Remove deprecated command line option to print reasons for rule execu…

…tion
NBISweden · Jun 14, 2024 · 4769cab · 4769cab
1 parent 1e9a163
commit 4769cab
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Showing 5 changed files with 5 additions and 5 deletions.
diff --git a/.github/workflows/gerp.yaml b/.github/workflows/gerp.yaml
@@ -67,7 +67,7 @@ jobs:
       - name: gerp_dry
         shell: bash -l {0}
         run: |
-          snakemake -npr --configfile .test/config/config_gerp.yaml -j 4 --cores 1 --use-singularity
+          snakemake -np -k --configfile .test/config/config_gerp.yaml -j 4 --cores 1 --use-singularity
 
       - name: gerp
         shell: bash -l {0}

diff --git a/.github/workflows/mitogenome_mapping.yaml b/.github/workflows/mitogenome_mapping.yaml
@@ -91,7 +91,7 @@ jobs:
       - name: mitogenome_mapping_dry
         shell: bash -l {0}
         run: |
-          snakemake -npr --configfile .test/config/config_mitogenomes.yaml -j 4 --cores 1 --use-singularity
+          snakemake -np -k --configfile .test/config/config_mitogenomes.yaml -j 4 --cores 1 --use-singularity
 
       - name: mitogenome_mapping
         shell: bash -l {0}

diff --git a/.github/workflows/mlRho_options.yaml b/.github/workflows/mlRho_options.yaml
@@ -73,7 +73,7 @@ jobs:
       - name: mlRho_options_dry
         shell: bash -l {0}
         run: |
-          snakemake -npr --configfile .test/config/config_mlRho_options.yaml -j 4 --cores 1 --use-singularity
+          snakemake -np -k --configfile .test/config/config_mlRho_options.yaml -j 4 --cores 1 --use-singularity
 
       - name: mlRho_options
         shell: bash -l {0}

diff --git a/.github/workflows/pca_roh.yaml b/.github/workflows/pca_roh.yaml
@@ -65,7 +65,7 @@ jobs:
       - name: pca_roh_dry
         shell: bash -l {0}
         run: |
-          snakemake -npr --configfile .test/config/config_pca_roh.yaml -j 4 --cores 1 --use-singularity
+          snakemake -np -k --configfile .test/config/config_pca_roh.yaml -j 4 --cores 1 --use-singularity
 
       - name: pca_roh
         shell: bash -l {0}

diff --git a/.github/workflows/snpeff.yaml b/.github/workflows/snpeff.yaml
@@ -67,7 +67,7 @@ jobs:
       - name: snpeff_dry
         shell: bash -l {0}
         run: |
-          snakemake -npr --configfile .test/config/config_snpeff.yaml -j 4 --cores 1 --use-singularity
+          snakemake -np -k --configfile .test/config/config_snpeff.yaml -j 4 --cores 1 --use-singularity
 
       - name: snpeff
         shell: bash -l {0}