From 3b4913eb99a9f13b8db277c7a681e6c3bb912e49 Mon Sep 17 00:00:00 2001
From: bioloni <nico.schcolnicov@gmail.com>
Date: Tue, 23 Jul 2024 22:01:01 +0000
Subject: [PATCH] Separated mkfastq test in CI, updated test

---
 .github/workflows/ci.yml            |  7 ++++---
 tests/pipeline/mkfastq.nf.test      |  6 +++---
 tests/pipeline/mkfastq.nf.test.snap | 22 ++++++++++++++++++++--
 3 files changed, 27 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index db835d84..c6080387 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -40,8 +40,7 @@ jobs:
       fail-fast: false
       matrix:
         NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
-        profile:
-          - docker
+        profile: ["bases2fastq", "bcl2fastq", "bclconvert", "fqtk", "sgdemux", "skip_tools"]
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
@@ -60,7 +59,9 @@ jobs:
 
       # Run nf-test
       - name: Run nf-test
-        run: nf-test test tests/pipeline/ --profile=test,${{ matrix.profile }} --junitxml=test.xml
+        run: |
+          nf-test test tests/pipeline/${{ matrix.profile }}.nf.test --profile=test,docker --junitxml=test.xml
+          nf-test test tests/pipeline/mkfastq.nf.test --profile=docker --junitxml=test.xml
 
       # If the test fails, output the software_versions.yml using the 'batcat' utility
       - name: Output log on failure
diff --git a/tests/pipeline/mkfastq.nf.test b/tests/pipeline/mkfastq.nf.test
index 04a16d9d..afea295a 100644
--- a/tests/pipeline/mkfastq.nf.test
+++ b/tests/pipeline/mkfastq.nf.test
@@ -30,15 +30,15 @@ nextflow_pipeline {
                 {assert snapshot(
                     //Check output files
                     path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/Sample1_S1_L001_summary.txt"),
-                    path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/Sample1_S1_L001_report.html"),
+                    path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/Sample1_S1_L001_report.html").exists(),
                     path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/Sample1_S1_L001_R1_001.fastq.gz"),
                     path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/Sample1_S1_L001_fastqc_data.txt"),
                     path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/Sample1_S1_L001.fastp.json"),
-                    path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/Sample1_S1_L001.fastp.html"),
+                    path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/Sample1_S1_L001.fastp.html").exists(),
                     path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/Sample1_S1_L001.fastp.fastq.gz.md5"),
                     path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/Sample1_S1_L001.fastp.fastq.gz"),
                     path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/InterOp/IndexMetricsOut.bin")
-                )}
+                ).match("file_assertions_mkfastq")}
             )
         }
     }
diff --git a/tests/pipeline/mkfastq.nf.test.snap b/tests/pipeline/mkfastq.nf.test.snap
index e90eda97..972c389b 100644
--- a/tests/pipeline/mkfastq.nf.test.snap
+++ b/tests/pipeline/mkfastq.nf.test.snap
@@ -5,8 +5,26 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-07-22T17:20:35.469557836"
+        "timestamp": "2024-07-23T21:48:45.441154457"
+    },
+    "file_assertions_mkfastq": {
+        "content": [
+            "Sample1_S1_L001_summary.txt:md5,510c6b8a26ff8d530950c05b3ca5a1c6",
+            true,
+            "Sample1_S1_L001_R1_001.fastq.gz:md5,0675fb6365322eaafb33c0f8e862b54b",
+            "Sample1_S1_L001_fastqc_data.txt:md5,0adf4e2617f55fabba0663583c1f65b7",
+            "Sample1_S1_L001.fastp.json:md5,14d9d03ea4803a563a2f4e84940d7a11",
+            true,
+            "Sample1_S1_L001.fastp.fastq.gz.md5:md5,c3cd96f3a22fb6afbaa1df324814d54c",
+            "Sample1_S1_L001.fastp.fastq.gz:md5,64639ff33d4b07d62a9079f88cbbd373",
+            "IndexMetricsOut.bin:md5,9e688c58a5487b8eaf69c9e1005ad0bf"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-23T21:48:45.470338496"
     }
 }
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