From a9aac457cd8619beffd367ec492efea8b0026400 Mon Sep 17 00:00:00 2001
From: Lucas Taniguti <lucas.biotec07@gmail.com>
Date: Sun, 17 Dec 2023 21:44:17 -0300
Subject: [PATCH] =?UTF-8?q?=F0=9F=92=9A=20Update=20pytest=20command=20and?=
 =?UTF-8?q?=20disk=20size=20calculation?=
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---
 .github/workflows/release.yml | 4 ++--
 tasks/clair3/haploid.wdl      | 3 +++
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index bac3b22..96d1f9f 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -67,12 +67,12 @@ jobs:
         run: pip install -r tests/requirements.txt
 
       - name: Run test ${{ matrix.tag }}
-        run: pytest --tag ${{ matrix.tag }} --basetemp /tmp/ci tests/tasks
+        run: pytest --git-aware --tag ${{ matrix.tag }} --basetemp temp-dir tests/tasks
 
       - uses: actions/upload-artifact@v4
         with:
           name: miniwdl-command
-          path: /tmp/ci/*/_LAST/command
+          path: temp-dir/**/command
 
   release:
     needs: [test]
diff --git a/tasks/clair3/haploid.wdl b/tasks/clair3/haploid.wdl
index 3e178fa..8f7a392 100644
--- a/tasks/clair3/haploid.wdl
+++ b/tasks/clair3/haploid.wdl
@@ -15,6 +15,8 @@ task Clair3Haploid {
         Boolean stub = false
     }
 
+    Int disk_size = ceil((size(alignment, "GB") + size(reference, "GB") + size(model_tar, "GB")) * 2)
+
     command <<<
     set -e
 
@@ -53,6 +55,7 @@ task Clair3Haploid {
         docker: "docker.io/hkubal/clair3:v1.0.4"
         cpu: threads
         memory: "8G"  # TODO: check if it's enough
+        disks: "local-disk " + disk_size + " HDD"
     }
 
     output {