Merge branch 'release/1.6.0'

DataBiosphere · Apr 30, 2018 · 7457845 · 7457845
2 parents 3802615 + 5e50c26
commit 7457845
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Showing 19 changed files with 2 additions and 2 deletions.
diff --git a/...workflow-wrapping-alignment-workflow.json → ...workflow-wrapping-alignment-workflow.json b/...workflow-wrapping-alignment-workflow.json → ...workflow-wrapping-alignment-workflow.json
diff --git a/...-workflow-wrapping-alignment-workflow.wdl → ...-workflow-wrapping-alignment-workflow.wdl b/...-workflow-wrapping-alignment-workflow.wdl → ...-workflow-wrapping-alignment-workflow.wdl
@@ -1,5 +1,5 @@
-import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/topmed-firecloud-demo/functional-equivalence-wdl/FunctionalEquivalence.wdl" as TopMed_aligner
-import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.4.0/functional-equivalence-checker/topmed-alignment-checker.wdl" as checker
+import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.6.0/aligner/functional-equivalence-wdl/FunctionalEquivalence.wdl" as TopMed_aligner
+import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.6.0/aligner/functional-equivalence-checker/topmed-alignment-checker.wdl" as checker
 
 workflow checkerWorkflow {
   #File referenceFasta

diff --git a/...ence-checker/topmed-alignment-checker.wdl → ...ence-checker/topmed-alignment-checker.wdl b/...ence-checker/topmed-alignment-checker.wdl → ...ence-checker/topmed-alignment-checker.wdl
diff --git a/...quivalence-wdl/FunctionalEquivalence.json → ...quivalence-wdl/FunctionalEquivalence.json b/...quivalence-wdl/FunctionalEquivalence.json → ...quivalence-wdl/FunctionalEquivalence.json
diff --git a/...equivalence-wdl/FunctionalEquivalence.wdl → ...equivalence-wdl/FunctionalEquivalence.wdl b/...equivalence-wdl/FunctionalEquivalence.wdl → ...equivalence-wdl/FunctionalEquivalence.wdl
diff --git a/functional-equivalence-wdl/README.md → aligner/functional-equivalence-wdl/README.md b/functional-equivalence-wdl/README.md → aligner/functional-equivalence-wdl/README.md
diff --git a/topmed-cwl/tasks/ApplyBQSR.yaml → aligner/topmed-cwl/tasks/ApplyBQSR.yaml b/topmed-cwl/tasks/ApplyBQSR.yaml → aligner/topmed-cwl/tasks/ApplyBQSR.yaml
diff --git a/topmed-cwl/tasks/BaseRecalibrator.yaml → ...er/topmed-cwl/tasks/BaseRecalibrator.yaml b/topmed-cwl/tasks/BaseRecalibrator.yaml → ...er/topmed-cwl/tasks/BaseRecalibrator.yaml
diff --git a/topmed-cwl/tasks/ConvertToCram.yaml → aligner/topmed-cwl/tasks/ConvertToCram.yaml b/topmed-cwl/tasks/ConvertToCram.yaml → aligner/topmed-cwl/tasks/ConvertToCram.yaml
diff --git a/...ed-cwl/tasks/CreateSequenceGroupingTSV.py → ...ed-cwl/tasks/CreateSequenceGroupingTSV.py b/...ed-cwl/tasks/CreateSequenceGroupingTSV.py → ...ed-cwl/tasks/CreateSequenceGroupingTSV.py
diff --git a/...-cwl/tasks/CreateSequenceGroupingTSV.yaml → ...-cwl/tasks/CreateSequenceGroupingTSV.yaml b/...-cwl/tasks/CreateSequenceGroupingTSV.yaml → ...-cwl/tasks/CreateSequenceGroupingTSV.yaml
diff --git a/...ks/Expression_createsequencegrouping.yaml → ...ks/Expression_createsequencegrouping.yaml b/...ks/Expression_createsequencegrouping.yaml → ...ks/Expression_createsequencegrouping.yaml
diff --git a/topmed-cwl/tasks/GatherBamFiles.yaml → aligner/topmed-cwl/tasks/GatherBamFiles.yaml b/topmed-cwl/tasks/GatherBamFiles.yaml → aligner/topmed-cwl/tasks/GatherBamFiles.yaml
diff --git a/topmed-cwl/tasks/GatherBqsrReports.yaml → ...r/topmed-cwl/tasks/GatherBqsrReports.yaml b/topmed-cwl/tasks/GatherBqsrReports.yaml → ...r/topmed-cwl/tasks/GatherBqsrReports.yaml
diff --git a/topmed-cwl/tasks/GetBwaVersion.yaml → aligner/topmed-cwl/tasks/GetBwaVersion.yaml b/topmed-cwl/tasks/GetBwaVersion.yaml → aligner/topmed-cwl/tasks/GetBwaVersion.yaml
diff --git a/topmed-cwl/tasks/MarkDuplicates.yaml → aligner/topmed-cwl/tasks/MarkDuplicates.yaml b/topmed-cwl/tasks/MarkDuplicates.yaml → aligner/topmed-cwl/tasks/MarkDuplicates.yaml
diff --git a/...-cwl/tasks/SamToFastqAndBwaMemAndMba.yaml → ...-cwl/tasks/SamToFastqAndBwaMemAndMba.yaml b/...-cwl/tasks/SamToFastqAndBwaMemAndMba.yaml → ...-cwl/tasks/SamToFastqAndBwaMemAndMba.yaml
diff --git a/topmed-cwl/tasks/SortSam.yaml → aligner/topmed-cwl/tasks/SortSam.yaml b/topmed-cwl/tasks/SortSam.yaml → aligner/topmed-cwl/tasks/SortSam.yaml
diff --git a/topmed-cwl/workflow/alignment_pipeline.yaml → ...pmed-cwl/workflow/alignment_pipeline.yaml b/topmed-cwl/workflow/alignment_pipeline.yaml → ...pmed-cwl/workflow/alignment_pipeline.yaml