fix: pipe of stdout (#631)

* fix pipe of stderr * free CI space --------- Co-authored-by: Johannes Koester <[email protected]>
IKIM-Essen · Feb 22, 2024 · a48a357 · a48a357
1 parent c6fc415
commit a48a357
Show file tree

Hide file tree

Showing 2 changed files with 35 additions and 2 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -76,6 +76,23 @@ jobs:
         seq_method: [shotgun, amplicon]
     steps:
       - uses: actions/checkout@v4
+
+      - name: Free Disk Space (Ubuntu)
+        uses: jlumbroso/[email protected]
+        with:
+          # this might remove tools that are actually needed,
+          # if set to "true" but frees about 6 GB
+          tool-cache: false
+
+          # all of these default to true, but feel free to set to
+          # "false" if necessary for your workflow
+          android: true
+          dotnet: true
+          haskell: true
+          large-packages: true
+          docker-images: false
+          swap-storage: true
+
       - uses: actions/setup-python@v4
         with:
           python-version: '3.11'
@@ -194,6 +211,22 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
+      - name: Free Disk Space (Ubuntu)
+        uses: jlumbroso/[email protected]
+        with:
+          # this might remove tools that are actually needed,
+          # if set to "true" but frees about 6 GB
+          tool-cache: false
+
+          # all of these default to true, but feel free to set to
+          # "false" if necessary for your workflow
+          android: true
+          dotnet: true
+          haskell: true
+          large-packages: true
+          docker-images: false
+          swap-storage: true
+
       # - name: Cache conda dependencies
       #   uses: actions/cache@v2
       #   with:

diff --git a/workflow/rules/ref.smk b/workflow/rules/ref.smk
@@ -163,7 +163,7 @@ rule get_genome_db_for_kraken:
     conda:
         "../envs/unix.yaml"
     shell:
-        "mkdir {output} && curl -SL https://genome-idx.s3.amazonaws.com/kraken/k2_standard_08gb_20220926.tar.gz | tar zxvf - -C {output} 2> {log}"
+        "(mkdir {output} && curl -SL https://genome-idx.s3.amazonaws.com/kraken/k2_standard_08gb_20220926.tar.gz | tar zxvf - -C {output}) 2> {log}"
 
 
 rule get_taxonomie_db_for_krona:
@@ -221,7 +221,7 @@ rule update_lineages:
 
 rule get_gisaid_provision:
     output:
-        temp("resources/gisaid/provision.json"),
+        "resources/gisaid/provision.json",
     log:
         "logs/get_gisaid_provision.log",
     conda: