From 59818c2b86ff3ad1dd53eb5bb0edeaabb882abe8 Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.a.miller@protonmail.com>
Date: Wed, 27 Oct 2021 11:42:34 -0500
Subject: [PATCH] ci(bam_sort_samtools): Depend on paths-filter instead of
 pytest-workflow

Co-authored-by: Harshil Patel <drpatelhh@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
---
 tests/config/pytest_modules.yml               |  7 ++++--
 .../nf-core/bam_sort_samtools/test.yml        | 24 +++++++++----------
 2 files changed, 17 insertions(+), 14 deletions(-)

diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index eedbdc36..1bc8bdf5 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1163,7 +1163,7 @@ samtools/idxstats:
   - modules/samtools/idxstats/**
   - tests/modules/samtools/idxstats/**
 
-samtools/index:
+samtools/index: &samtools/index
   - modules/samtools/index/**
   - tests/modules/samtools/index/**
 
@@ -1175,7 +1175,7 @@ samtools/mpileup:
   - modules/samtools/mpileup/**
   - tests/modules/samtools/mpileup/**
 
-samtools/sort:
+samtools/sort: &samtools/sort
   - modules/samtools/sort/**
   - tests/modules/samtools/sort/**
 
@@ -1386,6 +1386,9 @@ subworkflows/bam_stats_samtools: &subworkflows/bam_stats_samtools
 subworkflows/bam_sort_samtools:
   - subworkflows/nf-core/bam_sort_samtools/**
   - tests/subworkflows/nf-core/bam_sort_samtools/**
+  - *samtools/sort
+  - *samtools/index
+  - *subworkflows/bam_stats_samtools
 
 subworkflows/sra_fastq:
   - subworkflows/nf-core/sra_fastq/**
diff --git a/tests/subworkflows/nf-core/bam_sort_samtools/test.yml b/tests/subworkflows/nf-core/bam_sort_samtools/test.yml
index e2fc27d8..88ea9d5a 100644
--- a/tests/subworkflows/nf-core/bam_sort_samtools/test.yml
+++ b/tests/subworkflows/nf-core/bam_sort_samtools/test.yml
@@ -4,12 +4,12 @@
     - subworkflows/bam_sort_samtools
     - subworkflows/bam_stats_samtools
     # Modules
-    - samtools
-    - samtools/index
-    - samtools/sort
-    - samtools/stats
-    - samtools/idxstats
-    - samtools/flagstat
+    # - samtools
+    # - samtools/index
+    # - samtools/sort
+    # - samtools/stats
+    # - samtools/idxstats
+    # - samtools/flagstat
   files:
     - path: ./output/samtools/test.sorted.bam
       md5sum: e4c77897d6824ce4df486d1b100618af
@@ -28,12 +28,12 @@
     - subworkflows/bam_sort_samtools
     - subworkflows/bam_stats_samtools
     # Modules
-    - samtools
-    - samtools/index
-    - samtools/sort
-    - samtools/stats
-    - samtools/idxstats
-    - samtools/flagstat
+    # - samtools
+    # - samtools/index
+    # - samtools/sort
+    # - samtools/stats
+    # - samtools/idxstats
+    # - samtools/flagstat
   files:
     - path: ./output/samtools/test.sorted.bam
       md5sum: bbb2db225f140e69a4ac577f74ccc90f