /tools/samtools/faidx/samtools_faidx.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/samtools/faidx/samtools_faidx.cwl -------------------------------------------------------------------------------- /tools/samtools/faidx/samtools_faidx.yml.sample: -------------------------------------------------------------------------------- 1 | reference: 2 | class: File 3 | path: _INPUT_FASTA_ 4 | -------------------------------------------------------------------------------- /tools/samtools/faidx/test/samtools_faidx.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/samtools/faidx/test/samtools_faidx.sh -------------------------------------------------------------------------------- /tools/samtools/index_bam/samtools_index_bam.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/samtools/index_bam/samtools_index_bam.cwl -------------------------------------------------------------------------------- /tools/samtools/index_bam/samtools_index_bam.yml.sample: -------------------------------------------------------------------------------- 1 | input_bam: 2 | class: File 3 | path: _INPUT_BAM_ 4 | -------------------------------------------------------------------------------- /tools/samtools/index_bam/test/samtools_index_bam.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/samtools/index_bam/test/samtools_index_bam.sh -------------------------------------------------------------------------------- /tools/samtools/sam2bam/samtools_sam2bam.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/samtools/sam2bam/samtools_sam2bam.cwl -------------------------------------------------------------------------------- /tools/samtools/sam2bam/samtools_sam2bam.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/samtools/sam2bam/samtools_sam2bam.yml.sample -------------------------------------------------------------------------------- /tools/samtools/sam2bam/test/samtools_sam2bam.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/samtools/sam2bam/test/samtools_sam2bam.sh -------------------------------------------------------------------------------- /tools/samtools/sort/samtools_sort.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/samtools/sort/samtools_sort.cwl -------------------------------------------------------------------------------- /tools/samtools/sort/samtools_sort.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/samtools/sort/samtools_sort.yml.sample -------------------------------------------------------------------------------- /tools/samtools/sort/test/samtools_sort.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/samtools/sort/test/samtools_sort.sh -------------------------------------------------------------------------------- /tools/star/index/star_index.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/star/index/star_index.cwl -------------------------------------------------------------------------------- /tools/star/index/star_index.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/star/index/star_index.yml.sample -------------------------------------------------------------------------------- /tools/star/index/test/star_index.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/star/index/test/star_index.sh -------------------------------------------------------------------------------- /tools/star/mapping/paired_end/star_mapping_pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/star/mapping/paired_end/star_mapping_pe.cwl -------------------------------------------------------------------------------- /tools/star/mapping/paired_end/star_mapping_pe.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/star/mapping/paired_end/star_mapping_pe.yml.sample -------------------------------------------------------------------------------- /tools/star/mapping/paired_end/test/star_mapping_pe.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/star/mapping/paired_end/test/star_mapping_pe.sh -------------------------------------------------------------------------------- /tools/star/mapping/single_end/star_mapping_se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/star/mapping/single_end/star_mapping_se.cwl -------------------------------------------------------------------------------- /tools/star/mapping/single_end/star_mapping_se.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/star/mapping/single_end/star_mapping_se.yml.sample -------------------------------------------------------------------------------- /tools/star/mapping/single_end/test/star_mapping_se.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/star/mapping/single_end/test/star_mapping_se.sh -------------------------------------------------------------------------------- /tools/star/mapping_genomeLoad/star_load.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/star/mapping_genomeLoad/star_load.cwl -------------------------------------------------------------------------------- /tools/star/mapping_genomeLoad/star_load.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/star/mapping_genomeLoad/star_load.yml.sample -------------------------------------------------------------------------------- /tools/star/mapping_genomeLoad/test/star_load.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/star/mapping_genomeLoad/test/star_load.sh -------------------------------------------------------------------------------- /tools/stringtie/assemble/stringtie_assemble.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/stringtie/assemble/stringtie_assemble.cwl -------------------------------------------------------------------------------- /tools/stringtie/assemble/stringtie_assemble.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/stringtie/assemble/stringtie_assemble.yml.sample -------------------------------------------------------------------------------- /tools/stringtie/assemble/test/stringtie_assemble.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/stringtie/assemble/test/stringtie_assemble.sh -------------------------------------------------------------------------------- /tools/tophat2/mapping/paired_end/tophat2_mapping_pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/tophat2/mapping/paired_end/tophat2_mapping_pe.cwl -------------------------------------------------------------------------------- /tools/tophat2/mapping/paired_end/tophat2_mapping_pe.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/tophat2/mapping/paired_end/tophat2_mapping_pe.yml.sample -------------------------------------------------------------------------------- /tools/tophat2/mapping/single_end/tophat2_mapping_se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/tophat2/mapping/single_end/tophat2_mapping_se.cwl -------------------------------------------------------------------------------- /tools/tophat2/mapping/single_end/tophat2_mapping_se.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/tophat2/mapping/single_end/tophat2_mapping_se.yml.sample -------------------------------------------------------------------------------- /tools/trinity/trinity-pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/trinity/trinity-pe.cwl -------------------------------------------------------------------------------- /tools/trinity/trinity-se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/trinity/trinity-se.cwl -------------------------------------------------------------------------------- /tools/trinity/trinity-version.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/trinity/trinity-version.cwl -------------------------------------------------------------------------------- /tools/utils/grep.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/utils/grep.cwl -------------------------------------------------------------------------------- /tools/utils/grep.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/tools/utils/grep.yml -------------------------------------------------------------------------------- /workflows/assembler/assembler-version.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/assembler/assembler-version.cwl -------------------------------------------------------------------------------- /workflows/assembler/nucleotides.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/assembler/nucleotides.cwl -------------------------------------------------------------------------------- /workflows/assembler/nucleotides.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/assembler/nucleotides.yml -------------------------------------------------------------------------------- /workflows/assembler/nucleotides2.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/assembler/nucleotides2.cwl -------------------------------------------------------------------------------- /workflows/assembler/nucleotides2.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/assembler/nucleotides2.yml -------------------------------------------------------------------------------- /workflows/assembler/nucleotids.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/assembler/nucleotids.sh -------------------------------------------------------------------------------- /workflows/assembler/nucleotids2.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/assembler/nucleotids2.sh -------------------------------------------------------------------------------- /workflows/bowtie/BowtieWorkflow-pe-pfastq-ver.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/bowtie/BowtieWorkflow-pe-pfastq-ver.cwl -------------------------------------------------------------------------------- /workflows/bowtie/BowtieWorkflow-pe-pfastq-ver.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/bowtie/BowtieWorkflow-pe-pfastq-ver.yml -------------------------------------------------------------------------------- /workflows/bowtie/BowtieWorkflow-pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/bowtie/BowtieWorkflow-pe.cwl -------------------------------------------------------------------------------- /workflows/bowtie/BowtieWorkflow-pe.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/bowtie/BowtieWorkflow-pe.yml -------------------------------------------------------------------------------- /workflows/bowtie/BowtieWorkflow-se-pfastq-ver.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/bowtie/BowtieWorkflow-se-pfastq-ver.cwl -------------------------------------------------------------------------------- /workflows/bowtie/BowtieWorkflow-se-pfastq-ver.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/bowtie/BowtieWorkflow-se-pfastq-ver.yml -------------------------------------------------------------------------------- /workflows/bowtie/BowtieWorkflow-se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/bowtie/BowtieWorkflow-se.cwl -------------------------------------------------------------------------------- /workflows/bowtie/BowtieWorkflow-se.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/bowtie/BowtieWorkflow-se.yml -------------------------------------------------------------------------------- /workflows/bowtie2/Bowtie2Workflow-pe-pfastq-ver.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/bowtie2/Bowtie2Workflow-pe-pfastq-ver.cwl -------------------------------------------------------------------------------- /workflows/bowtie2/Bowtie2Workflow-pe-pfastq-ver.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/bowtie2/Bowtie2Workflow-pe-pfastq-ver.yml -------------------------------------------------------------------------------- /workflows/bowtie2/Bowtie2Workflow-pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/bowtie2/Bowtie2Workflow-pe.cwl -------------------------------------------------------------------------------- /workflows/bowtie2/Bowtie2Workflow-pe.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/bowtie2/Bowtie2Workflow-pe.yml -------------------------------------------------------------------------------- /workflows/bowtie2/Bowtie2Workflow-se-pfastq-ver.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/bowtie2/Bowtie2Workflow-se-pfastq-ver.cwl -------------------------------------------------------------------------------- /workflows/bowtie2/Bowtie2Workflow-se-pfastq-ver.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/bowtie2/Bowtie2Workflow-se-pfastq-ver.yml -------------------------------------------------------------------------------- /workflows/bowtie2/Bowtie2Workflow-se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/bowtie2/Bowtie2Workflow-se.cwl -------------------------------------------------------------------------------- /workflows/bowtie2/Bowtie2Workflow-se.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/bowtie2/Bowtie2Workflow-se.yml -------------------------------------------------------------------------------- /workflows/bwa/BwaWorkflow-pe-pfastq-ver.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/bwa/BwaWorkflow-pe-pfastq-ver.cwl -------------------------------------------------------------------------------- /workflows/bwa/BwaWorkflow-pe-pfastq-ver.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/bwa/BwaWorkflow-pe-pfastq-ver.yml -------------------------------------------------------------------------------- /workflows/bwa/BwaWorkflow-pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/bwa/BwaWorkflow-pe.cwl -------------------------------------------------------------------------------- /workflows/bwa/BwaWorkflow-pe.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/bwa/BwaWorkflow-pe.yml -------------------------------------------------------------------------------- /workflows/bwa/BwaWorkflow-se-pfastq-ver.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/bwa/BwaWorkflow-se-pfastq-ver.cwl -------------------------------------------------------------------------------- /workflows/bwa/BwaWorkflow-se-pfastq-ver.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/bwa/BwaWorkflow-se-pfastq-ver.yml -------------------------------------------------------------------------------- /workflows/bwa/BwaWorkflow-se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/bwa/BwaWorkflow-se.cwl -------------------------------------------------------------------------------- /workflows/bwa/BwaWorkflow-se.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/bwa/BwaWorkflow-se.yml -------------------------------------------------------------------------------- /workflows/download-fastq/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/download-fastq/README.md -------------------------------------------------------------------------------- /workflows/download-fastq/download-fastq.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/download-fastq/download-fastq.cwl -------------------------------------------------------------------------------- /workflows/download-fastq/download-fastq.packed.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/download-fastq/download-fastq.packed.cwl -------------------------------------------------------------------------------- /workflows/download-fastq/download-fastq.single.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/download-fastq/download-fastq.single.cwl -------------------------------------------------------------------------------- /workflows/download-fastq/download-fastq.single.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/download-fastq/download-fastq.single.yml -------------------------------------------------------------------------------- /workflows/download-fastq/download-fastq.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/download-fastq/download-fastq.yml -------------------------------------------------------------------------------- /workflows/fastqc/fastqc_wf.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/fastqc/fastqc_wf.cwl -------------------------------------------------------------------------------- /workflows/fastqc/fastqc_wf.yml.sample: -------------------------------------------------------------------------------- 1 | nthreads: _NTHREADS_ 2 | run_ids: [_RUN_ID_] 3 | -------------------------------------------------------------------------------- /workflows/hisat2-cufflinks/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2-cufflinks/README.md -------------------------------------------------------------------------------- /workflows/hisat2-cufflinks/paired_end/hisat2-cufflinks_wf_pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2-cufflinks/paired_end/hisat2-cufflinks_wf_pe.cwl -------------------------------------------------------------------------------- /workflows/hisat2-cufflinks/paired_end/hisat2-cufflinks_wf_pe.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2-cufflinks/paired_end/hisat2-cufflinks_wf_pe.yml.sample -------------------------------------------------------------------------------- /workflows/hisat2-cufflinks/paired_end/test/hisat2-cufflinks_wf_pe.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2-cufflinks/paired_end/test/hisat2-cufflinks_wf_pe.sh -------------------------------------------------------------------------------- /workflows/hisat2-cufflinks/paired_end/test/hisat2-cufflinks_wf_pe_setup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2-cufflinks/paired_end/test/hisat2-cufflinks_wf_pe_setup.sh -------------------------------------------------------------------------------- /workflows/hisat2-cufflinks/single_end/hisat2-cufflinks_wf_se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2-cufflinks/single_end/hisat2-cufflinks_wf_se.cwl -------------------------------------------------------------------------------- /workflows/hisat2-cufflinks/single_end/hisat2-cufflinks_wf_se.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2-cufflinks/single_end/hisat2-cufflinks_wf_se.yml.sample -------------------------------------------------------------------------------- /workflows/hisat2-cufflinks/single_end/test/hisat2-cufflinks_wf_se.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2-cufflinks/single_end/test/hisat2-cufflinks_wf_se.sh -------------------------------------------------------------------------------- /workflows/hisat2-cufflinks/single_end/test/hisat2-cufflinks_wf_se_setup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2-cufflinks/single_end/test/hisat2-cufflinks_wf_se_setup.sh -------------------------------------------------------------------------------- /workflows/hisat2-eXpress/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2-eXpress/README.md -------------------------------------------------------------------------------- /workflows/hisat2-eXpress/paired_end/hisat2-eXpress_wf_pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2-eXpress/paired_end/hisat2-eXpress_wf_pe.cwl -------------------------------------------------------------------------------- /workflows/hisat2-eXpress/paired_end/hisat2-eXpress_wf_pe.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2-eXpress/paired_end/hisat2-eXpress_wf_pe.yml.sample -------------------------------------------------------------------------------- /workflows/hisat2-eXpress/paired_end/test/hisat2-eXpress_wf_pe.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2-eXpress/paired_end/test/hisat2-eXpress_wf_pe.sh -------------------------------------------------------------------------------- /workflows/hisat2-eXpress/paired_end/test/hisat2-eXpress_wf_pe_setup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2-eXpress/paired_end/test/hisat2-eXpress_wf_pe_setup.sh -------------------------------------------------------------------------------- /workflows/hisat2-eXpress/single_end/hisat2-eXpress_wf_se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2-eXpress/single_end/hisat2-eXpress_wf_se.cwl -------------------------------------------------------------------------------- /workflows/hisat2-eXpress/single_end/hisat2-eXpress_wf_se.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2-eXpress/single_end/hisat2-eXpress_wf_se.yml.sample -------------------------------------------------------------------------------- /workflows/hisat2-eXpress/single_end/test/hisat2-eXpress_wf_se.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2-eXpress/single_end/test/hisat2-eXpress_wf_se.sh -------------------------------------------------------------------------------- /workflows/hisat2-eXpress/single_end/test/hisat2-eXpress_wf_se_setup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2-eXpress/single_end/test/hisat2-eXpress_wf_se_setup.sh -------------------------------------------------------------------------------- /workflows/hisat2-stringtie/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2-stringtie/README.md -------------------------------------------------------------------------------- /workflows/hisat2-stringtie/paired_end/hisat2-stringtie_wf_pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2-stringtie/paired_end/hisat2-stringtie_wf_pe.cwl -------------------------------------------------------------------------------- /workflows/hisat2-stringtie/paired_end/hisat2-stringtie_wf_pe.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2-stringtie/paired_end/hisat2-stringtie_wf_pe.yml.sample -------------------------------------------------------------------------------- /workflows/hisat2-stringtie/paired_end/test/hisat2-stringtie_wf_pe.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2-stringtie/paired_end/test/hisat2-stringtie_wf_pe.sh -------------------------------------------------------------------------------- /workflows/hisat2-stringtie/paired_end/test/hisat2-stringtie_wf_pe_setup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2-stringtie/paired_end/test/hisat2-stringtie_wf_pe_setup.sh -------------------------------------------------------------------------------- /workflows/hisat2-stringtie/single_end/hisat2-stringtie_wf_se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2-stringtie/single_end/hisat2-stringtie_wf_se.cwl -------------------------------------------------------------------------------- /workflows/hisat2-stringtie/single_end/hisat2-stringtie_wf_se.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2-stringtie/single_end/hisat2-stringtie_wf_se.yml.sample -------------------------------------------------------------------------------- /workflows/hisat2-stringtie/single_end/test/hisat2-stringtie_wf_se.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2-stringtie/single_end/test/hisat2-stringtie_wf_se.sh -------------------------------------------------------------------------------- /workflows/hisat2-stringtie/single_end/test/hisat2-stringtie_wf_se_setup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2-stringtie/single_end/test/hisat2-stringtie_wf_se_setup.sh -------------------------------------------------------------------------------- /workflows/hisat2/Hisat2Workflow-pe-pfastq-ver.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2/Hisat2Workflow-pe-pfastq-ver.cwl -------------------------------------------------------------------------------- /workflows/hisat2/Hisat2Workflow-pe-pfastq-ver.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2/Hisat2Workflow-pe-pfastq-ver.yml -------------------------------------------------------------------------------- /workflows/hisat2/Hisat2Workflow-pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2/Hisat2Workflow-pe.cwl -------------------------------------------------------------------------------- /workflows/hisat2/Hisat2Workflow-pe.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2/Hisat2Workflow-pe.yml -------------------------------------------------------------------------------- /workflows/hisat2/Hisat2Workflow-se-pfastq-ver.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2/Hisat2Workflow-se-pfastq-ver.cwl -------------------------------------------------------------------------------- /workflows/hisat2/Hisat2Workflow-se-pfastq-ver.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2/Hisat2Workflow-se-pfastq-ver.yml -------------------------------------------------------------------------------- /workflows/hisat2/Hisat2Workflow-se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2/Hisat2Workflow-se.cwl -------------------------------------------------------------------------------- /workflows/hisat2/Hisat2Workflow-se.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/hisat2/Hisat2Workflow-se.yml -------------------------------------------------------------------------------- /workflows/kallisto/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/kallisto/README.md -------------------------------------------------------------------------------- /workflows/kallisto/paired_end/kallisto_wf_pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/kallisto/paired_end/kallisto_wf_pe.cwl -------------------------------------------------------------------------------- /workflows/kallisto/paired_end/kallisto_wf_pe.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/kallisto/paired_end/kallisto_wf_pe.yml.sample -------------------------------------------------------------------------------- /workflows/kallisto/paired_end/test/kallisto_wf_pe.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/kallisto/paired_end/test/kallisto_wf_pe.sh -------------------------------------------------------------------------------- /workflows/kallisto/paired_end/test/kallisto_wf_pe_setup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/kallisto/paired_end/test/kallisto_wf_pe_setup.sh -------------------------------------------------------------------------------- /workflows/kallisto/single_end/kallisto_wf_se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/kallisto/single_end/kallisto_wf_se.cwl -------------------------------------------------------------------------------- /workflows/kallisto/single_end/kallisto_wf_se.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/kallisto/single_end/kallisto_wf_se.yml.sample -------------------------------------------------------------------------------- /workflows/kallisto/single_end/test/kallisto_wf_se.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/kallisto/single_end/test/kallisto_wf_se.sh -------------------------------------------------------------------------------- /workflows/kallisto/single_end/test/kallisto_wf_se_setup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/kallisto/single_end/test/kallisto_wf_se_setup.sh -------------------------------------------------------------------------------- /workflows/last/LastWorkflow-pe-pfastq-ver.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/last/LastWorkflow-pe-pfastq-ver.cwl -------------------------------------------------------------------------------- /workflows/last/LastWorkflow-pe-pfastq-ver.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/last/LastWorkflow-pe-pfastq-ver.yml -------------------------------------------------------------------------------- /workflows/last/LastWorkflow-pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/last/LastWorkflow-pe.cwl -------------------------------------------------------------------------------- /workflows/last/LastWorkflow-pe.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/last/LastWorkflow-pe.yml -------------------------------------------------------------------------------- /workflows/last/LastWorkflow-se-pfastq-ver.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/last/LastWorkflow-se-pfastq-ver.cwl -------------------------------------------------------------------------------- /workflows/last/LastWorkflow-se-pfastq-ver.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/last/LastWorkflow-se-pfastq-ver.yml -------------------------------------------------------------------------------- /workflows/last/LastWorkflow-se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/last/LastWorkflow-se.cwl -------------------------------------------------------------------------------- /workflows/last/LastWorkflow-se.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/last/LastWorkflow-se.yml -------------------------------------------------------------------------------- /workflows/sailfish/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/sailfish/README.md -------------------------------------------------------------------------------- /workflows/sailfish/paired_end/sailfish_wf_pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/sailfish/paired_end/sailfish_wf_pe.cwl -------------------------------------------------------------------------------- /workflows/sailfish/paired_end/sailfish_wf_pe.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/sailfish/paired_end/sailfish_wf_pe.yml.sample -------------------------------------------------------------------------------- /workflows/sailfish/paired_end/test/sailfish_wf_pe.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/sailfish/paired_end/test/sailfish_wf_pe.sh -------------------------------------------------------------------------------- /workflows/sailfish/paired_end/test/sailfish_wf_pe_setup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/sailfish/paired_end/test/sailfish_wf_pe_setup.sh -------------------------------------------------------------------------------- /workflows/sailfish/single_end/sailfish_wf_se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/sailfish/single_end/sailfish_wf_se.cwl -------------------------------------------------------------------------------- /workflows/sailfish/single_end/sailfish_wf_se.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/sailfish/single_end/sailfish_wf_se.yml.sample -------------------------------------------------------------------------------- /workflows/sailfish/single_end/test/sailfish_wf_se.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/sailfish/single_end/test/sailfish_wf_se.sh -------------------------------------------------------------------------------- /workflows/sailfish/single_end/test/sailfish_wf_se_setup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/sailfish/single_end/test/sailfish_wf_se_setup.sh -------------------------------------------------------------------------------- /workflows/salmon/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/salmon/README.md -------------------------------------------------------------------------------- /workflows/salmon/paired_end/salmon_wf_pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/salmon/paired_end/salmon_wf_pe.cwl -------------------------------------------------------------------------------- /workflows/salmon/paired_end/salmon_wf_pe.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/salmon/paired_end/salmon_wf_pe.yml.sample -------------------------------------------------------------------------------- /workflows/salmon/paired_end/test/salmon_wf_pe.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/salmon/paired_end/test/salmon_wf_pe.sh -------------------------------------------------------------------------------- /workflows/salmon/paired_end/test/salmon_wf_pe_setup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/salmon/paired_end/test/salmon_wf_pe_setup.sh -------------------------------------------------------------------------------- /workflows/salmon/single_end/salmon_wf_se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/salmon/single_end/salmon_wf_se.cwl -------------------------------------------------------------------------------- /workflows/salmon/single_end/salmon_wf_se.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/salmon/single_end/salmon_wf_se.yml.sample -------------------------------------------------------------------------------- /workflows/salmon/single_end/test/salmon_wf_se.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/salmon/single_end/test/salmon_wf_se.sh -------------------------------------------------------------------------------- /workflows/salmon/single_end/test/salmon_wf_se_setup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/salmon/single_end/test/salmon_wf_se_setup.sh -------------------------------------------------------------------------------- /workflows/star-cufflinks/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-cufflinks/README.md -------------------------------------------------------------------------------- /workflows/star-cufflinks/paired_end/star-cufflinks_wf_pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-cufflinks/paired_end/star-cufflinks_wf_pe.cwl -------------------------------------------------------------------------------- /workflows/star-cufflinks/paired_end/star-cufflinks_wf_pe.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-cufflinks/paired_end/star-cufflinks_wf_pe.yml.sample -------------------------------------------------------------------------------- /workflows/star-cufflinks/paired_end/test/star-cufflinks_wf_pe.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-cufflinks/paired_end/test/star-cufflinks_wf_pe.sh -------------------------------------------------------------------------------- /workflows/star-cufflinks/paired_end/test/star-cufflinks_wf_pe_setup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-cufflinks/paired_end/test/star-cufflinks_wf_pe_setup.sh -------------------------------------------------------------------------------- /workflows/star-cufflinks/single_end/star-cufflinks_wf_se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-cufflinks/single_end/star-cufflinks_wf_se.cwl -------------------------------------------------------------------------------- /workflows/star-cufflinks/single_end/star-cufflinks_wf_se.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-cufflinks/single_end/star-cufflinks_wf_se.yml.sample -------------------------------------------------------------------------------- /workflows/star-cufflinks/single_end/test/star-cufflinks_wf_se.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-cufflinks/single_end/test/star-cufflinks_wf_se.sh -------------------------------------------------------------------------------- /workflows/star-cufflinks/single_end/test/star-cufflinks_wf_se_setup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-cufflinks/single_end/test/star-cufflinks_wf_se_setup.sh -------------------------------------------------------------------------------- /workflows/star-eXpress/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-eXpress/README.md -------------------------------------------------------------------------------- /workflows/star-eXpress/paired_end/star-eXpress_wf_pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-eXpress/paired_end/star-eXpress_wf_pe.cwl -------------------------------------------------------------------------------- /workflows/star-eXpress/paired_end/star-eXpress_wf_pe.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-eXpress/paired_end/star-eXpress_wf_pe.yml.sample -------------------------------------------------------------------------------- /workflows/star-eXpress/paired_end/test/star-eXpress_wf_pe.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-eXpress/paired_end/test/star-eXpress_wf_pe.sh -------------------------------------------------------------------------------- /workflows/star-eXpress/single_end/star-eXpress_wf_se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-eXpress/single_end/star-eXpress_wf_se.cwl -------------------------------------------------------------------------------- /workflows/star-eXpress/single_end/star-eXpress_wf_se.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-eXpress/single_end/star-eXpress_wf_se.yml.sample -------------------------------------------------------------------------------- /workflows/star-eXpress/single_end/test/star-eXpress_wf_se.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-eXpress/single_end/test/star-eXpress_wf_se.sh -------------------------------------------------------------------------------- /workflows/star-rsem/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-rsem/README.md -------------------------------------------------------------------------------- /workflows/star-rsem/paired_end/star-rsem_wf_pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-rsem/paired_end/star-rsem_wf_pe.cwl -------------------------------------------------------------------------------- /workflows/star-rsem/paired_end/star-rsem_wf_pe.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-rsem/paired_end/star-rsem_wf_pe.yml.sample -------------------------------------------------------------------------------- /workflows/star-rsem/paired_end/test/star-rsem_wf_pe.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-rsem/paired_end/test/star-rsem_wf_pe.sh -------------------------------------------------------------------------------- /workflows/star-rsem/paired_end/test/star-rsem_wf_pe_setup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-rsem/paired_end/test/star-rsem_wf_pe_setup.sh -------------------------------------------------------------------------------- /workflows/star-rsem/single_end/star-rsem_wf_se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-rsem/single_end/star-rsem_wf_se.cwl -------------------------------------------------------------------------------- /workflows/star-rsem/single_end/star-rsem_wf_se.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-rsem/single_end/star-rsem_wf_se.yml.sample -------------------------------------------------------------------------------- /workflows/star-rsem/single_end/test/star-rsem_wf_se.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-rsem/single_end/test/star-rsem_wf_se.sh -------------------------------------------------------------------------------- /workflows/star-rsem/single_end/test/star-rsem_wf_se_setup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-rsem/single_end/test/star-rsem_wf_se_setup.sh -------------------------------------------------------------------------------- /workflows/star-stringtie/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-stringtie/README.md -------------------------------------------------------------------------------- /workflows/star-stringtie/paired_end/star-stringtie_wf_pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-stringtie/paired_end/star-stringtie_wf_pe.cwl -------------------------------------------------------------------------------- /workflows/star-stringtie/paired_end/star-stringtie_wf_pe.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-stringtie/paired_end/star-stringtie_wf_pe.yml.sample -------------------------------------------------------------------------------- /workflows/star-stringtie/paired_end/test/star-stringtie_wf_pe.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-stringtie/paired_end/test/star-stringtie_wf_pe.sh -------------------------------------------------------------------------------- /workflows/star-stringtie/paired_end/test/star-stringtie_wf_pe_setup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-stringtie/paired_end/test/star-stringtie_wf_pe_setup.sh -------------------------------------------------------------------------------- /workflows/star-stringtie/single_end/star-stringtie_wf_se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-stringtie/single_end/star-stringtie_wf_se.cwl -------------------------------------------------------------------------------- /workflows/star-stringtie/single_end/star-stringtie_wf_se.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-stringtie/single_end/star-stringtie_wf_se.yml.sample -------------------------------------------------------------------------------- /workflows/star-stringtie/single_end/test/star-stringtie_wf_se.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-stringtie/single_end/test/star-stringtie_wf_se.sh -------------------------------------------------------------------------------- /workflows/star-stringtie/single_end/test/star-stringtie_wf_se_setup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star-stringtie/single_end/test/star-stringtie_wf_se_setup.sh -------------------------------------------------------------------------------- /workflows/star/StarWorkflow-pe-pfastq-ver.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star/StarWorkflow-pe-pfastq-ver.cwl -------------------------------------------------------------------------------- /workflows/star/StarWorkflow-pe-pfastq-ver.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star/StarWorkflow-pe-pfastq-ver.yml -------------------------------------------------------------------------------- /workflows/star/StarWorkflow-pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star/StarWorkflow-pe.cwl -------------------------------------------------------------------------------- /workflows/star/StarWorkflow-pe.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star/StarWorkflow-pe.yml -------------------------------------------------------------------------------- /workflows/star/StarWorkflow-se-pfastq-ver.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star/StarWorkflow-se-pfastq-ver.cwl -------------------------------------------------------------------------------- /workflows/star/StarWorkflow-se-pfastq-ver.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star/StarWorkflow-se-pfastq-ver.yml -------------------------------------------------------------------------------- /workflows/star/StarWorkflow-se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star/StarWorkflow-se.cwl -------------------------------------------------------------------------------- /workflows/star/StarWorkflow-se.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/star/StarWorkflow-se.yml -------------------------------------------------------------------------------- /workflows/tophat2-cufflinks/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/tophat2-cufflinks/README.md -------------------------------------------------------------------------------- /workflows/tophat2-cufflinks/paired_end/test/tophat2-cufflinks_wf_pe.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/tophat2-cufflinks/paired_end/test/tophat2-cufflinks_wf_pe.sh -------------------------------------------------------------------------------- /workflows/tophat2-cufflinks/paired_end/test/tophat2-cufflinks_wf_pe_setup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/tophat2-cufflinks/paired_end/test/tophat2-cufflinks_wf_pe_setup.sh -------------------------------------------------------------------------------- /workflows/tophat2-cufflinks/paired_end/tophat2-cufflinks_wf_pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/tophat2-cufflinks/paired_end/tophat2-cufflinks_wf_pe.cwl -------------------------------------------------------------------------------- /workflows/tophat2-cufflinks/paired_end/tophat2-cufflinks_wf_pe.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/tophat2-cufflinks/paired_end/tophat2-cufflinks_wf_pe.yml.sample -------------------------------------------------------------------------------- /workflows/tophat2-cufflinks/single_end/test/tophat2-cufflinks_wf_se.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/tophat2-cufflinks/single_end/test/tophat2-cufflinks_wf_se.sh -------------------------------------------------------------------------------- /workflows/tophat2-cufflinks/single_end/test/tophat2-cufflinks_wf_se_setup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/tophat2-cufflinks/single_end/test/tophat2-cufflinks_wf_se_setup.sh -------------------------------------------------------------------------------- /workflows/tophat2-cufflinks/single_end/tophat2-cufflinks_wf_se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/tophat2-cufflinks/single_end/tophat2-cufflinks_wf_se.cwl -------------------------------------------------------------------------------- /workflows/tophat2-cufflinks/single_end/tophat2-cufflinks_wf_se.yml.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/tophat2-cufflinks/single_end/tophat2-cufflinks_wf_se.yml.sample -------------------------------------------------------------------------------- /workflows/tophat2/Tophat2Workflow-pe-pfastq-ver.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/tophat2/Tophat2Workflow-pe-pfastq-ver.cwl -------------------------------------------------------------------------------- /workflows/tophat2/Tophat2Workflow-pe-pfastq-ver.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/tophat2/Tophat2Workflow-pe-pfastq-ver.yml -------------------------------------------------------------------------------- /workflows/tophat2/Tophat2Workflow-pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/tophat2/Tophat2Workflow-pe.cwl -------------------------------------------------------------------------------- /workflows/tophat2/Tophat2Workflow-pe.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/tophat2/Tophat2Workflow-pe.yml -------------------------------------------------------------------------------- /workflows/tophat2/Tophat2Workflow-se-pfastq-ver.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/tophat2/Tophat2Workflow-se-pfastq-ver.cwl -------------------------------------------------------------------------------- /workflows/tophat2/Tophat2Workflow-se-pfastq-ver.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/tophat2/Tophat2Workflow-se-pfastq-ver.yml -------------------------------------------------------------------------------- /workflows/tophat2/Tophat2Workflow-se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/tophat2/Tophat2Workflow-se.cwl -------------------------------------------------------------------------------- /workflows/tophat2/Tophat2Workflow-se.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/tophat2/Tophat2Workflow-se.yml -------------------------------------------------------------------------------- /workflows/trinity/TrinityWorkflow-pe-pfastq-ver.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/trinity/TrinityWorkflow-pe-pfastq-ver.cwl -------------------------------------------------------------------------------- /workflows/trinity/TrinityWorkflow-pe-pfastq-ver.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/trinity/TrinityWorkflow-pe-pfastq-ver.yml -------------------------------------------------------------------------------- /workflows/trinity/TrinityWorkflow-pe.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/trinity/TrinityWorkflow-pe.cwl -------------------------------------------------------------------------------- /workflows/trinity/TrinityWorkflow-pe.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/trinity/TrinityWorkflow-pe.yml -------------------------------------------------------------------------------- /workflows/trinity/TrinityWorkflow-se-pfastq-ver.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/trinity/TrinityWorkflow-se-pfastq-ver.cwl -------------------------------------------------------------------------------- /workflows/trinity/TrinityWorkflow-se-pfastq-ver.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/trinity/TrinityWorkflow-se-pfastq-ver.yml -------------------------------------------------------------------------------- /workflows/trinity/TrinityWorkflow-se.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/trinity/TrinityWorkflow-se.cwl -------------------------------------------------------------------------------- /workflows/trinity/TrinityWorkflow-se.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/HEAD/workflows/trinity/TrinityWorkflow-se.yml --------------------------------------------------------------------------------