{"id":64508,"date":"2026-04-25T19:13:41","date_gmt":"2026-04-25T11:13:41","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=64508"},"modified":"2026-04-23T19:17:01","modified_gmt":"2026-04-23T11:17:01","slug":"%e7%94%9f%e4%bf%a1%e4%ba%ba%e7%94%a8-codex-%e7%9a%84%e8%bf%9b%e9%98%b6%e7%89%88%ef%bc%9a%e5%88%ab%e5%86%8d%e5%8f%aa%e5%bc%80%e4%ba%a4%e4%ba%92%e7%aa%97%e5%8f%a3%e4%ba%86","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=64508","title":{"rendered":"\u751f\u4fe1\u4eba\u7528 Codex \u7684\u8fdb\u9636\u7248\uff1a\u522b\u518d\u53ea\u5f00\u4ea4\u4e92\u7a97\u53e3\u4e86"},"content":{"rendered":"\n<h1 class=\"wp-block-heading\"><\/h1>\n\n\n\n<p><\/p>\n\n\n\n<h2 class=\"wp-block-heading\">1. \u5148\u56fa\u5b9a\u5de5\u4f5c\u76ee\u5f55\uff0c\u518d\u5f00\u5de5<\/h2>\n\n\n\n<p><code>codex -C ~\/projects\/rnaseq_lung<\/code><\/p>\n\n\n\n<p>\u522b\u5c0f\u770b&nbsp;-C\u3002\u751f\u4fe1\u9879\u76ee\u6700\u6015\u4e32\u76ee\u5f55\uff0c\u5c24\u5176\u4f60\u540c\u65f6\u5f00\u7740&nbsp;bulk RNA-seq\u3001WES\u3001single-cell&nbsp;\u4e09\u4e2a\u9879\u76ee\u7684\u65f6\u5019\u3002\u5148\u8fdb\u76ee\u6807\u76ee\u5f55\uff0c\u518d\u8ba9\u5b83\u5e72\u6d3b\uff0c\u9519\u8bef\u4f1a\u5c11\u5f88\u591a\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">2. \u7528&nbsp;exec&nbsp;\u505a\u4e00\u6b21\u6027\u4efb\u52a1\uff0c\u4e0d\u8981\u4ec0\u4e48\u90fd\u8fdb\u4ea4\u4e92<\/h2>\n\n\n\n<p><code>codex exec -C ~\/projects\/wes \"\u627e\u51fa\u8fd9\u4e2a\u9879\u76ee\u91cc TMB \u662f\u4ece\u54ea\u4e2a VCF \u7b97\u51fa\u6765\u7684\"<\/code><\/p>\n\n\n\n<p>exec&nbsp;\u9002\u5408\u8fd9\u7c7b\u4e8b\uff1a<\/p>\n\n\n\n<ul>\n<li>\u67e5\u6d41\u7a0b\u5165\u53e3<\/li>\n\n\n\n<li>\u627e\u67d0\u4e2a\u7ed3\u679c\u6587\u4ef6\u4ece\u54ea\u4e00\u6b65\u751f\u6210<\/li>\n\n\n\n<li>\u603b\u7ed3\u4e00\u4e2a\u76ee\u5f55\u4e0b\u7684\u811a\u672c\u804c\u8d23<\/li>\n\n\n\n<li>\u6279\u91cf\u6539\u53c2\u6570<\/li>\n\n\n\n<li>\u8865\u4e00\u4e2a\u4e00\u6b21\u6027\u7edf\u8ba1\u811a\u672c<\/li>\n<\/ul>\n\n\n\n<p>\u5b83\u7684\u4f18\u70b9\u5f88\u7b80\u5355\uff1a\u8dd1\u5b8c\u5c31\u7ed3\u675f\uff0c\u9002\u5408\u6302\u5230\u5de5\u4f5c\u6d41\u91cc\uff0c\u4e0d\u7528\u4e00\u76f4\u76ef\u7ec8\u7aef\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">3. \u7ed3\u679c\u76f4\u63a5\u5199\u6587\u4ef6\uff0c\u522b\u624b\u52a8\u590d\u5236<\/h2>\n\n\n\n<p><code>codex exec -C ~\/projects\/scRNA \\ -o pipeline_note.md \\ \"\u603b\u7ed3\u8fd9\u4e2a\u9879\u76ee\u4ece\u539f\u59cb\u77e9\u9635\u5230 cell type annotation \u7684\u5b8c\u6574\u6d41\u7a0b\"<\/code><\/p>\n\n\n\n<p>\u8fd9\u6761\u5bf9\u751f\u4fe1\u7279\u522b\u6709\u7528\u3002\u5f88\u591a\u65f6\u5019\u4f60\u8981\u7684\u4e0d\u662f\u201c\u770b\u4e00\u773c\u7b54\u6848\u201d\uff0c\u800c\u662f\uff1a<\/p>\n\n\n\n<ul>\n<li>\u7ed9\u540c\u4e8b\u53d1\u4e00\u4efd\u8bf4\u660e<\/li>\n\n\n\n<li>\u7559\u4e00\u4efd\u9879\u76ee\u7b14\u8bb0<\/li>\n\n\n\n<li>\u8ba9\u4e0b\u5468\u7684\u81ea\u5df1\u770b\u5f97\u61c2<\/li>\n<\/ul>\n\n\n\n<p>\u80fd\u76f4\u63a5\u843d\u6587\u4ef6\uff0c\u5c31\u522b\u4eba\u5de5\u590d\u5236\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">4. \u60f3\u8981\u7ed3\u6784\u5316\u7ed3\u679c\uff0c\u7528&nbsp;&#8211;output-schema<\/h2>\n\n\n\n<p>\u8fd9\u662f\u8fdb\u9636\u91cc\u6700\u503c\u94b1\u7684\u4e00\u6761\u3002<\/p>\n\n\n\n<p>\u5148\u51c6\u5907\u4e00\u4e2a JSON Schema\uff0c\u6bd4\u5982\u4f60\u8981\u5b83\u8f93\u51fa\uff1a<\/p>\n\n\n\n<ul>\n<li>\u8f93\u5165\u6587\u4ef6<\/li>\n\n\n\n<li>\u4e3b\u6d41\u7a0b\u6b65\u9aa4<\/li>\n\n\n\n<li>\u5173\u952e\u811a\u672c<\/li>\n\n\n\n<li>\u6700\u7ec8\u4ea7\u7269<\/li>\n<\/ul>\n\n\n\n<p>\u7136\u540e\uff1a<\/p>\n\n\n\n<p><code>codex exec -C ~\/projects\/chipseq \\ --output-schema schema.json \\ -o summary.json \\ \"\u8bfb\u53d6\u5f53\u524d\u4ed3\u5e93\u5e76\u6309 schema \u8f93\u51fa\u6d41\u7a0b\u6458\u8981\"<\/code><\/p>\n\n\n\n<p>\u8fd9\u6bd4\u8ba9\u5b83\u5410\u4e00\u6bb5\u81ea\u7531\u6587\u672c\u7a33\u5f97\u591a\u3002\u540e\u9762\u4f60\u53ef\u4ee5\u628a&nbsp;summary.json&nbsp;\u518d\u5582\u7ed9\u522b\u7684\u811a\u672c\uff0c\u505a\u9879\u76ee\u7d22\u5f15\u3001\u6587\u6863\u751f\u6210\u3001\u6d41\u7a0b\u68c0\u67e5\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">5. \u60f3\u505a\u6279\u5904\u7406\uff0c\u7528&nbsp;&#8211;json<\/h2>\n\n\n\n<p><code>codex exec -C ~\/projects\/atacseq --json \\ \"\u68c0\u67e5\u5f53\u524d\u9879\u76ee\u91cc bigWig \u548c peak \u6587\u4ef6\u7684\u751f\u6210\u8def\u5f84\"<\/code><\/p>\n\n\n\n<p>&#8211;json&nbsp;\u4f1a\u628a\u8fc7\u7a0b\u4e8b\u4ef6\u6309 JSONL \u6253\u51fa\u6765\u3002\u8fd9\u4e2a\u9002\u5408\uff1a<\/p>\n\n\n\n<ul>\n<li>\u4f60\u60f3\u8bb0\u5f55\u6267\u884c\u8fc7\u7a0b<\/li>\n\n\n\n<li>\u4f60\u8981\u628a\u7ed3\u679c\u63a5\u8fdb\u522b\u7684\u7a0b\u5e8f<\/li>\n\n\n\n<li>\u4f60\u5728\u505a\u6279\u91cf\u81ea\u52a8\u5316<\/li>\n<\/ul>\n\n\n\n<p>\u5982\u679c\u4f60\u540e\u9762\u771f\u60f3\u628a Codex \u63a5\u8fdb\u81ea\u5df1\u7684\u751f\u4fe1\u5de5\u5177\u94fe\uff0c\u8fd9\u4e2a\u9009\u9879\u6bd4\u4ea4\u4e92\u754c\u9762\u66f4\u91cd\u8981\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">6. \u957f\u4efb\u52a1\u522b\u91cd\u5f00\uff0c\u76f4\u63a5\u7eed\u8dd1<\/h2>\n\n\n\n<p><code>codex resume --last<\/code><\/p>\n\n\n\n<p>\u8fd9\u5bf9\u5927\u9879\u76ee\u5f88\u597d\u7528\u3002\u6bd4\u5982\u4f60\u6628\u5929\u5df2\u7ecf\u8ba9\u5b83\u8bfb\u5b8c&nbsp;Snakemake&nbsp;\u4e3b\u6d41\u7a0b\uff0c\u4eca\u5929\u53ea\u60f3\u63a5\u7740\u95ee\uff1a<\/p>\n\n\n\n<p><code>\u7ee7\u7eed\u5f80\u4e0b\u627e\u5dee\u5f02\u5206\u6790\u7ed3\u679c\u662f\u5728\u54ea\u4e00\u6b65\u6c47\u603b\u6210\u6700\u7ec8\u8868\u683c\u7684<\/code><\/p>\n\n\n\n<p>\u4e0d\u7528\u91cd\u590d\u89e3\u91ca\u80cc\u666f\uff0c\u6548\u7387\u4f1a\u9ad8\u5f88\u591a\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">7. \u7528&nbsp;review&nbsp;\u770b\u4f60\u521a\u6539\u5b8c\u7684\u811a\u672c<\/h2>\n\n\n\n<p><code>codex review<\/code><\/p>\n\n\n\n<p>\u8fd9\u4e2a\u5f88\u9002\u5408\u751f\u4fe1\u91cc\u7684\u201c\u5c0f\u6539\u52a8\u9ad8\u98ce\u9669\u201d\u573a\u666f\uff0c\u6bd4\u5982\uff1a<\/p>\n\n\n\n<ul>\n<li>\u6837\u672c\u5206\u7ec4\u8868\u5217\u540d\u6539\u4e86<\/li>\n\n\n\n<li>\u8def\u5f84\u4ece\u7edd\u5bf9\u8def\u5f84\u6539\u76f8\u5bf9\u8def\u5f84<\/li>\n\n\n\n<li>R&nbsp;\u811a\u672c\u591a\u52a0\u4e86\u4e00\u4e2a\u53c2\u6570<\/li>\n\n\n\n<li>Nextflow&nbsp;channel \u63a5\u9519\u4e86<\/li>\n\n\n\n<li>\u8f93\u51fa\u6587\u4ef6\u540d\u6539\u4e86\u4f46\u4e0b\u6e38\u6ca1\u540c\u6b65<\/li>\n<\/ul>\n\n\n\n<p>\u8fd9\u4e9b\u95ee\u9898\u4e0d\u96be\uff0c\u4f46\u7279\u522b\u5bb9\u6613\u62d6\u5230\u6d41\u7a0b\u8dd1\u5230\u4e00\u534a\u624d\u70b8\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">8. \u4f1a\u8bdd\u578b\u5f00\u53d1\u91cc\uff0capply&nbsp;\u5f88\u6709\u7528<\/h2>\n\n\n\n<p><code>codex apply &lt;TASK_ID&gt;<\/code><\/p>\n\n\n\n<p>\u5982\u679c\u4f60\u662f\u5728\u67d0\u4e9b\u4efb\u52a1\u6d41\u6216\u8fdc\u7aef\u4efb\u52a1\u91cc\u8ba9 Codex \u5148\u4ea7\u51fa diff\uff0c\u518d\u843d\u56de\u672c\u5730\u5de5\u4f5c\u6811\uff0c\u8fd9\u6761\u547d\u4ee4\u5c31\u5f88\u597d\u7528\u3002\u666e\u901a\u804a\u5929\u5f0f\u4f7f\u7528\u4e0d\u4e00\u5b9a\u5929\u5929\u78b0\uff0c\u4f46\u4e00\u65e6\u4f60\u5f00\u59cb\u628a Codex \u5f53\u534a\u81ea\u52a8\u5f00\u53d1\u5de5\u5177\uff0c\u8fd9\u6761\u5c31\u4f1a\u51fa\u73b0\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><\/h2>\n","protected":false},"excerpt":{"rendered":"<p>1. \u5148\u56fa\u5b9a\u5de5\u4f5c\u76ee\u5f55\uff0c\u518d\u5f00\u5de5 codex -C ~\/projects\/rnaseq_lung \u522b\u5c0f\u770b&#038;nbsp [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/64508"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=64508"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/64508\/revisions"}],"predecessor-version":[{"id":64509,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/64508\/revisions\/64509"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=64508"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=64508"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=64508"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}