From 6ca17c2d5d08a7f28568dc34bd250f812898a3f2 Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Wed, 30 Aug 2023 07:09:28 -0700 Subject: [PATCH 01/17] Update dist-immune-build.yml --- .github/workflows/dist-immune-build.yml | 8 -------- 1 file changed, 8 deletions(-) diff --git a/.github/workflows/dist-immune-build.yml b/.github/workflows/dist-immune-build.yml index 07e97ee..672e3e2 100755 --- a/.github/workflows/dist-immune-build.yml +++ b/.github/workflows/dist-immune-build.yml @@ -5,16 +5,8 @@ defaults: on: push: paths: -<<<<<<< HEAD:.github/workflows/dist-immune-build.yml - 'metrics/distance/*' - 'metrics/imm-subtypes/*' -======= - - 'metrics/*' - - 'metrics/*/*' - - 'simulatedData/*' - - 'signatureMatrices/*' ->>>>>>> main:.github/workflows/metrics-docker-build.yml - jobs: build-and-push-tools: runs-on: ubuntu-latest From 189186449f9cc208e673588bcb0cab145d2af49d Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Wed, 30 Aug 2023 07:11:02 -0700 Subject: [PATCH 02/17] Update combine_results.R --- metrics/figures/combine_results.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metrics/figures/combine_results.R b/metrics/figures/combine_results.R index 8ff07dd..b240694 100644 --- 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 From f89918bb02367d2c1be49811d86ab515a7f3791c Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Wed, 30 Aug 2023 07:12:51 -0700 Subject: [PATCH 03/17] Update README.md --- README.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 7730413..d475284 100644 --- 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/metrics-fig-cor-build.yml/badge.svg) | Builds metrics and figure docker images | +![Immune subtypes docker builds](https://github.com/pnnl-compBio/decomprolute/actions/workflows/metrics-dist-immune-build.yml/badge.svg) | Builds immune subtypes and distance metric docker images | ## How to contribute From b8878175f7cf35bd10f5129308b14bd532987132 Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Wed, 30 Aug 2023 07:13:25 -0700 Subject: [PATCH 04/17] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index d475284..abb396e 100644 --- a/README.md +++ b/README.md @@ -11,8 +11,8 @@ Status of docker builds: | ![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 | -| ![Figures and correlation docker builds](https://github.com/pnnl-compBio/decomprolute/actions/workflows/metrics-fig-cor-build.yml/badge.svg) | Builds metrics and figure docker images | -![Immune subtypes docker builds](https://github.com/pnnl-compBio/decomprolute/actions/workflows/metrics-dist-immune-build.yml/badge.svg) | Builds immune subtypes and distance metric 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 From f8d55db0a1faadd0a8c6365ce7e27f1c59eb3b21 Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Wed, 30 Aug 2023 07:14:55 -0700 Subject: [PATCH 05/17] Update README.md From 04c867df36ccfe030edbad271c664f46e4966fba Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Wed, 30 Aug 2023 07:16:33 -0700 Subject: [PATCH 06/17] Update dist-immune-build.yml --- .github/workflows/dist-immune-build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/dist-immune-build.yml b/.github/workflows/dist-immune-build.yml index 672e3e2..2729e25 100755 --- 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: ./ From 0ff81f4f1d996de538d09a650903897e5c25e20a Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Wed, 30 Aug 2023 07:16:50 -0700 Subject: [PATCH 07/17] Update fig-cor-build.yml --- .github/workflows/fig-cor-build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/fig-cor-build.yml b/.github/workflows/fig-cor-build.yml index 201fbd8..c96b6cb 100755 --- 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: ./ From e5573ae873cb905c5d3d158048751553677f584c Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Wed, 30 Aug 2023 07:18:11 -0700 Subject: [PATCH 08/17] Update immune_subtypes.R --- metrics/imm-subtypes/immune_subtypes.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metrics/imm-subtypes/immune_subtypes.R b/metrics/imm-subtypes/immune_subtypes.R index 8218f26..04d9a0f 100644 --- 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'), From 96a715dd943e750257219c0cc97aad1709bb0202 Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Wed, 30 Aug 2023 07:19:46 -0700 Subject: [PATCH 09/17] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index abb396e..e5bf86b 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,7 @@ Status of docker builds: | ![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 | | ![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 | +| ![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 From e958749f2ac4b944826d0f0fd567a68e5fac3b73 Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Wed, 30 Aug 2023 12:20:38 -0700 Subject: [PATCH 10/17] Update dist-immune-build.yml From e9fa5ff76eed200fe91d10f55e57ce5a3eef768a Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Mon, 11 Sep 2023 12:13:55 -0700 Subject: [PATCH 11/17] Update Dockerfile --- simulatedData/Dockerfile | 1 - 1 file changed, 1 deletion(-) diff --git a/simulatedData/Dockerfile b/simulatedData/Dockerfile index fd11f7c..7a7151d 100644 --- 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'] From 175770e36a16fee1626cca7a31d242d1e6ca14ee Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Mon, 11 Sep 2023 12:15:02 -0700 Subject: [PATCH 12/17] Update docker-build-prot-dat.yml --- .github/workflows/docker-build-prot-dat.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-build-prot-dat.yml b/.github/workflows/docker-build-prot-dat.yml index bc273d6..fd1cc6c 100644 --- 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/*" From f001627329f37d30303a3cd3ef099ccf1f0761b0 Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Tue, 12 Sep 2023 07:39:49 -0700 Subject: [PATCH 13/17] Update simul-data-comparison.cwl --- metrics/data-sim/simul-data-comparison.cwl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metrics/data-sim/simul-data-comparison.cwl b/metrics/data-sim/simul-data-comparison.cwl index 4f3edfa..4050fa1 100644 --- a/metrics/data-sim/simul-data-comparison.cwl +++ b/metrics/data-sim/simul-data-comparison.cwl @@ -38,7 +38,7 @@ inputs: default: 100 repNumber: ##if you wanted to run this numer times type: int - defalut 0 + default: 0 outputs: cell-cor-tab: From 0d0b928378b4df4285df0a384bba34342f5d5f30 Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Tue, 12 Sep 2023 07:48:58 -0700 Subject: [PATCH 14/17] Update simul-data-comparison.cwl --- metrics/data-sim/simul-data-comparison.cwl | 1 + 1 file changed, 1 insertion(+) diff --git a/metrics/data-sim/simul-data-comparison.cwl b/metrics/data-sim/simul-data-comparison.cwl index 4050fa1..dff163d 100644 --- a/metrics/data-sim/simul-data-comparison.cwl +++ b/metrics/data-sim/simul-data-comparison.cwl @@ -88,6 +88,7 @@ steps: in: metricType: valueFrom: "cellType" + repNumber: repNumber files: source: - run-all-algs-by-mrna/cell-cor-file From 14e4880e9e5fb7818c17a9869189991015b94949 Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Tue, 12 Sep 2023 07:52:16 -0700 Subject: [PATCH 15/17] Update simul-data-comparison.cwl --- metrics/data-sim/simul-data-comparison.cwl | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/metrics/data-sim/simul-data-comparison.cwl b/metrics/data-sim/simul-data-comparison.cwl index dff163d..b37ced3 100644 --- a/metrics/data-sim/simul-data-comparison.cwl +++ b/metrics/data-sim/simul-data-comparison.cwl @@ -52,11 +52,11 @@ steps: run-all-algs-by-mrna: run: call-deconv-on-sim.cwl when: $(inputs.simType.trim() == 'mrna') - scatter: [protAlg,permutation,signature] + scatter: [protAlg,simulation,signature] scatterMethod: flat_crossproduct in: protAlg: prot-algorithms - permutation: mrna-perms + simulation: mrna-perms signature: rna-sigs sample: sample sampleType: @@ -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: From 473b93a8e88c55aa8435bc9a4990e4edf7f8015d Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Thu, 14 Sep 2023 10:51:21 -0700 Subject: [PATCH 16/17] Update getAllDatasets.py --- protData/getAllDatasets.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/protData/getAllDatasets.py b/protData/getAllDatasets.py index b34daf8..d263119 100644 --- a/protData/getAllDatasets.py +++ b/protData/getAllDatasets.py @@ -22,7 +22,7 @@ def getCancerObj(cancertype): dat = cptac.Lscc() elif cancertype == 'luad': dat = cptac.Luad() - elif cancertype == 'ov': + elif cancertype == 'ovarian': dat = cptac.Ov() elif cancertype =='pdac': dat = cptac.Pdac() From ffd9728eb420736e2973cf96e7d4cd052629a554 Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Thu, 14 Sep 2023 10:51:46 -0700 Subject: [PATCH 17/17] Update getAllDatasets.py --- mRNAData/getAllDatasets.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mRNAData/getAllDatasets.py b/mRNAData/getAllDatasets.py index bc5a596..dffa7ad 100644 --- a/mRNAData/getAllDatasets.py +++ b/mRNAData/getAllDatasets.py @@ -22,7 +22,7 @@ def getCancerObj(cancertype): dat = cptac.Lscc() elif cancertype == 'luad': dat = cptac.Luad() - elif cancertype == 'ov': + elif cancertype == 'ovarian': dat = cptac.Ov() elif cancertype =='pdac': dat = cptac.Pdac()