Merge branch 'main' into dev

PNNL-CompBio · Sep 27, 2023 · 8417cb2 · 8417cb2
2 parents 823c8dc + fce1e8f
commit 8417cb2
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diff --git a/.github/workflows/dist-immune-build.yml b/.github/workflows/dist-immune-build.yml
@@ -1,4 +1,4 @@
-name: Docker-build-metrics
+name: Docker-distance-immune-metrics
 defaults:
   run:
     working-directory: ./

diff --git a/.github/workflows/docker-build-prot-dat.yml b/.github/workflows/docker-build-prot-dat.yml
@@ -4,7 +4,7 @@ defaults:
     working-directory: ./
 on:
   push:
-    branches:
+    paths:
       - "protData/*"
       - "signature_matrices/*"
       - "simulatedData/*"

diff --git a/.github/workflows/fig-cor-build.yml b/.github/workflows/fig-cor-build.yml
@@ -1,4 +1,4 @@
-name: Docker-build-metrics
+name: Docker-metrics-figures-correlations
 defaults:
   run:
     working-directory: ./

diff --git a/README.md b/README.md
@@ -8,10 +8,11 @@ Status of docker builds:
 
 | Status | Description |
 | --- | --- |
-| ![Protein docker builds](https://github.com/pnnl-compBio/decomprolute/actions/workflows/docker-build-1.yml/badge.svg) | Collects CPTAC protein data |
-| ![mRNA docker builds](https://github.com/pnnl-compBio/decomprolute/actions/workflows/docker-build-2.yml/badge.svg)| Collects CPTAC mRNA data |
+| ![Protein docker builds](https://github.com/pnnl-compBio/decomprolute/actions/workflows/docker-build-prot-dat.yml/badge.svg) | Collects CPTAC protein data |
+| ![mRNA docker builds](https://github.com/pnnl-compBio/decomprolute/actions/workflows/docker-build-mrna-imput.yml/badge.svg)| Collects CPTAC mRNA data |
 | ![Algorithm docker builds](https://github.com/pnnl-compBio/decomprolute/actions/workflows/decon-alg-docker.yml/badge.svg) | Builds deconvolution docker images |
-| ![Metrics docker builds](https://github.com/pnnl-compBio/decomprolute/actions/workflows/metrics-docker-build.yml/badge.svg) | Builds metrics and figure docker images |
+| ![Figures and correlation docker builds](https://github.com/pnnl-compBio/decomprolute/actions/workflows/fig-cor-build.yml/badge.svg) | Builds metrics and figure docker images |
+| ![Immune subtypes docker builds](https://github.com/pnnl-compBio/decomprolute/actions/workflows/dist-immune-build.yml/badge.svg) | Builds immune subtypes and distance metric docker images |
 
 ## How to contribute
 

diff --git a/metrics/data-sim/simul-data-comparison.cwl b/metrics/data-sim/simul-data-comparison.cwl
@@ -69,11 +69,11 @@ steps:
    run-all-algs-by-prot:
      run: call-deconv-on-sim.cwl
      when: $(inputs.simType.trim() == 'prot')
-     scatter: [protAlg,permutation,signature]
+     scatter: [protAlg,simulation,signature]
      scatterMethod: flat_crossproduct
      in:
         protAlg: prot-algorithms
-        permutation: prot-perms
+        simulation: prot-perms
         signature: prot-sigs
         sample: sample
         sampleType:
@@ -88,6 +88,7 @@ steps:
       in:
         metricType:
             valueFrom: "cellType"
+        repNumber: repNumber
         files:
             source:
               - run-all-algs-by-mrna/cell-cor-file

diff --git a/metrics/figures/combine_results.R b/metrics/figures/combine_results.R
@@ -3,7 +3,7 @@
 #' 1 - assess correlations for each patient/disease
 #' 2- assess correlations for each celltype/matrix
 #'
-#'
+#' We generally only use correlation right now
 #' to run:
 #' Rscript  combine_results.R --metricType sample --metric correlation --repNumber 0 */*corr.tsv
 #' Rscript  combine_results.R --metricType cellType --metric correlation  --repNumber 0  */*corrXcelltypes.tsv

diff --git a/metrics/imm-subtypes/immune_subtypes.R b/metrics/imm-subtypes/immune_subtypes.R
@@ -3,7 +3,7 @@ library(argparser)
 library(ggplot2)
 library(reshape2)
 library(nationalparkcolors)
-
+#general colors used
 pal <- c(park_palette('GeneralGrant'),
          park_palette('Redwoods'),
          park_palette('DeathValley'),

diff --git a/simulatedData/Dockerfile b/simulatedData/Dockerfile
@@ -10,5 +10,4 @@ COPY mapSimDataMatrices.R /bin/
 RUN chmod 777 /bin/getSimDataMatrices.R
 RUN chmod 777 /bin/mapSimDataMatrices.R
 
-
 #VOLUME ['/tmp']