gnomaddir: Directory
readmeinfo: string[]
-outputs: []
-# stagednpydir:
-# type: Directory
-# outputSource: stage-output/stagednpydir
-# stagedonehotnpydir:
-# type: Directory
-# outputSource: stage-output/stagedonehotnpydir
-# stagedannotationdir:
-# type: Directory
-# outputSource: stage-output/stagedannotationdir
-# readme:
-# type: File
-# outputSource: genreadme/readme
+outputs:
+ stagednpydir:
+ type: Directory
+ outputSource: stage-output/stagednpydir
+ stagedonehotnpydir:
+ type: Directory
+ outputSource: stage-output/stagedonehotnpydir
+ stagedannotationdir:
+ type: Directory
+ outputSource: stage-output/stagedannotationdir
+ readme:
+ type: File
+ outputSource: genreadme/readme
steps:
batch-dirs:
randomseed: randomseed
out: [samplescsv]
-# lightning-slice-numpy:
-# run: lightning-slice-numpy.cwl
-# in:
-# matchgenome: matchgenome
-# libdir: lightning-slice/libdir
-# regions: regions
-# threads: threads
-# mergeoutput: mergeoutput
-# expandregions: expandregions
-# samplescsv: lightning-choose-samples/samplescsv
-# out: [outdir, npys, chunktagoffsetcsv]
+ lightning-slice-numpy:
+ run: lightning-slice-numpy.cwl
+ in:
+ matchgenome: matchgenome
+ libdir: lightning-slice/libdir
+ regions: regions
+ threads: threads
+ mergeoutput: mergeoutput
+ expandregions: expandregions
+ samplescsv: lightning-choose-samples/samplescsv
+ out: [outdir, npys, chunktagoffsetcsv]
lightning-slice-numpy-onehot_chi2:
run: lightning-slice-numpy-onehot.cwl
samplescsv: lightning-choose-samples/samplescsv
pcacomponents: pcacomponents
out: [outdir, pcanpy, pcasamplescsv]
+
+ lightning-slice-numpy-onehot:
+ run: lightning-slice-numpy-onehot.cwl
+ in:
+ matchgenome: matchgenome
+ libdir: lightning-slice/libdir
+ regions: regions
+ mergeoutput: mergeoutput
+ expandregions: expandregions
+ samplescsv: lightning-choose-samples/samplescsv
+ out: [outdir, npys]
lightning-plot_1-2:
run: lightning-plot.cwl
valueFrom: "3"
out: [png]
-# lightning-anno2vcf-onehot:
-# run: lightning-anno2vcf.cwl
-# in:
-# annodir: lightning-slice-numpy-onehot/outdir
-# out: [vcfdir]
-
-# make-libname:
-# run: make-libname.cwl
-# in:
-# matchgenome: matchgenome
-# genomeversion: genomeversion
-# out: [libname]
-
-# annotate-wf:
-# run: ../annotation/annotate-wf.cwl
-# in:
-# sample: make-libname/libname
-# chrs: chrs
-# vcfdir: lightning-anno2vcf-onehot/vcfdir
-# snpeffdatadir: snpeffdatadir
-# genomeversion: genomeversion
-# dbsnp: dbsnp
-# gnomaddir: gnomaddir
-# out: [annotatedvcf, summary]
-
-# stage-output:
-# run: stage-output.cwl
-# in:
-# libname: make-libname/libname
-# npyfiles:
-# source: [lightning-slice-numpy/npys, lightning-slice-numpy/chunktagoffsetcsv]
-# linkMerge: merge_flattened
-# onehotnpyfiles: lightning-slice-numpy-onehot/npys
-# pcapngs:
-# source: [lightning-plot_1-2/png, lightning-plot_2-3/png]
-# linkMerge: merge_flattened
-# bed: lightning-tiling-stats/bed
-# annotatedvcf: annotate-wf/annotatedvcf
-# summary: annotate-wf/summary
-# out: [stagednpydir, stagedonehotnpydir, stagedannotationdir]
-
-# genreadme:
-# run: genreadme.cwl
-# in:
-# samplescsv: lightning-choose-samples/samplescsv
-# readmeinfo: readmeinfo
-# out: [readme]
+ lightning-anno2vcf-onehot:
+ run: lightning-anno2vcf.cwl
+ in:
+ annodir: lightning-slice-numpy-onehot/outdir
+ out: [vcfdir]
+
+ make-libname:
+ run: make-libname.cwl
+ in:
+ matchgenome: matchgenome
+ genomeversion: genomeversion
+ out: [libname]
+
+ annotate-wf:
+ run: ../annotation/annotate-wf.cwl
+ in:
+ sample: make-libname/libname
+ chrs: chrs
+ vcfdir: lightning-anno2vcf-onehot/vcfdir
+ snpeffdatadir: snpeffdatadir
+ genomeversion: genomeversion
+ dbsnp: dbsnp
+ gnomaddir: gnomaddir
+ out: [annotatedvcf, summary]
+
+ stage-output:
+ run: stage-output.cwl
+ in:
+ libname: make-libname/libname
+ npyfiles:
+ source: [lightning-slice-numpy/npys, lightning-slice-numpy/chunktagoffsetcsv]
+ linkMerge: merge_flattened
+ onehotnpyfiles: lightning-slice-numpy-onehot/npys
+ pcapngs:
+ source: [lightning-plot_1-2/png, lightning-plot_2-3/png]
+ linkMerge: merge_flattened
+ bed: lightning-tiling-stats/bed
+ annotatedvcf: annotate-wf/annotatedvcf
+ summary: annotate-wf/summary
+ out: [stagednpydir, stagedonehotnpydir, stagedannotationdir]
+
+ genreadme:
+ run: genreadme.cwl
+ in:
+ samplescsv: lightning-choose-samples/samplescsv
+ readmeinfo: readmeinfo
+ out: [readme]