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.dockstore.yml
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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