refs #20821

[lightning.git] / cwl / lightning / fasta2numpy-test-release-wf.cwl

diff --git a/cwl/lightning/fasta2numpy-test-release-wf.cwl b/cwl/lightning/fasta2numpy-test-release-wf.cwl
index 7b860ccc2b76a3fda4cbb2129a860243233e44dc..dbf8d8632bc46d645915158bb1c7ed60d23caffb 100644 (file)
--- a/cwl/lightning/fasta2numpy-test-release-wf.cwl
+++ b/cwl/lightning/fasta2numpy-test-release-wf.cwl
@@ -56,6 +56,15 @@ inputs:
   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
@@ -110,6 +119,29 @@ steps:
       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-onehot_logisticregression:
+    run: lightning-slice-numpy-onehot.cwl
+    in:
+      matchgenome: matchgenome
+      libdir: lightning-slice/libdir
+      regions: regions
+      mergeoutput: mergeoutput
+      expandregions: expandregions
+      samplescsv: lightning-slice-numpy-pca/pcasamplescsv
+    out: [outdir, npys]
+
   lightning-slice-numpy-pca:
     run: lightning-slice-numpy-pca.cwl
     in:
@@ -122,8 +154,8 @@ steps:
       samplescsv: lightning-choose-samples/samplescsv
       pcacomponents: pcacomponents
     out: [outdir, pcanpy, pcasamplescsv]
-
-  lightning-slice-numpy:
+  
+  lightning-slice-numpy-onehot:
     run: lightning-slice-numpy-onehot.cwl
     in:
       matchgenome: matchgenome
@@ -131,7 +163,7 @@ steps:
       regions: regions
       mergeoutput: mergeoutput
       expandregions: expandregions
-      samplescsv: lightning-slice-numpy-pca/pcasamplescsv
+      samplescsv: lightning-choose-samples/samplescsv
     out: [outdir, npys]
 
   lightning-plot_1-2:
@@ -161,7 +193,7 @@ steps:
   lightning-anno2vcf-onehot:
     run: lightning-anno2vcf.cwl
     in:
-      annodir: lightning-slice-numpy/outdir
+      annodir: lightning-slice-numpy-onehot/outdir
     out: [vcfdir]
 
   make-libname:
@@ -183,6 +215,22 @@ steps:
       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: