Add flag -k to keep going when a job fails until none of the jobs can…

… be started anymore
NBISweden · Jun 16, 2024 · 9df5bc6 · 9df5bc6
1 parent 5d53485
commit 9df5bc6
Show file tree

Hide file tree

Showing 5 changed files with 5 additions and 5 deletions.
diff --git a/.github/workflows/gerp.yaml b/.github/workflows/gerp.yaml
@@ -72,4 +72,4 @@ jobs:
       - name: gerp
         shell: bash -l {0}
         run: |
-          snakemake --configfile .test/config/config_gerp.yaml -j 4 --cores 1 --use-singularity
+          snakemake -k --configfile .test/config/config_gerp.yaml -j 4 --cores 1 --use-singularity
diff --git a/.github/workflows/mitogenome_mapping.yaml b/.github/workflows/mitogenome_mapping.yaml
@@ -96,5 +96,5 @@ jobs:
       - name: mitogenome_mapping
         shell: bash -l {0}
         run: |
-          snakemake --configfile .test/config/config_mitogenomes.yaml -j 4 --cores 1 --use-singularity
+          snakemake -k --configfile .test/config/config_mitogenomes.yaml -j 4 --cores 1 --use-singularity
 
diff --git a/.github/workflows/mlRho_options.yaml b/.github/workflows/mlRho_options.yaml
@@ -78,4 +78,4 @@ jobs:
       - name: mlRho_options
         shell: bash -l {0}
         run: |
-          snakemake --configfile .test/config/config_mlRho_options.yaml -j 4 --cores 1 --use-singularity
+          snakemake -k --configfile .test/config/config_mlRho_options.yaml -j 4 --cores 1 --use-singularity
diff --git a/.github/workflows/pca_roh.yaml b/.github/workflows/pca_roh.yaml
@@ -70,4 +70,4 @@ jobs:
       - name: pca_roh
         shell: bash -l {0}
         run: |
-          snakemake --configfile .test/config/config_pca_roh.yaml -j 4 --cores 1 --use-singularity
+          snakemake -k --configfile .test/config/config_pca_roh.yaml -j 4 --cores 1 --use-singularity
diff --git a/.github/workflows/snpeff.yaml b/.github/workflows/snpeff.yaml
@@ -72,4 +72,4 @@ jobs:
       - name: snpeff
         shell: bash -l {0}
         run: |
-          snakemake --configfile .test/config/config_snpeff.yaml -j 4 --cores 1 --use-singularity
+          snakemake -k --configfile .test/config/config_snpeff.yaml -j 4 --cores 1 --use-singularity