20461 Updating Resource requirements

Updating resource requirements to be able to run on pirca

Arvados-DCO-1.1-Signed-off-by: Alex Coleman <alex.coleman@curii.com>

diff --git a/cwl/lightning/fasta2numpy-wf.cwl b/cwl/lightning/fasta2numpy-wf.cwl
index 68248de2995bfebbb2ba8aef29b505ce605170a1..9ca9642937dd989431030580b3f15c4601134b6a 100644 (file)
--- a/cwl/lightning/fasta2numpy-wf.cwl
+++ b/cwl/lightning/fasta2numpy-wf.cwl
@@ -55,19 +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:
@@ -119,17 +119,17 @@ 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:
+    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
@@ -165,6 +165,17 @@ steps:
       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
@@ -190,50 +201,50 @@ 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-anno2vcf.cwl b/cwl/lightning/lightning-anno2vcf.cwl
index fb23d5c1d4f0a468cdf1852cd0db24b5c92f6df7..ae8568fdb23f2ee0c0d322f3b64251e36d786e8c 100644 (file)
--- a/cwl/lightning/lightning-anno2vcf.cwl
+++ b/cwl/lightning/lightning-anno2vcf.cwl
@@ -14,7 +14,7 @@ hints:
     dockerPull: lightning
   ResourceRequirement:
     coresMin: 64
-    ramMin: 500000
+    ramMin: 200000 #500000
   arv:RuntimeConstraints:
     keep_cache: 83000
     outputDirType: keep_output_dir

diff --git a/cwl/lightning/lightning-import.cwl b/cwl/lightning/lightning-import.cwl
index 693e15372d73ba3df0accadbe83167f5d4a8aa24..25a1c0d0fd6de7cc6d7879d06b37628b91c812e8 100644 (file)
--- a/cwl/lightning/lightning-import.cwl
+++ b/cwl/lightning/lightning-import.cwl
@@ -14,8 +14,8 @@ hints:
     dockerPull: lightning
     arv:dockerCollectionPDH: 1f430e6dd9b6be0ae78d4cffde9b1fef+892
   ResourceRequirement:
-    coresMin: 96
-    ramMin: 670000
+    coresMin: 30#96
+    ramMin: 200000#670000
   arv:RuntimeConstraints:
     keep_cache: 6200
     outputDirType: keep_output_dir

diff --git a/cwl/lightning/lightning-slice-numpy-onehot.cwl b/cwl/lightning/lightning-slice-numpy-onehot.cwl
index 42c3e007884d358183bb79826605ce183a5d96eb..ac28b441b9faf24b50d8ea300dffc0539a15cf00 100644 (file)
--- a/cwl/lightning/lightning-slice-numpy-onehot.cwl
+++ b/cwl/lightning/lightning-slice-numpy-onehot.cwl
@@ -14,7 +14,7 @@ hints:
     dockerPull: lightning
   ResourceRequirement:
     coresMin: 64
-    ramMin: 660000
+    ramMin: 200000#660000
   arv:RuntimeConstraints:
     keep_cache: 83000
     outputDirType: keep_output_dir

diff --git a/cwl/lightning/lightning-slice-numpy-pca.cwl b/cwl/lightning/lightning-slice-numpy-pca.cwl
index 1e85f04dab3a0e7a9f97b2b66bfe37c1b19be9df..b4818eb6acff00e421bf7d92908b59f490d9d17f 100644 (file)
--- a/cwl/lightning/lightning-slice-numpy-pca.cwl
+++ b/cwl/lightning/lightning-slice-numpy-pca.cwl
@@ -14,7 +14,7 @@ hints:
     dockerPull: lightning
   ResourceRequirement:
     coresMin: 64
-    ramMin: 1500000
+    ramMin: 200000 #1500000
   arv:RuntimeConstraints:
     keep_cache: 83000
     outputDirType: keep_output_dir

diff --git a/cwl/lightning/lightning-slice-numpy.cwl b/cwl/lightning/lightning-slice-numpy.cwl
index 9cd8452bf4a7c90f8b2aff97d9deedf0a6923d46..ba462a35d51aa947c1ab15f885370fc3455e286b 100644 (file)
--- a/cwl/lightning/lightning-slice-numpy.cwl
+++ b/cwl/lightning/lightning-slice-numpy.cwl
@@ -14,7 +14,7 @@ hints:
     dockerPull: lightning
   ResourceRequirement:
     coresMin: 64
-    ramMin: 660000
+    ramMin: 200000#660000
   arv:RuntimeConstraints:
     keep_cache: 83000
     outputDirType: keep_output_dir

diff --git a/cwl/lightning/lightning-slice.cwl b/cwl/lightning/lightning-slice.cwl
index d30edb19a2d9c24132c4c8c3b2b749feac736bd2..502fdf9532f26eab2e39ab55cb1867307bf6abc8 100644 (file)
--- a/cwl/lightning/lightning-slice.cwl
+++ b/cwl/lightning/lightning-slice.cwl
@@ -14,8 +14,8 @@ hints:
     dockerPull: lightning
     arv:dockerCollectionPDH: 1f430e6dd9b6be0ae78d4cffde9b1fef+892
   ResourceRequirement:
-    coresMin: 96
-    ramMin: 660000
+    coresMin: 30#96
+    ramMin: 200000#660000
   arv:RuntimeConstraints:
     keep_cache: 6200
     outputDirType: keep_output_dir