diff --git a/.github/workflows/gene-essentiality.yml b/.github/workflows/gene-essentiality.yml index c6b87481..a7bb642d 100644 --- a/.github/workflows/gene-essentiality.yml +++ b/.github/workflows/gene-essentiality.yml @@ -17,7 +17,7 @@ jobs: - name: Run gene essentiality id: essentiality run: | - TEST_RESULTS=$(/usr/local/bin/matlab -nodisplay -nosplash -nodesktop -r "addpath(genpath('.')); ihuman = readYAMLmodel('Human-GEM.yml'); taskStruct = parseTaskList('data/metabolicTasks/metabolicTasks_Essential.txt'); eGenes = estimateEssentialGenes(ihuman, 'Hart2015_RNAseq.txt', taskStruct);output = transpose(evaluateHart2015Essentiality(eGenes)); fid = fopen('data/testResults/gene-essential.csv','w'); fprintf(fid,[repmat('%s,',1,13) '%s\n'],output{:,1}); fprintf(fid,['%s,%d,%d,%d,%d' repmat(',%.4g',1,9) '\n'],output{:,2:end}); fclose(fid); disp(evaluateHart2015Essentiality(eGenes));" | awk 'NR>9 && !/^\.+/') + TEST_RESULTS=$(/usr/local/bin/matlab -nodisplay -nosplash -nodesktop -r "addpath(genpath('.')); ihuman = readYAMLmodel('model/Human-GEM.yml'); taskStruct = parseTaskList('data/metabolicTasks/metabolicTasks_Essential.txt'); eGenes = estimateEssentialGenes(ihuman, 'Hart2015_RNAseq.txt', taskStruct);output = transpose(evaluateHart2015Essentiality(eGenes)); fid = fopen('data/testResults/gene-essential.csv','w'); fprintf(fid,[repmat('%s,',1,13) '%s\n'],output{:,1}); fprintf(fid,['%s,%d,%d,%d,%d' repmat(',%.4g',1,9) '\n'],output{:,2:end}); fclose(fid); disp(evaluateHart2015Essentiality(eGenes));" | awk 'NR>9 && !/^\.+/') PARSED_RESULTS="${TEST_RESULTS//'%'/'%25'}" PARSED_RESULTS="${PARSED_RESULTS//$'\n'/'
'}" PARSED_RESULTS="${PARSED_RESULTS//$'\r'/'
'}" @@ -42,6 +42,7 @@ jobs: uses: NejcZdovc/comment-pr@v2 with: file: "commentGeneEssential.md" + identifier: "GITHUB_COMMENT_GENE" env: GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}} TEST_RESULTS: ${{steps.essentiality.outputs.results}} diff --git a/.github/workflows/macaw-tests.yml b/.github/workflows/macaw-tests.yml index ef0eaee4..d123b75c 100644 --- a/.github/workflows/macaw-tests.yml +++ b/.github/workflows/macaw-tests.yml @@ -52,6 +52,7 @@ jobs: uses: NejcZdovc/comment-pr@v2 with: file: "commentMacaw.md" + identifier: "GITHUB_COMMENT_MACAW" env: GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}} TEST_RESULTS: ${{steps.macaw-run.outputs.results}}