MANIFEST.in
README.md
setup.py
./__init__.py
./workflows_create.py
./workflows_init.py
biowardrobe_cwl_workflows.egg-info/PKG-INFO
biowardrobe_cwl_workflows.egg-info/SOURCES.txt
biowardrobe_cwl_workflows.egg-info/dependency_links.txt
biowardrobe_cwl_workflows.egg-info/entry_points.txt
biowardrobe_cwl_workflows.egg-info/requires.txt
biowardrobe_cwl_workflows.egg-info/top_level.txt
biowardrobe_cwl_workflows.egg-info/zip-safe
expressiontools/fastqc-results-trigger.cwl
expressiontools/files-to-folder.cwl
expressiontools/get-file-by-name.cwl
metadata/chipseq-header.cwl
metadata/rnaseq-header.cwl
subworkflows/allele-alignreads-se-pe.cwl
subworkflows/allele-process-reference.cwl
subworkflows/allele-process-strain.cwl
subworkflows/allele-vcf-alignreads-se-pe.cwl
subworkflows/bam-bedgraph-bigwig.cwl
subworkflows/chipseq-gen-bigwig.cwl
subworkflows/heatmap-prepare.cwl
subworkflows/xenbase-fastq-bowtie-bigwig-se-pe.cwl
subworkflows/xenbase-sra-to-fastq-pe.cwl
subworkflows/xenbase-sra-to-fastq-se.cwl
tools/atdp.cwl
tools/bamtools-stats.cwl
tools/bedtools-genomecov.cwl
tools/bowtie-alignreads.cwl
tools/bowtie-build.cwl
tools/bowtie2-build.cwl
tools/bowtie2.cwl
tools/bzip2-compress.cwl
tools/crossmap.cwl
tools/custom-bash.cwl
tools/custom-bedops.cwl
tools/deseq-advanced.cwl
tools/extract-fastq.cwl
tools/fastq-dump.cwl
tools/fastqc.cwl
tools/fastx-quality-stats.cwl
tools/geep.cwl
tools/group-isoforms.cwl
tools/halliftover.cwl
tools/homer-annotate-peaks-hist.cwl
tools/homer-make-metagene-profile.cwl
tools/homer-make-tag-directory.cwl
tools/iaintersect.cwl
tools/linux-sort.cwl
tools/macs2-callpeak-biowardrobe-only.cwl
tools/macs2-callpeak.cwl
tools/macs2-island-count.cwl
tools/macs2-stat.cwl
tools/makegff.cwl
tools/picard-markduplicates.cwl
tools/plugin-plot-dna.cwl
tools/plugin-plot-rna.cwl
tools/python-get-stat-chipseq.cwl
tools/python-get-stat-rnaseq.cwl
tools/python-make-biowardrobe-isoforms.cwl
tools/reads-counting.cwl
tools/rename.cwl
tools/rose.cwl
tools/rsem-calculate-expression.cwl
tools/samtools-index.cwl
tools/samtools-merge.cwl
tools/samtools-rmdup.cwl
tools/samtools-sort-index.cwl
tools/samtools-sort.cwl
tools/samtools-view.cwl
tools/satscript.cwl
tools/split-heatmap.cwl
tools/star-alignreads.cwl
tools/star-genomegenerate.cwl
tools/trimgalore.cwl
tools/trimmomatic.cwl
tools/ucsc-bedgraphtobigwig.cwl
tools/ucsc-bedtobigbed.cwl
tools/ucsc-bigwigtowig.cwl
tools/metadata/atdp-metadata.yaml
tools/metadata/bamtools-metadata.yaml
tools/metadata/bedtools-metadata.yaml
tools/metadata/bowtie-metadata.yaml
tools/metadata/bowtie2-metadata.yaml
tools/metadata/bzip2-metadata.yaml
tools/metadata/crossmap-metadata.yaml
tools/metadata/deseq-metadata.yaml
tools/metadata/fastqc-metadata.yaml
tools/metadata/fastx-toolkit-metadata.yaml
tools/metadata/geep-metadata.yaml
tools/metadata/hal-metadata.yaml
tools/metadata/homer-metadata.yaml
tools/metadata/iaintersect-metadata.yaml
tools/metadata/macs2-metadata.yaml
tools/metadata/makegff-metadata.yaml
tools/metadata/mea-metadata.yaml
tools/metadata/picard-metadata.yaml
tools/metadata/rose-metadata.yaml
tools/metadata/rsem-metadata.yaml
tools/metadata/samtools-metadata.yaml
tools/metadata/sratoolkit-metadata.yaml
tools/metadata/star-metadata.yaml
tools/metadata/trimgalore-metadata.yaml
tools/metadata/trimmomatic-metadata.yaml
tools/metadata/ucsc-metadata.yaml
workflows/allele-rnaseq-pe.cwl
workflows/allele-rnaseq-se.cwl
workflows/allele-vcf-rnaseq-pe.cwl
workflows/allele-vcf-rnaseq-se.cwl
workflows/bowtie-index.cwl
workflows/chipseq-pe.cwl
workflows/chipseq-se.cwl
workflows/genome-indices.cwl
workflows/heatmap.cwl
workflows/rnaseq-pe-dutp-mitochondrial.cwl
workflows/rnaseq-pe-dutp.cwl
workflows/rnaseq-pe.cwl
workflows/rnaseq-se-dutp-mitochondrial.cwl
workflows/rnaseq-se-dutp.cwl
workflows/rnaseq-se.cwl
workflows/star-index.cwl
workflows/super-enhancer.cwl
workflows/trim-chipseq-pe.cwl
workflows/trim-chipseq-se.cwl
workflows/trim-rnaseq-pe-dutp.cwl
workflows/trim-rnaseq-pe.cwl
workflows/trim-rnaseq-se-dutp.cwl
workflows/trim-rnaseq-se.cwl
workflows/xenbase-chipseq-pe.cwl
workflows/xenbase-chipseq-se.cwl
workflows/xenbase-rnaseq-pe.cwl
workflows/xenbase-rnaseq-se.cwl