├── .all-contributorsrc ├── .dockstore.yml ├── .github └── workflows │ └── ci.yml ├── CONTRIBUTING.md ├── GATK ├── GATK-ApplyBQSR.cwl ├── GATK-BaseRecalibrator.cwl ├── GATK-CNNScoreVariants.cwl ├── GATK-FilterMutectCalls.cwl ├── GATK-FilterVariantTranches.cwl ├── GATK-FixMateInformation.cwl ├── GATK-HaplotypeCaller.cwl ├── GATK-MarkDuplicates.cwl ├── GATK-SelectVariants.cwl ├── GATK-SplitNCigarReads.cwl └── GATK-VariantFiltration.cwl ├── Kallisto ├── Kallisto-Index.cwl └── Kallisto-Quant.cwl ├── LICENSE ├── Lancet └── Lancet.cwl ├── Pizzly └── Pizzly.cwl ├── README.md ├── STAR ├── STAR-Align.cwl └── STAR-Index.cwl ├── bamtools ├── bamtools_stats.cwl └── tests │ └── bamtools_stats_t1.json ├── bandage ├── bandage-image.cwl └── bandage-info.cwl ├── bash ├── Gunzip.cwl ├── bedgraph_sort.cwl ├── custom_bash.cwl ├── extract_fastq.cwl └── tests │ ├── custom_bash_t1.json │ ├── custom_bash_t2.json │ ├── custom_bash_t3.json │ ├── custom_bash_t4.json │ ├── custom_bash_t5.json │ ├── extract_fastq_t1.json │ ├── extract_fastq_t2.json │ ├── extract_fastq_t3.json │ └── extract_fastq_t4.json ├── bedtools ├── bedtools_bamtobed_1.cwl ├── bedtools_bamtobed_2.cwl ├── bedtools_bedtobam.cwl ├── bedtools_genomecov.cwl ├── bedtools_genomecov_bed2bedgraph.cwl ├── bedtools_getfasta.cwl ├── bedtools_intersect.cwl ├── bedtools_merge.cwl ├── bedtools_slop_clip_to_chrom_boundaries.cwl └── tests │ ├── bedtools_bamtobed_2_t1.json │ ├── bedtools_bamtobed_2_t2.json │ ├── bedtools_genomecov_t1.json │ ├── bedtools_genomecov_t2.json │ ├── bedtools_genomecov_t3.json │ ├── bedtools_genomecov_t4.json │ ├── bedtools_genomecov_t5.json │ ├── bedtools_getfasta_t1.json │ ├── bedtools_getfasta_t2.json │ ├── bedtools_intersect_t1.json │ ├── bedtools_intersect_t2.json │ ├── bedtools_intersect_t3.json │ ├── bedtools_merge_t1.json │ └── bedtools_merge_t2.json ├── bismark ├── bismark_align.cwl ├── bismark_extract_methylation.cwl ├── bismark_prepare_genome.cwl ├── bismark_report.cwl └── tests │ ├── bismark_align_t1.json │ ├── bismark_extract_methylation_t1.json │ ├── bismark_methylation_se_t1.json │ ├── bismark_prepare_genome_t1.json │ └── bismark_report_t1.json ├── bowtie ├── bowtie_align.cwl ├── bowtie_build.cwl └── tests │ ├── bowtie_align_t1.json │ ├── bowtie_align_t2.json │ ├── bowtie_align_t3.json │ ├── bowtie_align_t4.json │ ├── bowtie_align_t5.json │ ├── bowtie_align_t6.json │ ├── bowtie_align_t7.json │ ├── bowtie_align_t8.json │ ├── bowtie_align_t9.json │ └── bowtie_build_t1.json ├── bowtie2 ├── bowtie2.cwl ├── bowtie2_align.cwl └── bowtie2_build.cwl ├── bwa ├── BWA-Index.cwl ├── BWA-Mem.cwl ├── BWA-Mem2-index.cwl ├── BWA-Mem2-paired-end-test.yml ├── BWA-Mem2-paired-name_sorted-test.yml ├── BWA-Mem2-paired-rg-test.yml ├── BWA-Mem2-paired-unsorted-test.yml ├── BWA-Mem2-paired.cwl ├── BWA-Mem2-single-test.yml ├── BWA-Mem2-single.cwl ├── BWA-Mem2.cwl ├── ReadGroup.cwl ├── ReadGroupType.yml └── tests │ ├── bwa-index-t1.yml │ └── bwa-mem-t1.yml ├── bzip2 ├── bzip2_compress.cwl └── tests │ └── bzip2_compress_t1.json ├── cellranger ├── cellranger-aggr.cwl ├── cellranger-arc-aggr.cwl ├── cellranger-arc-count.cwl ├── cellranger-arc-mkref.cwl ├── cellranger-count.cwl ├── cellranger-mkref.cwl └── cellranger-reanalyze.cwl ├── ci.py ├── crossmap ├── crossmap.cwl └── tests │ ├── crossmap-t1.json │ ├── crossmap-t2.json │ ├── crossmap-t3.json │ ├── crossmap-t4.json │ ├── crossmap-t5.json │ └── crossmap-t6.json ├── cutadapt └── cutadapt-paired.cwl ├── deeptools ├── deeptools_alignmentsieve.cwl ├── deeptools_bamCoverage.cwl ├── deeptools_plotCoverage.cwl ├── deeptools_plotFingerprint.cwl └── tests │ ├── deeptools_alignmentsieve_t1.json │ └── deeptools_alignmentsieve_t2.json ├── deseq ├── deseq_advanced.cwl └── tests │ ├── deseq_advanced_t1.json │ ├── deseq_advanced_t2.json │ ├── deseq_advanced_t3.json │ ├── deseq_advanced_t4.json │ ├── deseq_advanced_t5.json │ └── deseq_advanced_t6.json ├── fastp └── fastp.cwl ├── fastqc ├── fastqc_1.cwl ├── fastqc_2.cwl └── tests │ ├── fastqc_2_t1.json │ ├── fastqc_2_t2.json │ └── fastqc_2_t3.json ├── fastx_toolkit ├── fastx_quality_stats.cwl └── tests │ ├── fastx_quality_stats_t1.json │ └── fastx_quality_stats_t2.json ├── gat └── gat-run.cwl ├── gffread └── gffread.cwl ├── graph-genome-segmentation ├── component_segmentation.Dockerfile └── component_segmentation.cwl ├── gsea └── gseapy.cwl ├── hal ├── halliftover.cwl └── tests │ ├── halliftover-1.json │ └── halliftover-2.json ├── haltools └── halliftover.cwl ├── homer ├── homer-annotate-peaks-hist.cwl ├── homer-make-metagene-profile.cwl ├── homer-make-tag-directory.cwl └── tests │ ├── homer-annotate-peaks-hist-1.json │ ├── homer-annotate-peaks-hist-2.json │ ├── homer-annotate-peaks-hist-3.json │ ├── homer-make-tag-directory-1.json │ ├── homer-make-tag-directory-2.json │ ├── homer-make-tag-directory-3.json │ ├── homer-make-tag-directory-4.json │ ├── homer-make-tag-directory-5.json │ ├── homer-make-tag-directory-6.json │ └── homer-make-tag-directory-7.json ├── hopach ├── hopach.cwl └── tests │ ├── hopach-1.json │ ├── hopach-2.json │ ├── hopach-3.json │ └── hopach-4.json ├── intervene └── intervene.cwl ├── iqtree └── iqtree.cwl ├── ivar ├── docker_container.txt ├── ivar_trim.cwl ├── software_requirement.yml └── tests │ └── ivar_trim_t1.json ├── kraken2 ├── kraken2.cwl └── tests │ ├── kraken2-t1.json │ ├── kraken2-t2.json │ └── kraken2-t3.json ├── lofreq ├── lofreq_call.cwl └── lofreq_viterbi.cwl ├── mafft ├── mafft.cwl └── tests │ └── mafft_test1.yml ├── manorm └── manorm.cwl ├── mashmap └── MashMap.cwl ├── megahit └── megahit.cwl ├── metfrag ├── metfrag.cwl └── metfrag_README.md ├── minimap2 ├── minimap2_paf.cwl └── minimap2_sam.cwl ├── multiqc └── multiqc.cwl ├── nanoplot └── nanoplot.cwl ├── nextclade ├── nextclade.cwl └── tests │ └── nextclade_t1.yml ├── nucleoatac └── nucleoatac.cwl ├── odgi ├── odgi_bin.cwl ├── odgi_build.cwl ├── odgi_pathindex.cwl ├── odgi_sort.cwl └── odgi_viz.cwl ├── pca ├── pca.cwl └── tests │ └── pca_t1.json ├── phantompeakqualtools └── phantompeakqualtools.cwl ├── picard ├── picard_AddOrReplaceReadGroups.cwl ├── picard_CreateSequenceDictionary.cwl ├── picard_MarkDuplicates.cwl └── picard_SortSam.cwl ├── preseq ├── preseq_lc_extrap.cwl └── tests │ ├── preseq-lc-extrap-t1.json │ ├── preseq-lc-extrap-t2.json │ ├── preseq-lc-extrap-t3.json │ └── preseq-lc-extrap-t4.json ├── qualimap └── qualimap_rnaseq.cwl ├── rgt └── rgt-thor.cwl ├── rose └── rose.cwl ├── samtools ├── samtools_faidx.cwl ├── samtools_fastq.cwl ├── samtools_index.cwl ├── samtools_merge.cwl ├── samtools_sort.cwl ├── samtools_stats.cwl ├── samtools_view_count_alignments.cwl ├── samtools_view_filter.cwl └── samtools_view_sam2bam.cwl ├── seqkit └── seqkit_rmdup.cwl ├── sirius ├── sirius.cwl └── sirius_README.md ├── snp-sites ├── snp-sites.cwl └── tests │ └── snp-sites-test1.yml ├── spades └── spades.cwl ├── sratoolkit ├── fastq_dump.cwl ├── metadata │ └── sratoolkit_metadata.yaml ├── 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