{"action":"created","comment":{"url":"https://api.github.com/repos/genialis/resolwe-bio/pulls/comments/80761593","pull_request_review_id":1794477,"id":80761593,"diff_hunk":"@@ -114,24 +113,166 @@\n       if [[ '.{{ src.file }}' =~ \\.(xls)$ ]]; then\n         re-import \"{{ src.file_temp|default:src.file }}\" \"{{ src.file }}\" \"xls\" \"xls\" 0.3 extract\n         convert_DE_excel_table.py '{{ src.file }}' > \"${NAME}.tab\"\n-        parse_diffexp.py ${NAME}.tab ${GENE_ID} ${LOG_FC} ${FDR} ${LOGODDS} ${FWER} ${PVALUE} ${STAT}\n+        parse_diffexp.py ${NAME}.tab ${GENE_ID} ${LOGFC} ${FDR} ${LOGODDS} ${FWER} ${PVALUE} ${STAT} --output de_data.json\n         re-checkrc\n         re-progress 0.7\n         gzip \"${NAME}.tab\"\n       elif [[ '.{{ src.file }}' =~ \\.(xlsx)$ ]]; then\n         re-import \"{{ src.file_temp|default:src.file }}\" \"{{ src.file }}\" \"xlsx\" \"xlsx\" 0.3 extract\n         convert_DE_excel_table.py '{{ src.file }}' > \"${NAME}.tab\"\n-        parse_diffexp.py ${NAME}.tab ${GENE_ID} ${LOG_FC} ${FDR} ${LOGODDS} ${FWER} ${PVALUE} ${STAT}\n+        parse_diffexp.py ${NAME}.tab ${GENE_ID} ${LOGFC} ${FDR} ${LOGODDS} ${FWER} ${PVALUE} ${STAT} --output de_data.json\n         re-checkrc\n         re-progress 0.7\n         gzip \"${NAME}.tab\"\n       else\n         re-import \"{{ src.file_temp|default:src.file }}\" \"{{ src.file }}\" \"diff|tab|gz\" \"tab\" 0.3\n-        parse_diffexp.py ${NAME}.tab ${GENE_ID} ${LOG_FC} ${FDR} ${LOGODDS} ${FWER} ${PVALUE} ${STAT}\n+        parse_diffexp.py ${NAME}.tab ${GENE_ID} ${LOGFC} ${FDR} ${LOGODDS} ${FWER} ${PVALUE} ${STAT} --output de_data.json\n+        re-checkrc\n+        re-progress 0.7\n+      fi\n+      re-save-file raw ${NAME}.tab.gz\n+      re-save-file de_file de_file.tab.gz\n+      re-save de_json de_data.json\n+      re-save source \"{{source}}\"\n+\n+- slug: upload-diffexp-inputs","path":"resolwe_bio/processes/import_data/differential_exp.yml","position":46,"original_position":46,"commit_id":"9a0aecbfc89d274c1352a7894d1b262c6c6ad3be","original_commit_id":"9a0aecbfc89d274c1352a7894d1b262c6c6ad3be","user":{"login":"mstajdohar","id":1026716,"avatar_url":"https://avatars.githubusercontent.com/u/1026716?v=3","gravatar_id":"","url":"https://api.github.com/users/mstajdohar","html_url":"https://github.com/mstajdohar","followers_url":"https://api.github.com/users/mstajdohar/followers","following_url":"https://api.github.com/users/mstajdohar/following{/other_user}","gists_url":"https://api.github.com/users/mstajdohar/gists{/gist_id}","starred_url":"https://api.github.com/users/mstajdohar/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mstajdohar/subscriptions","organizations_url":"https://api.github.com/users/mstajdohar/orgs","repos_url":"https://api.github.com/users/mstajdohar/repos","events_url":"https://api.github.com/users/mstajdohar/events{/privacy}","received_events_url":"https://api.github.com/users/mstajdohar/received_events","type":"User","site_admin":false},"body":"Refactor the `upload-diffexp` process and remove the `upload-diffexp-inputs`. Add `case` and `control` fields as optional fields to the `upload-diffexp` process. This way you will not have to repeat the process logic and bioinformaticians will only have to remember one slug.","created_at":"2016-09-27T18:24:45Z","updated_at":"2016-09-27T18:52:38Z","html_url":"https://github.com/genialis/resolwe-bio/pull/112#discussion_r80761593","pull_request_url":"https://api.github.com/repos/genialis/resolwe-bio/pulls/112","_links":{"self":{"href":"https://api.github.com/repos/genialis/resolwe-bio/pulls/comments/80761593"},"html":{"href":"https://github.com/genialis/resolwe-bio/pull/112#discussion_r80761593"},"pull_request":{"href":"https://api.github.com/repos/genialis/resolwe-bio/pulls/112"}}},"pull_request":{"url":"https://api.github.com/repos/genialis/resolwe-bio/pulls/112","id":86271913,"html_url":"https://github.com/genialis/resolwe-bio/pull/112","diff_url":"https://github.com/genialis/resolwe-bio/pull/112.diff","patch_url":"https://github.com/genialis/resolwe-bio/pull/112.patch","issue_url":"https://api.github.com/repos/genialis/resolwe-bio/issues/112","number":112,"state":"open","locked":false,"title":"Set expression objects as inputs on import of DE 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