add main to logic

.github/workflows/align.yml

@@ -23,6 +23,7 @@ on:
       - 'workflow/scripts/makewindows.py'
       - 'test/fastq/**'
       - '**align.yml'
+      - '**__main__.py'
 
   pull_request:
     branches:
@@ -46,6 +47,7 @@ on:
       - 'workflow/scripts/makewindows.py'
       - 'test/fastq/**'
       - '**align.yml'
+      - '**__main__.py'
 
 env:
   CACHE_NUMBER: 0  # increase to reset cache manually

.github/workflows/demux.yml

@@ -17,6 +17,7 @@ on:
       - '**demux.yml'
       - 'BC_files.py'
       - 'test/data/demux/**'
+      - '**__main__.py'
 
   pull_request:
     branches:
@@ -34,7 +35,7 @@ on:
       - '**demux.yml'
       - 'BC_files.py'
       - 'test/data/demux/**'
-
+      - '**__main__.py'
 
 env:
   CACHE_NUMBER: 0  # increase to reset cache manually

.github/workflows/impute.yml

@@ -19,6 +19,7 @@ on:
       - 'workflow/report/Impute.Rmd'
       - 'workflow/report/StitchCollate.Rmd'
       - 'workflow/scripts/stitch_impute.R'
+      - '**__main__.py'
 
   pull_request:
     branches:
@@ -38,6 +39,7 @@ on:
       - 'workflow/report/Impute.Rmd'
       - 'workflow/report/StitchCollate.Rmd'
       - 'workflow/scripts/stitch_impute.R'
+      - '**__main__.py'
 
 env:
   CACHE_NUMBER: 0  # increase to reset cache manually

.github/workflows/phase.yml

@@ -20,6 +20,7 @@ on:
       - 'workflow/report/HapCut2.Rmd'
       - 'workflow/scripts/parsePhaseBlocks.py'
       - 'workflow/scripts/summarizeHaplobocks.py'
+      - '**__main__.py'
 
   pull_request:
     branches:
@@ -40,6 +41,7 @@ on:
       - 'workflow/report/HapCut2.Rmd'
       - 'workflow/scripts/parsePhaseBlocks.py'
       - 'workflow/scripts/summarizeHaplobocks.py'
+      - '**__main__.py'
 
 env:
   CACHE_NUMBER: 0  # increase to reset cache manually

.github/workflows/preflight.yml

@@ -20,6 +20,7 @@ on:
       - 'workflow/report/PreflightFastq.Rmd'
       - 'workflow/report/PreflightBam.Rmd'
       - '**preflight.yml'
+      - '**__main__.py'
 
   pull_request:
     branches:
@@ -40,6 +41,7 @@ on:
       - 'workflow/report/PreflightFastq.Rmd'
       - 'workflow/report/PreflightBam.Rmd'
       - '**preflight.yml'
+      - '**__main__.py'
 
 env:
   CACHE_NUMBER: 0  # increase to reset cache manually

.github/workflows/qc.yml

@@ -15,6 +15,7 @@ on:
       - '**validations.py'
       - 'test/fastq/**'
       - '**qc.yml'
+      - '**__main__.py'
 
   pull_request:
     branches:
@@ -30,6 +31,7 @@ on:
       - '**validations.py'
       - 'test/fastq/**'
       - '**qc.yml'
+      - '**__main__.py'
 
 env:
   CACHE_NUMBER: 0  # increase to reset cache manually

.github/workflows/variants_snp.yml

@@ -19,6 +19,7 @@ on:
       - 'workflow/scripts/makewindows.py'
       - 'test/bam/**'
       - '**variants_snp.yml'
+      - '**__main__.py'
 
   pull_request:
     branches:
@@ -38,6 +39,7 @@ on:
       - 'workflow/scripts/makewindows.py'
       - 'test/bam/**'
       - '**variants_snp.yml'
+      - '**__main__.py'
 
 env:
   CACHE_NUMBER: 0  # increase to reset cache manually

.github/workflows/variants_sv.yml

@@ -21,6 +21,7 @@ on:
       - 'workflow/report/Leviathan**.Rmd'
       - 'workflow/report/Naibr**.Rmd'
       - 'workflow/scripts/inferSV.py'
+      - '**__main__.py'
 
   pull_request:
     branches:
@@ -42,6 +43,7 @@ on:
       - 'workflow/report/Leviathan**.Rmd'
       - 'workflow/report/Naibr**.Rmd'
       - 'workflow/scripts/inferSV.py'
+      - '**__main__.py'
 
 env:
   CACHE_NUMBER: 0  # increase to reset cache manually