From 4f1b56bf4043743c1cb63b85e433742b677a6ac8 Mon Sep 17 00:00:00 2001
From: Alexander Thomas <77535027+alethomas@users.noreply.github.com>
Date: Tue, 16 Jan 2024 10:04:56 +0100
Subject: [PATCH] fix: remove -r flag (#624)

* remove -r flag

* fix
---
 .github/workflows/main.yml | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 828c4acb..c7da6a58 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -69,7 +69,7 @@ jobs:
       #- Pre-Commit
     strategy:
       matrix:
-        rule: [all, all -npr]
+        rule: [all, all -np]
         # disable ont actions
         technology: [all, illumina, ont, ion]
         # technology: [all, illumina, ion]
@@ -141,11 +141,11 @@ jobs:
         with:
           directory: .tests
           snakefile: workflow/Snakefile
-          args: "-pr --use-conda --show-failed-logs --cores 2 --resources ncbi_api_requests=1 --conda-cleanup-pkgs cache --conda-frontend mamba ${{ matrix.rule }}"
+          args: "-p --use-conda --show-failed-logs --cores 2 --resources ncbi_api_requests=1 --conda-cleanup-pkgs cache --conda-frontend mamba ${{ matrix.rule }}"
 
       - name: Test report
         uses: snakemake/snakemake-github-action@v1.25.1
-        if: startsWith(matrix.rule, 'all -npr') != true
+        if: startsWith(matrix.rule, 'all -np') != true
         with:
           directory: .tests
           snakefile: workflow/Snakefile
@@ -153,14 +153,14 @@ jobs:
 
       - name: Upload report
         uses: actions/upload-artifact@v3
-        if: matrix.technology == 'all' && matrix.rule != 'all -npr'
+        if: matrix.technology == 'all' && matrix.rule != 'all -np'
         with:
           name: report-rule-${{ matrix.rule }}-${{ matrix.technology }}-${{ matrix.seq_method }}
           path: .tests/results/patient-reports/2022-01-01.zip
 
       - name: Upload logs
         uses: actions/upload-artifact@v3
-        if: matrix.technology == 'all' && matrix.rule != 'all -npr'
+        if: matrix.technology == 'all' && matrix.rule != 'all -np'
         with:
           name: log-rule-${{ matrix.rule }}-technology-${{ matrix.technology }}
           path: .tests/logs/
@@ -319,11 +319,11 @@ jobs:
         with:
           directory: .tests
           snakefile: workflow/Snakefile
-          args: "-pr --use-conda --show-failed-logs --cores 2 --resources ncbi_api_requests=1 --conda-cleanup-pkgs cache --conda-frontend mamba ${{ matrix.rule }}"
+          args: "-p --use-conda --show-failed-logs --cores 2 --resources ncbi_api_requests=1 --conda-cleanup-pkgs cache --conda-frontend mamba ${{ matrix.rule }}"
 
       - name: Test report
         uses: snakemake/snakemake-github-action@v1.25.1
-        if: startsWith(matrix.rule, 'all -npr') != true
+        if: startsWith(matrix.rule, 'all -np') != true
         with:
           directory: .tests
           snakefile: workflow/Snakefile