.dockstore.yml

version: 1.2
tools:
# bamtools
  - subclass: CWL
    primaryDescriptorPath: /bamtools/bamtools_stats.cwl
    name: bamtools_stats
    publish: true
    testParameterFiles:
      - /bamtools/tests/bamtools_stats_t1.json
# bandage
  - subclass: CWL
    primaryDescriptorPath: /bandage/bandage-image.cwl
    name: bandage-image
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /bandage/bandage-info.cwl
    name: bandage-info
    publish: true
# bash
  - subclass: CWL
    primaryDescriptorPath: /bash/Gunzip.cwl
    name: Gunzip
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /bash/bedgraph_sort.cwl
    name: bedgraph_sort
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /bash/custom_bash.cwl
    name: custom_bash
    publish: true
    testParameterFiles:
      - /bash/tests/custom_bash_t1.json
      - /bash/tests/custom_bash_t2.json
      - /bash/tests/custom_bash_t3.json
      - /bash/tests/custom_bash_t4.json
      - /bash/tests/custom_bash_t5.json
  - subclass: CWL
    primaryDescriptorPath: /bash/extract_fastq.cwl
    name: extract_fastq
    publish: true
    testParameterFiles:
      - /bash/tests/extract_fastq_t1.json
      - /bash/tests/extract_fastq_t2.json
      - /bash/tests/extract_fastq_t3.json
      - /bash/tests/extract_fastq_t4.json
# bedtools
  - subclass: CWL
    primaryDescriptorPath: /bedtools/bedtools_bamtobed_1.cwl
    name: bedtools_bamtobed_1
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /bedtools/bedtools_bamtobed_2.cwl
    name: bedtools_bamtobed_2
    publish: true
    testParameterFiles:
      - /bedtools/tests/bedtools_bamtobed_2_t1.json
      - /bedtools/tests/bedtools_bamtobed_2_t2.json
  - subclass: CWL
    primaryDescriptorPath: /bedtools/bedtools_bedtobam.cwl
    name: bedtools_bedtobam
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /bedtools/bedtools_genomecov.cwl
    name: bedtools_genomecov
    publish: true
    testParameterFiles:
      - /bedtools/tests/bedtools_genomecov_t1.json
      - /bedtools/tests/bedtools_genomecov_t2.json
      - /bedtools/tests/bedtools_genomecov_t3.json
      - /bedtools/tests/bedtools_genomecov_t4.json
      - /bedtools/tests/bedtools_genomecov_t5.json
  - subclass: CWL
    primaryDescriptorPath: /bedtools/bedtools_genomecov_bed2bedgraph.cwl
    name: bedtools_genomecov_bed2bedgraph
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /bedtools/bedtools_getfasta.cwl
    name: bedtools_getfasta
    publish: true
    testParameterFiles:
      - /bedtools/tests/bedtools_getfasta_t1.json
      - /bedtools/tests/bedtools_getfasta_t2.json
  - subclass: CWL
    primaryDescriptorPath: /bedtools/bedtools_intersect.cwl
    name: bedtools_intersect
    publish: true
    testParameterFiles:
      - /bedtools/tests/bedtools_intersect_t1.json
      - /bedtools/tests/bedtools_intersect_t2.json
      - /bedtools/tests/bedtools_intersect_t3.json
  - subclass: CWL
    primaryDescriptorPath: /bedtools/bedtools_merge.cwl
    name: bedtools_merge
    publish: true
    testParameterFiles:
      - /bedtools/tests/bedtools_merge_t1.json
      - /bedtools/tests/bedtools_merge_t2.json
  - subclass: CWL
    primaryDescriptorPath: /bedtools/bedtools_slop_clip_to_chrom_boundaries.cwl
    name: bedtools_slop_clip_to_chrom_boundaries
    publish: true
# bismark
  - subclass: CWL
    primaryDescriptorPath: /bismark/bismark_align.cwl
    name: bismark_align
    publish: true
    testParameterFiles:
      - /bismark/tests/bismark_align_t1.json
  - subclass: CWL
    primaryDescriptorPath: /bismark/bismark_extract_methylation.cwl
    name: bismark_extract_methylation
    publish: true
    testParameterFiles:
      - /bismark/tests/bismark_extract_methylation_t1.json
      - /bismark/tests/bismark_methylation_se_t1.json
  - subclass: CWL
    primaryDescriptorPath: /bismark/bismark_prepare_genome.cwl
    name: bismark_prepare_genome
    publish: true
    testParameterFiles:
      - /bismark/tests/bismark_prepare_genome_t1.json
  - subclass: CWL
    primaryDescriptorPath: /bismark/bismark_report.cwl
    name: bismark_report
    publish: true
    testParameterFiles:
      - /bismark/tests/bismark_report_t1.json
# bowtie
  - subclass: CWL
    primaryDescriptorPath: /bowtie/bowtie_align.cwl
    name: bowtie_align
    publish: true
    testParameterFiles:
      - /bowtie/tests/bowtie_align_t1.json
      - /bowtie/tests/bowtie_align_t2.json
      - /bowtie/tests/bowtie_align_t3.json
      - /bowtie/tests/bowtie_align_t4.json
      - /bowtie/tests/bowtie_align_t5.json
      - /bowtie/tests/bowtie_align_t6.json
      - /bowtie/tests/bowtie_align_t7.json
      - /bowtie/tests/bowtie_align_t8.json
      - /bowtie/tests/bowtie_align_t9.json
  - subclass: CWL
    primaryDescriptorPath: /bowtie/bowtie_build.cwl
    name: bowtie_build
    publish: true
    testParameterFiles:
      - /bowtie/tests/bowtie_build_t1.json
# bowtie2
  - subclass: CWL
    primaryDescriptorPath: /bowtie2/bowtie2.cwl
    name: bowtie2
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /bowtie2/bowtie2_align.cwl
    name: bowtie2_align
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /bowtie2/bowtie2_build.cwl
    name: bowtie2_build
    publish: true
# bwa
  - subclass: CWL
    primaryDescriptorPath: /bwa/BWA-Index.cwl
    name: BWA-Index
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /bwa/BWA-Mem.cwl
    name: BWA-Mem
    publish: true
# bzip2
  - subclass: CWL
    primaryDescriptorPath: /bzip2/bzip2_compress.cwl
    name: bzip2_compress
    publish: true
    testParameterFiles:
      - /bzip2/tests/bzip2_compress_t1.json
# crossmap
  - subclass: CWL
    primaryDescriptorPath: /crossmap/crossmap.cwl
    name: crossmap
    publish: true
    testParameterFiles:
      - /crossmap/tests/crossmap-t1.json
      - /crossmap/tests/crossmap-t2.json
      - /crossmap/tests/crossmap-t3.json
      - /crossmap/tests/crossmap-t4.json
      - /crossmap/tests/crossmap-t5.json
      - /crossmap/tests/crossmap-t6.json
# cutadapt
  - subclass: CWL
    primaryDescriptorPath: /cutadapt/cutadapt-paired.cwl
    name: cutadapt-paired
    publish: true
# deeptools
  - subclass: CWL
    primaryDescriptorPath: /deeptools/deeptools_alignmentsieve.cwl
    name: deeptools_alignmentsieve
    publish: true
    testParameterFiles:
      - /deeptools/tests/deeptools_alignmentsieve_t1.json
      - /deeptools/tests/deeptools_alignmentsieve_t2.json
  - subclass: CWL
    primaryDescriptorPath: /deeptools/deeptools_bamCoverage.cwl
    name: deeptools_bamCoverage
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /deeptools/deeptools_plotCoverage.cwl
    name: deeptools_plotCoverage
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /deeptools/deeptools_plotFingerprint.cwl
    name: deeptools_plotFingerprint
    publish: true
# deseq
  - subclass: CWL
    primaryDescriptorPath: /deseq/deseq_advanced.cwl
    name: deseq_advanced
    publish: true
    testParameterFiles:
      - /deseq/tests/deseq_advanced_t1.json
      - /deseq/tests/deseq_advanced_t2.json
      - /deseq/tests/deseq_advanced_t3.json
      - /deseq/tests/deseq_advanced_t4.json
      - /deseq/tests/deseq_advanced_t5.json
      - /deseq/tests/deseq_advanced_t6.json
# fastp
  - subclass: CWL
    primaryDescriptorPath: /fastp/fastp.cwl
    name: fastp
    publish: true
# fastqc
  - subclass: CWL
    primaryDescriptorPath: /fastqc/fastqc_1.cwl
    name: fastqc_1
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /fastqc/fastqc_2.cwl
    name: fastqc_2
    publish: true
    testParameterFiles:
      - /fastqc/tests/fastqc_2_t1.json
      - /fastqc/tests/fastqc_2_t2.json
      - /fastqc/tests/fastqc_2_t3.json
# fastx_toolkit
  - subclass: CWL
    primaryDescriptorPath: /fastx_toolkit/fastx_quality_stats.cwl
    name: fastx_quality_stats
    publish: true
    testParameterFiles:
      - /fastx_toolkit/tests/fastx_quality_stats_t1.json
      - /fastx_toolkit/tests/fastx_quality_stats_t2.json
# GATK
  - subclass: CWL
    primaryDescriptorPath: /GATK/GATK-ApplyBQSR.cwl
    name: GATK-ApplyBQSR
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /GATK/GATK-BaseRecalibrator.cwl
    name: GATK-BaseRecalibrator
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /GATK/GATK-CNNScoreVariants.cwl
    name: GATK-CNNScoreVariants
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /GATK/GATK-FilterMutectCalls.cwl
    name: GATK-FilterMutectCalls
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /GATK/GATK-FilterVariantTranches.cwl
    name: GATK-FilterVariantTranches
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /GATK/GATK-FixMateInformation.cwl
    name: GATK-FixMateInformation
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /GATK/GATK-HaplotypeCaller.cwl
    name: GATK-HaplotypeCaller
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /GATK/GATK-MarkDuplicates.cwl
    name: GATK-MarkDuplicates
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /GATK/GATK-SelectVariants.cwl
    name: GATK-SelectVariants
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /GATK/GATK-SplitNCigarReads.cwl
    name: GATK-SplitNCigarReads
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /GATK/GATK-VariantFiltration.cwl
    name: GATK-VariantFiltration
    publish: true
# graph-genome-segmentation
  - subclass: CWL
    primaryDescriptorPath: /graph-genome-segmentation/component_segmentation.cwl
    name: component_segmentation
    publish: true
# hal
  - subclass: CWL
    primaryDescriptorPath: /hal/halliftover.cwl
    name: halliftover
    publish: true
    testParameterFiles:
      - /hal/tests/halliftover-1.json
      - /hal/tests/halliftover-2.json
# homer
  - subclass: CWL
    primaryDescriptorPath: /homer/homer-annotate-peaks-hist.cwl
    name: homer-annotate-peaks-hist
    publish: true
    testParameterFiles:
      - /homer/tests/homer-annotate-peaks-hist-1.json
      - /homer/tests/homer-annotate-peaks-hist-2.json
      - /homer/tests/homer-annotate-peaks-hist-3.json
  - subclass: CWL
    primaryDescriptorPath: /homer/homer-make-metagene-profile.cwl
    name: homer-make-metagene-profile
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /homer/homer-make-tag-directory.cwl
    name: homer-make-tag-directory
    publish: true
    testParameterFiles:
      - /homer/tests/homer-make-tag-directory-1.json
      - /homer/tests/homer-make-tag-directory-2.json
      - /homer/tests/homer-make-tag-directory-3.json
      - /homer/tests/homer-make-tag-directory-4.json
      - /homer/tests/homer-make-tag-directory-5.json
      - /homer/tests/homer-make-tag-directory-6.json
      - /homer/tests/homer-make-tag-directory-7.json
# hopach
  - subclass: CWL
    primaryDescriptorPath: /hopach/hopach.cwl
    name: hopach
    publish: true
    testParameterFiles:
      - /hopach/tests/hopach-1.json
      - /hopach/tests/hopach-2.json
      - /hopach/tests/hopach-3.json
      - /hopach/tests/hopach-4.json
# ivar
  - subclass: CWL
    primaryDescriptorPath: /ivar/ivar_trim.cwl
    name: ivar_trim
    publish: true
    testParameterFiles:
      - /ivar/tests/ivar_trim_t1.json
# Kallisto
  - subclass: CWL
    primaryDescriptorPath: /Kallisto/Kallisto-Index.cwl
    name: Kallisto-Index
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /Kallisto/Kallisto-Quant.cwl
    name: Kallisto-Quant
    publish: true
# kraken2
  - subclass: CWL
    primaryDescriptorPath: /kraken2/kraken2.cwl
    name: kraken2
    publish: true
    testParameterFiles:
      - /kraken2/tests/kraken2-t1.json
      - /kraken2/tests/kraken2-t2.json
      - /kraken2/tests/kraken2-t3.json
# Lancet
  - subclass: CWL
    primaryDescriptorPath: /Lancet/Lancet.cwl
    name: Lancet
    publish: true
# lofreq
  - subclass: CWL
    primaryDescriptorPath: /lofreq/lofreq_call.cwl
    name: lofreq_call
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /lofreq/lofreq_viterbi.cwl
    name: lofreq_viterbi
    publish: true
# mafft
  - subclass: CWL
    primaryDescriptorPath: /mafft/mafft.cwl
    name: mafft
    publish: true
    testParameterFiles:
      - /mafft/tests/mafft_test1.yml
# manorm
  - subclass: CWL
    primaryDescriptorPath: /manorm/manorm.cwl
    name: manorm
    publish: true
# mashmap
  - subclass: CWL
    primaryDescriptorPath: /mashmap/MashMap.cwl
    name: MashMap
    publish: true
# minimap2
  - subclass: CWL
    primaryDescriptorPath: /minimap2/minimap2_paf.cwl
    name: minimap2_paf
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /minimap2/minimap2_sam.cwl
    name: minimap2_sam
    publish: true
# multiqc
  - subclass: CWL
    primaryDescriptorPath: /multiqc/multiqc.cwl
    name: multiqc
    publish: true
# nanoplot
  - subclass: CWL
    primaryDescriptorPath: /nanoplot/nanoplot.cwl
    name: nanoplot
    publish: true
# nextclade
  - subclass: CWL
    primaryDescriptorPath: /nextclade/nextclade.cwl
    name: nextclade
    publish: true
    testParameterFiles:
      - /nextclade/tests/nextclade_t1.yml
# nucleoatac
  - subclass: CWL
    primaryDescriptorPath: /nucleoatac/nucleoatac.cwl
    name: nucleoatac
    publish: true
# odgi
  - subclass: CWL
    primaryDescriptorPath: /odgi/odgi_bin.cwl
    name: odgi_bin
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /odgi/odgi_build.cwl
    name: odgi_build
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /odgi/odgi_pathindex.cwl
    name: odgi_pathindex
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /odgi/odgi_sort.cwl
    name: odgi_sort
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /odgi/odgi_viz.cwl
    name: odgi_viz
    publish: true
# pca
  - subclass: CWL
    primaryDescriptorPath: /pca/pca.cwl
    name: pca
    publish: true
    testParameterFiles:
      - /pca/tests/pca_t1.json
# phantompeakqualtools
  - subclass: CWL
    primaryDescriptorPath: /phantompeakqualtools/phantompeakqualtools.cwl
    name: phantompeakqualtools
    publish: true
# picard
  - subclass: CWL
    primaryDescriptorPath: /picard/picard_AddOrReplaceReadGroups.cwl
    name: picard_AddOrReplaceReadGroups
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /picard/picard_CreateSequenceDictionary.cwl
    name: picard_CreateSequenceDictionary
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /picard/picard_MarkDuplicates.cwl
    name: picard_MarkDuplicates
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /picard/picard_SortSam.cwl
    name: picard_SortSam
    publish: true
# Pizzly
  - subclass: CWL
    primaryDescriptorPath: /Pizzly/Pizzly.cwl
    name: Pizzly
    publish: true
# preseq
  - subclass: CWL
    primaryDescriptorPath: /preseq/preseq_lc_extrap.cwl
    name: preseq_lc_extrap
    publish: true
    testParameterFiles:
      - /preseq/tests/preseq-lc-extrap-t1.json
      - /preseq/tests/preseq-lc-extrap-t2.json
      - /preseq/tests/preseq-lc-extrap-t3.json
      - /preseq/tests/preseq-lc-extrap-t4.json
# qualimap
  - subclass: CWL
    primaryDescriptorPath: /qualimap/qualimap_rnaseq.cwl
    name: qualimap_rnaseq
    publish: true
# samtools
  - subclass: CWL
    primaryDescriptorPath: /samtools/samtools_faidx.cwl
    name: samtools_faidx
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /samtools/samtools_fastq.cwl
    name: samtools_fastq
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /samtools/samtools_index.cwl
    name: samtools_index
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /samtools/samtools_merge.cwl
    name: samtools_merge
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /samtools/samtools_sort.cwl
    name: samtools_sort
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /samtools/samtools_stats.cwl
    name: samtools_stats
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /samtools/samtools_view_count_alignments.cwl
    name: samtools_view_count_alignments
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /samtools/samtools_view_filter.cwl
    name: samtools_view_filter
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /samtools/samtools_view_sam2bam.cwl
    name: samtools_view_sam2bam
    publish: true
# seqkit
  - subclass: CWL
    primaryDescriptorPath: /seqkit/seqkit_rmdup.cwl
    name: seqkit_rmdup
    publish: true
# spades
  - subclass: CWL
    primaryDescriptorPath: /spades/spades.cwl
    name: spades
    publish: true
# sratoolkit
  - subclass: CWL
    primaryDescriptorPath: /sratoolkit/fastq_dump.cwl
    name: fastq_dump
    publish: true
    testParameterFiles:
      - /sratoolkit/tests/fastq_dump_t1.json
      - /sratoolkit/tests/fastq_dump_t2.json
      - /sratoolkit/tests/fastq_dump_t3.json
      - /sratoolkit/tests/fastq_dump_t4.json
      - /sratoolkit/tests/fastq_dump_t5.json
  - subclass: CWL
    primaryDescriptorPath: /sratoolkit/prefetch.cwl
    name: prefetch
    publish: true
# STAR
  - subclass: CWL
    primaryDescriptorPath: /STAR/STAR-Align.cwl
    name: STAR-Align
    publish: true
  - subclass: CWL
    primaryDescriptorPath: /STAR/STAR-Index.cwl
    name: STAR-Index
    publish: true
# subread
  - subclass: CWL
    primaryDescriptorPath: /subread/featureCounts.cwl
    name: featureCounts
    publish: true
# trim_galore
  - subclass: CWL
    primaryDescriptorPath: /trim_galore/trim_galore.cwl
    name: trim_galore
    publish: true
# unicycler
  - subclass: CWL
    primaryDescriptorPath: /unicycler/unicycler.cwl
    name: unicycler
    publish: true
# util
  - subclass: CWL
    primaryDescriptorPath: /util/awk.cwl
    name: awk
    publish: true
    testParameterFiles:
      - /util/tests/awk_test1.yml
  - subclass: CWL
    primaryDescriptorPath: /util/grep.cwl
    name: grep
    publish: true
    testParameterFiles:
      - /util/tests/grep_test1.yml
  - subclass: CWL
    primaryDescriptorPath: /util/rename.cwl
    name: rename
    publish: true

workflows:
# sratoolkit
  - subclass: CWL
    primaryDescriptorPath: /sratoolkit/prefetch_fastq.cwl
    name: prefetch_fastq
    publish: true