Change slice-numpy-onehot parameter

refs #19868

Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>

diff --git a/cwl/lightning/fasta2numpy-wf.cwl b/cwl/lightning/fasta2numpy-wf.cwl
index a804b9cfac4e33c9e0bc663a49da52a9472da890..68248de2995bfebbb2ba8aef29b505ce605170a1 100644 (file)
--- a/cwl/lightning/fasta2numpy-wf.cwl
+++ b/cwl/lightning/fasta2numpy-wf.cwl
@@ -11,6 +11,9 @@ requirements:
   SubworkflowFeatureRequirement: {}
   StepInputExpressionRequirement: {}
   MultipleInputFeatureRequirement: {}
+hints:
+  arv:UsePreemptible:
+    usePreemptible: true
 
 inputs:
   tagset:
@@ -52,19 +55,19 @@ inputs:
   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:
@@ -116,28 +119,38 @@ steps:
       randomseed: randomseed
     out: [samplescsv]
 
-  lightning-slice-numpy:
-    run: lightning-slice-numpy.cwl
+#  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
     in:
       matchgenome: matchgenome
       libdir: lightning-slice/libdir
       regions: regions
-      threads: threads
       mergeoutput: mergeoutput
       expandregions: expandregions
       samplescsv: lightning-choose-samples/samplescsv
-    out: [outdir, npys, chunktagoffsetcsv]
+    out: [outdir, npys]
 
-  lightning-slice-numpy-onehot:
+  lightning-slice-numpy-onehot_logisticregression:
     run: lightning-slice-numpy-onehot.cwl
     in:
       matchgenome: matchgenome
       libdir: lightning-slice/libdir
       regions: regions
-      threads: threads
       mergeoutput: mergeoutput
       expandregions: expandregions
-      samplescsv: lightning-choose-samples/samplescsv
+      samplescsv: lightning-slice-numpy-pca/pcasamplescsv
     out: [outdir, npys]
 
   lightning-slice-numpy-pca:
@@ -177,50 +190,50 @@ steps:
         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]

diff --git a/cwl/lightning/lightning-slice-numpy-onehot.cwl b/cwl/lightning/lightning-slice-numpy-onehot.cwl
index 15ca5471de70322e30050fadf09c17a9206d1e61..42c3e007884d358183bb79826605ce183a5d96eb 100644 (file)
--- a/cwl/lightning/lightning-slice-numpy-onehot.cwl
+++ b/cwl/lightning/lightning-slice-numpy-onehot.cwl
@@ -22,7 +22,6 @@ inputs:
   matchgenome: string
   libdir: Directory
   regions: File?
-  threads: int
   mergeoutput: string
   expandregions: int
   samplescsv: File
@@ -51,7 +50,7 @@ arguments:
     valueFrom: $(inputs.regions)
     separate: false
   - prefix: "-threads="
-    valueFrom: $(inputs.threads)
+    valueFrom: "20"
     separate: false
   - prefix: "-merge-output="
     valueFrom: $(inputs.mergeoutput)
@@ -63,5 +62,6 @@ arguments:
     valueFrom: $(inputs.samplescsv)
     separate: false
   - "-single-onehot=true"
-  - "-chi2-p-value=0.01"
+  - "-chi2-p-value=0.000001"
   - "-min-coverage=0.9"
+  - "-case-control-only=true"