From 7cafadcb2327fbcab5a839d6e149062f08b594f6 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Fri, 20 Oct 2023 15:59:06 -0400
Subject: [PATCH] refactor: move subworkflows

---
 .../CCBR/custom/filter_blacklist/test.yml     | 13 -------------
 .../{custom => }/filter_blacklist/main.nf     |  0
 .../filter_blacklist/nextflow.config          |  0
 .../CCBR/filter_blacklist/test.yml            | 19 +++++++++++++++++++
 .../filter_blacklist/test_filter_blacklist.py |  0
 5 files changed, 19 insertions(+), 13 deletions(-)
 delete mode 100644 tests/subworkflows/CCBR/custom/filter_blacklist/test.yml
 rename tests/subworkflows/CCBR/{custom => }/filter_blacklist/main.nf (100%)
 rename tests/subworkflows/CCBR/{custom => }/filter_blacklist/nextflow.config (100%)
 create mode 100644 tests/subworkflows/CCBR/filter_blacklist/test.yml
 rename tests/subworkflows/CCBR/{custom => }/filter_blacklist/test_filter_blacklist.py (100%)

diff --git a/tests/subworkflows/CCBR/custom/filter_blacklist/test.yml b/tests/subworkflows/CCBR/custom/filter_blacklist/test.yml
deleted file mode 100644
index a13d058..0000000
--- a/tests/subworkflows/CCBR/custom/filter_blacklist/test.yml
+++ /dev/null
@@ -1,13 +0,0 @@
-- name: filter_blacklist test_filter_blacklist_single
-  command: nextflow run ./tests/subworkflows/CCBR/custom/filter_blacklist/main.nf -entry test_filter_blacklist_single -c tests/config/nextflow.config -c tests/config/test_data_CCBR.config
-  files:
-    - path: output/bam/test.R1.fastq.gz
-- name: filter_blacklist test_filter_blacklist_paired
-  command: nextflow run ./tests/subworkflows/CCBR/custom/filter_blacklist/main.nf -entry test_filter_blacklist_paired -c tests/config/nextflow.config -c tests/config/test_data_CCBR.config
-  files:
-    - path: output/bam/test.R1.fastq.gz
-    - path: output/bam/test.R2.fastq.gz
-- name: filter_blacklist test_filter_blacklist_single stub
-  command: nextflow run ./tests/subworkflows/CCBR/custom/filter_blacklist/main.nf -entry test_filter_blacklist_single -c tests/config/nextflow.config -c tests/config/test_data_CCBR.config -stub
-  files:
-    - path: output/bam/test.R1.fastq.gz
diff --git a/tests/subworkflows/CCBR/custom/filter_blacklist/main.nf b/tests/subworkflows/CCBR/filter_blacklist/main.nf
similarity index 100%
rename from tests/subworkflows/CCBR/custom/filter_blacklist/main.nf
rename to tests/subworkflows/CCBR/filter_blacklist/main.nf
diff --git a/tests/subworkflows/CCBR/custom/filter_blacklist/nextflow.config b/tests/subworkflows/CCBR/filter_blacklist/nextflow.config
similarity index 100%
rename from tests/subworkflows/CCBR/custom/filter_blacklist/nextflow.config
rename to tests/subworkflows/CCBR/filter_blacklist/nextflow.config
diff --git a/tests/subworkflows/CCBR/filter_blacklist/test.yml b/tests/subworkflows/CCBR/filter_blacklist/test.yml
new file mode 100644
index 0000000..078b9b2
--- /dev/null
+++ b/tests/subworkflows/CCBR/filter_blacklist/test.yml
@@ -0,0 +1,19 @@
+- name: filter_blacklist test_filter_blacklist_single
+  command: nextflow run ./tests/subworkflows/CCBR/filter_blacklist/main.nf -entry test_filter_blacklist_single -c tests/config/nextflow.config -c tests/config/test_data_CCBR.config
+  tags:
+    - subworkflows/filter_blacklist
+  files:
+    - path: output/bam2fastq/test.R1.fastq.gz
+- name: filter_blacklist test_filter_blacklist_paired
+  command: nextflow run ./tests/subworkflows/CCBR/filter_blacklist/main.nf -entry test_filter_blacklist_paired -c tests/config/nextflow.config -c tests/config/test_data_CCBR.config
+  tags:
+    - subworkflows/filter_blacklist
+  files:
+    - path: output/bam2fastq/test.R1.fastq.gz
+    - path: output/bam2fastq/test.R2.fastq.gz
+- name: filter_blacklist test_filter_blacklist_single stub
+  command: nextflow run ./tests/subworkflows/CCBR/filter_blacklist/main.nf -entry test_filter_blacklist_single -c tests/config/nextflow.config -c tests/config/test_data_CCBR.config -stub
+  tags:
+    - subworkflows/filter_blacklist
+  files:
+    - path: output/bam2fastq/test.R1.fastq.gz
diff --git a/tests/subworkflows/CCBR/custom/filter_blacklist/test_filter_blacklist.py b/tests/subworkflows/CCBR/filter_blacklist/test_filter_blacklist.py
similarity index 100%
rename from tests/subworkflows/CCBR/custom/filter_blacklist/test_filter_blacklist.py
rename to tests/subworkflows/CCBR/filter_blacklist/test_filter_blacklist.py