make sure all 'rule all's are named 'rule workflow_all' and marked as…

… default target
bihealth · May 21, 2024 · 4bbee84 · 4bbee84
1 parent 327eba3
commit 4bbee84
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Showing 8 changed files with 16 additions and 8 deletions.
diff --git a/snappy_pipeline/workflows/adapter_trimming/Snakefile b/snappy_pipeline/workflows/adapter_trimming/Snakefile
@@ -32,9 +32,10 @@ localrules:
     adapter_trimming_link_out_fastq_run,
 
 
-rule all:
+rule adapter_trimming_all:
     input:
         wf.get_result_files(),
+    default_target: True
 
 
 # House-Keeping ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

diff --git a/snappy_pipeline/workflows/somatic_gene_fusion_calling/Snakefile b/snappy_pipeline/workflows/somatic_gene_fusion_calling/Snakefile
@@ -31,9 +31,10 @@ localrules:
     somatic_gene_fusion_calling_link_out_run,
 
 
-rule all:
+rule somatic_msi_calling_all:
     input:
         wf.get_result_files(),
+    default_target: True
 
 
 # House-Keeping ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

diff --git a/snappy_pipeline/workflows/somatic_hla_loh_calling/Snakefile b/snappy_pipeline/workflows/somatic_hla_loh_calling/Snakefile
@@ -58,9 +58,10 @@ localrules:
     somatic_hla_loh_calling_link_out_run,
 
 
-rule all:
+rule somatic_hla_loh_calling_all:
     input:
         wf.get_result_files(),
+    default_target: True
 
 
 # House-Keeping ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

diff --git a/snappy_pipeline/workflows/somatic_msi_calling/Snakefile b/snappy_pipeline/workflows/somatic_msi_calling/Snakefile
@@ -46,9 +46,10 @@ localrules:
     somatic_msi_calling_link_out_run,
 
 
-rule all:
+rule somatic_msi_calling_all:
     input:
         wf.get_result_files(),
+    default_target: True
 
 
 # House-Keeping ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

diff --git a/snappy_pipeline/workflows/variant_export_external/Snakefile b/snappy_pipeline/workflows/variant_export_external/Snakefile
@@ -36,9 +36,10 @@ localrules:
     variant_export_external_write_pedigree_run,
 
 
-rule all:
+rule variant_export_external_all:
     input:
         wf.get_result_files(),
+    default_target: True
 
 
 # House-Keeping ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

diff --git a/snappy_pipeline/workflows/variant_filtration/Snakefile b/snappy_pipeline/workflows/variant_filtration/Snakefile
@@ -47,9 +47,10 @@ localrules:
     variant_filtration_link_out_run,
 
 
-rule all:
+rule variant_filtration_all:
     input:
         wf.get_result_files(),
+    default_target: True
 
 
 # House-Keeping ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

diff --git a/snappy_pipeline/workflows/wgs_cnv_export_external/Snakefile b/snappy_pipeline/workflows/wgs_cnv_export_external/Snakefile
@@ -32,9 +32,10 @@ localrules:
     wgs_cnv_export_external_write_pedigree_run,
 
 
-rule all:
+rule wgs_cnv_export_external_all:
     input:
         wf.get_result_files(),
+    default_target: True
 
 
 # House-Keeping ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

diff --git a/snappy_pipeline/workflows/wgs_sv_export_external/Snakefile b/snappy_pipeline/workflows/wgs_sv_export_external/Snakefile
@@ -32,9 +32,10 @@ localrules:
     wgs_sv_export_external_write_pedigree_run,
 
 
-rule all:
+rule wgs_sv_export_external_all:
     input:
         wf.get_result_files(),
+    default_target: True
 
 
 # House-Keeping ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~