Adding release bugfix releated changes

[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
new file mode 100644 (file)
index 0000000..7b860cc
--- /dev/null
+++ b/cwl/lightning/fasta2numpy-test-release-wf.cwl
@@ -0,0 +1,191 @@
+# Copyright (C) The Lightning Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
+$namespaces:
+  arv: "http://arvados.org/cwl#"
+cwlVersion: v1.2
+class: Workflow
+requirements:
+  ScatterFeatureRequirement: {}
+  SubworkflowFeatureRequirement: {}
+  StepInputExpressionRequirement: {}
+  MultipleInputFeatureRequirement: {}
+hints:
+  arv:UsePreemptible:
+    usePreemptible: false 
+
+inputs:
+  tagset:
+    type: File
+  fastadirs:
+    type:
+      type: array
+      items: Directory
+  refdir:
+    type: Directory
+  batchsize:
+    type: int
+  regions:
+    type: File?
+  matchgenome:
+    type: string
+  threads:
+    type: int
+  mergeoutput:
+    type: string
+  expandregions:
+    type: int
+  phenotypesnofamilydir:
+    type: Directory
+  phenotypesdir:
+    type: Directory
+  trainingsetsize:
+    type: float
+  randomseed:
+    type: int
+  pcacomponents:
+    type: int
+  chrs: string[]
+  snpeffdatadir: Directory
+  genomeversion: string
+  dbsnp:
+    type: File
+    secondaryFiles: [.csi]
+  gnomaddir: Directory
+  readmeinfo: string[]
+
+outputs: 
+  readme:
+    type: File
+    outputSource: genreadme/readme
+
+steps:
+  batch-dirs:
+    run: batch-dirs.cwl
+    in:
+      dirs: fastadirs
+      batchsize: batchsize
+    out: [batches]
+
+  lightning-import_data:
+    run: lightning-import.cwl
+    scatter: fastadirs
+    in:
+      saveincomplete:
+        valueFrom: "false"
+      tagset: tagset
+      fastadirs: batch-dirs/batches
+    out: [lib]
+
+  lightning-import_refs:
+    run: lightning-import.cwl
+    in:
+      saveincomplete:
+        valueFrom: "true"
+      tagset: tagset
+      fastadirs: refdir
+    out: [lib]
+
+  lightning-slice:
+    run: lightning-slice.cwl
+    in:
+      datalibs: lightning-import_data/lib
+      reflib: lightning-import_refs/lib
+    out: [libdir]
+
+  lightning-tiling-stats:
+    run: lightning-tiling-stats.cwl
+    in:
+      libdir: lightning-slice/libdir
+    out: [bed]
+
+  lightning-choose-samples:
+    run: lightning-choose-samples.cwl
+    in:
+      matchgenome: matchgenome
+      libdir: lightning-slice/libdir
+      phenotypesdir: phenotypesnofamilydir
+      trainingsetsize: trainingsetsize
+      randomseed: randomseed
+    out: [samplescsv]
+
+  lightning-slice-numpy-pca:
+    run: lightning-slice-numpy-pca.cwl
+    in:
+      matchgenome: matchgenome
+      libdir: lightning-slice/libdir
+      regions: regions
+      threads: threads
+      mergeoutput: mergeoutput
+      expandregions: expandregions
+      samplescsv: lightning-choose-samples/samplescsv
+      pcacomponents: pcacomponents
+    out: [outdir, pcanpy, pcasamplescsv]
+
+  lightning-slice-numpy:
+    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-plot_1-2:
+    run: lightning-plot.cwl
+    in:
+      pcanpy: lightning-slice-numpy-pca/pcanpy
+      pcasamplescsv: lightning-slice-numpy-pca/pcasamplescsv
+      phenotypesdir: phenotypesdir
+      xcomponent:
+        valueFrom: "1"
+      ycomponent:
+        valueFrom: "2"
+    out: [png]
+
+  lightning-plot_2-3:
+    run: lightning-plot.cwl
+    in:
+      pcanpy: lightning-slice-numpy-pca/pcanpy
+      pcasamplescsv: lightning-slice-numpy-pca/pcasamplescsv
+      phenotypesdir: phenotypesdir
+      xcomponent:
+        valueFrom: "2"
+      ycomponent:
+        valueFrom: "3"
+    out: [png]
+
+  lightning-anno2vcf-onehot:
+    run: lightning-anno2vcf.cwl
+    in:
+      annodir: lightning-slice-numpy/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]
+
+  genreadme:
+    run: genreadme.cwl
+    in:
+      samplescsv: lightning-choose-samples/samplescsv
+      readmeinfo: readmeinfo
+    out: [readme]