Merge pull request #214 from PNNL-CompBio/dev

Dev

.github/workflows/alg-docker-build.yml

@@ -4,8 +4,9 @@ defaults:
     working-directory: ./
 on:
   push:
-    branches:
-      - "*"
+    paths:
+      - 'tumorDeconvAlgs/*'
+
 
 jobs:
   build-and-push-tools:
@@ -22,34 +23,6 @@ jobs:
         with:
           username: ${{ secrets.DOCKER }}
           password: ${{ secrets.DOCKERHUB_PASSWORD }}
-      - name: Build and push correlations
-        uses: docker/build-push-action@v4
-        with:
-          context: metrics/correlations
-          platforms: linux/amd64,linux/arm64/v8
-          push: true
-          tags: tumordeconv/correlation:latest
-      - name: Build and push distance
-        uses: docker/build-push-action@v4
-        with:
-          context: metrics/distance
-          platforms: linux/amd64,linux/arm64/v8
-          push: true
-          tags: tumordeconv/comparison:latest
-      - name: Build and push figures
-        uses: docker/build-push-action@v4
-        with:
-          context: metrics/figures
-          platforms: linux/amd64,linux/arm64/v8
-          push: true
-          tags: tumordeconv/figures:latest
-      - name: Build and push immune subtype
-        uses: docker/build-push-action@v4
-        with:
-          context: metrics/imm-subtypes
-          platforms: linux/amd64,linux/arm64/v8
-          push: true
-          tags: tumordeconv/imm-subtypes:latest
       - name: Build and push cibersort
         uses: docker/build-push-action@v4
         with:

.github/workflows/docker-build-2.yml

@@ -4,11 +4,11 @@ defaults:
     working-directory: ./
 on:
   push:
-    branches:
-      - "*"
+    paths:
+      - "mRNAData/*"
 
 jobs:
-  build-and-push-deconv-metrics:
+  build-and-push mrna:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout

.github/workflows/metrics-docker-build.yml

@@ -0,0 +1,53 @@
+name: Docker-build-metrics
+defaults:
+  run:
+    working-directory: ./
+on:
+  push:
+    paths:
+      - 'metrics/*'
+
+jobs:
+  build-and-push-tools:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+      - name: Login to DockerHub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKER }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+      - name: Build and push correlations
+        uses: docker/build-push-action@v4
+        with:
+          context: metrics/correlations
+          platforms: linux/amd64,linux/arm64
+          push: true
+          tags: tumordeconv/correlation:latest
+      - name: Build and push distance
+        uses: docker/build-push-action@v4
+        with:
+          context: metrics/distance
+          platforms: linux/amd64,linux/arm64
+          push: true
+          tags: tumordeconv/comparison:latest
+      - name: Build and push figures
+        uses: docker/build-push-action@v4
+        with:
+          context: metrics/figures
+          platforms: linux/amd64,linux/arm64
+          push: true
+          tags: tumordeconv/figures:latest
+      - name: Build and push immune subtype
+        uses: docker/build-push-action@v4
+        with:
+          context: metrics/imm-subtypes
+          platforms: linux/amd64,linux/arm64
+          push: true
+          tags: tumordeconv/imm-subtypes:latest
+

mRNAData/Dockerfile

@@ -1,8 +1,13 @@
-from amancevice/pandas
+from amancevice/pandas:1.4.0-slim
+#RUN echo "https://dl-cdn.alpinelinux.org/alpine/edge/community" >> /etc/apk/repositories
+#RUN apt update gcc fortran python-dev build-base wget freetype-dev libpng-dev openblas-dev py-numpy
+#RUN ln -s /usr/include/locale.h /usr/include/xlocale.h
+RUN pip install --no-cache-dir numpy scipy matplotlib
+
 RUN pip install --upgrade cptac
 COPY mRNADataSetsCLI.py /bin/
 RUN chmod 777 /bin/mRNADataSetsCLI.py
 COPY getAllDatasets.py /bin/
-RUN python /bin/getAllDatasets.py
+#RUN python /bin/getAllDatasets.py
 #VOLUME ['/tmp']
 WORKDIR ['/tmp']

metrics/correlations/deconv-corrXcelltypes-cwl-tool.cwl

@@ -36,8 +36,13 @@ inputs:
     default: "spearman"
   signature:
     type: string
+  sampleVal:
+    type: int
+    default: 100
   sampleType:
     type: string
+  sampleRep:
+    type: int
 
 outputs:
   corr:
@@ -47,7 +52,7 @@ outputs:
       outputEval: |
         ${
           var mat = inputs.signature
-          var name = inputs.sampleType + '-' + inputs.cancerType + '-' + inputs.mrnaAlg + '-to-' + inputs.protAlg +'-'+ mat + '-cellTypecorr.tsv'
+          var name = inputs.sampleType + '-' + inputs.cancerType + '-' + inputs.mrnaAlg + '-to-' +  inputs.protAlg +'-'+ mat + '-' + inputs.sampleVal + '-sample-' + inputs.sampleRep +'-cellTypecorr.tsv'
           self[0].basename = name;
           return self[0]
          }

metrics/data-sim/call-deconv-on-sim.cwl

@@ -11,36 +11,39 @@ requirements:
   - class: StepInputExpressionRequirement
 
 inputs:
-   signature:
+   signature:  ##name of matrix to sample from
      type: string
-   protAlg:
+   protAlg:    ##algorithm to run
      type: string
-   permutation:
+   simulation: ## permutation to test
      type: string
      default: '1'
-   dataType:
+   dataType:   ##mRNA or protein data
      type: string
      default: 'prot'
-   simType:
+   simType:    ##data simulated from mrna or protein
      type: string
      default: 'prot'
+   sample:     ##how much of the permuted sample do we test
+     type: int
+     default: 100
+   sampleRep:  ##
+     type: int
+     default: 1
 
 outputs:
-  matrix:
-     type: File
-     outputSource: get-sim-data/matrix
-  cellPred:
-     type: File
-     outputSource: get-sim-data/cellType
-  deconvoluted:
-     type: File
-     outputSource: deconv-prot/deconvoluted
-  deconv:
-     type: File
-     outputSource: match-prot-to-sig/updated-deconv
-#  mat-dist-file:
+#  matrix:
+#     type: File
+#     outputSource: get-sim-data/matrix
+#  cellPred:
+#     type: File
+#     outputSource: get-sim-data/cellType
+#  deconvoluted:
+#     type: File
+#     outputSource: deconv-prot/deconvoluted
+#  deconv:
 #     type: File
-#     outputSource: matrix-distance/dist     
+#     outputSource: match-prot-to-sig/updated-deconv
   cell-cor-file:
      type: File
      outputSource: celltype-cor/corr
@@ -50,12 +53,13 @@ steps:
      run: ../../signature_matrices/get-signature-matrix.cwl
      in:
       sigMatrixName: signature
+      subsample: sample
      out:
       [sigMatrix]
   get-sim-data:
      run: ../../simulatedData/sim-data-tool.cwl
      in:
-       repNumber: permutation
+       simNumber: simulation
        simType: simType
      out:
        [matrix,cellType]
@@ -77,12 +81,14 @@ steps:
   celltype-cor:
      run: ../correlations/deconv-corrXcelltypes-cwl-tool.cwl
      in:
-       cancerType: permutation
+       cancerType: simulation
        mrnaAlg:
           valueFrom: "cellFraction"
        protAlg: protAlg
        signature: signature
+       sampleVal: sample
        sampleType: simType
+       sampleRep: sampleRep
        proteomics:
          source: match-prot-to-sig/updated-deconv
        transcriptomics:
@@ -93,7 +99,7 @@ steps:
 #     in:
 #       matrixA: match-prot-to-sig/updated-deconv
 #       matrixB: match-prot-to-sig/updated-cell-matrix 
-#       cancerType: permutation
+#       cancerType: simulation
 #       aAlg: protAlg
 #       bAlg:
 #         valueFrom: "cellFraction"

metrics/data-sim/simul-data-comparison.cwl

@@ -33,6 +33,9 @@ inputs:
       default: ['LM7c','LM9']
    simType: 
       type: string
+   sample:
+      type: int
+      default: 100
 
 outputs:
    cell-cor-tab:
@@ -52,13 +55,14 @@ steps:
         protAlg: prot-algorithms
         permutation: mrna-perms
         signature: rna-sigs
+        sample: sample
         sampleType:
           valueFrom: 'normal'
         dataType:
           valueFrom: 'prot'
         simType: simType
      out:
-        [cell-cor-file, deconv, cellPred, deconvoluted, matrix]
+        [cell-cor-file]
    run-all-algs-by-prot:
      run: call-deconv-on-sim.cwl
      when: $(inputs.simType.trim() == 'prot')
@@ -68,13 +72,14 @@ steps:
         protAlg: prot-algorithms
         permutation: prot-perms
         signature: prot-sigs
+        sample: sample
         sampleType:
           valueFrom: 'normal'
         dataType:
           valueFrom: 'prot'
         simType: simType
      out:
-        [cell-cor-file,deconv, cellPred, deconvoluted, matrix]   
+        [cell-cor-file]
    get-celltype-cors:
       run: ../figures/plot-figs.cwl
       in: