Clean up pipeline tests

.github/workflows/ci.yml

@@ -22,7 +22,7 @@ permissions:
 
 jobs:
   test:
-    name: ${{ matrix.tags }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
+    name: ${{ matrix.tags }} | ${{ matrix.profile }} | NF-${{ matrix.NXF_VER }}
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
@@ -60,10 +60,15 @@ jobs:
           python-version: "3.11"
           architecture: "x64"
 
-      - name: Install pdiff to see diff between nf-test snapshots
-        run: |
-          python -m pip install --upgrade pip
-          pip install pdiff
+      - name: Cache pdiff
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
+        id: cache-pip-pdiff
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-pdiff
+
+      - name: Install pdiff
+        run: python -m pip install --upgrade pip pdiff cryptography
 
       - name: Run nf-test
         run: |

CHANGELOG.md

@@ -60,6 +60,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#433](https://github.com/genomic-medicine-sweden/nallo/pull/433) - Updated docs and README.
 - [#434](https://github.com/genomic-medicine-sweden/nallo/pull/434) - Updated the SVDB merge module to fix unstable CALL_SVS tests
 - [#435](https://github.com/genomic-medicine-sweden/nallo/pull/435) - Updated and refactored processes and workflows related to variant ranking
+- [#438](https://github.com/genomic-medicine-sweden/nallo/pull/438) - Updated pipeline tests to use functions in nft-utils instead of checking hardcoded paths
 - [#440](https://github.com/genomic-medicine-sweden/nallo/pull/440) - Updated hifiasm to 0.20 with new default parameters for telomeres and scaffolding ([#295](https://github.com/genomic-medicine-sweden/nallo/issues/295))
 
 ### `Removed`
@@ -77,6 +78,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#382](https://github.com/genomic-medicine-sweden/nallo/pull/382) - Fixed broken links and formatting in documentation
 - [#393](https://github.com/genomic-medicine-sweden/nallo/pull/393) - Fixed minimap2 preset for ONT data being overwritten to `map-ont` when it should have been `lr:hq`, due to different settings in index and alignment processes [#392](https://github.com/genomic-medicine-sweden/nallo/issues/392)
 - [#402](https://github.com/genomic-medicine-sweden/nallo/pull/402) - Fixed double sample names in HiFiCNV output
+- [#438](https://github.com/genomic-medicine-sweden/nallo/pull/438) - Fixed missing/malformed software versions in `ADD_FOUND_IN_TAG`, `ADD_MOST_SEVERE_CSQ`, `ADD_MOST_SEVERE_PLI`, `SAMPLESHEET_PED`, `SOMALIER_PED` and `TRGT`
 
 ### Parameters
 

modules/local/add_found_in_tag/main.nf

@@ -64,7 +64,7 @@ process ADD_FOUND_IN_TAG {
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
-        gawk: \$(awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//')
+        busybox-awk: \$(awk 2>&1 | sed -n 's/.*v\\([^ ]*\\) (.*/\\1/p')
     END_VERSIONS
     """
 
@@ -90,7 +90,7 @@ process ADD_FOUND_IN_TAG {
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
-        gawk: \$(awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//')
+        busybox-awk: \$(awk 2>&1 | sed -n 's/.*v\\([^ ]*\\) (.*/\\1/p')
     END_VERSIONS
     """
 }

modules/local/add_most_severe_consequence.nf

@@ -31,7 +31,7 @@ process ADD_MOST_SEVERE_CSQ {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        add_most_severe_consequence: v1.0
+        add_most_severe_consequence: 1.0
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """
@@ -43,7 +43,7 @@ process ADD_MOST_SEVERE_CSQ {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        add_most_severe_consequence: v1.0
+        add_most_severe_consequence: 1.0
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """

modules/local/add_most_severe_pli.nf

@@ -29,7 +29,7 @@ process ADD_MOST_SEVERE_PLI {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        add_most_severe_pli: v1.0
+        add_most_severe_pli: 1.0
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """
@@ -41,7 +41,7 @@ process ADD_MOST_SEVERE_PLI {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        add_most_severe_pli: v1.0
+        add_most_severe_pli: 1.0
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """

modules/local/create_pedigree_file/main.nf

@@ -36,7 +36,7 @@ process CREATE_PEDIGREE_FILE {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        create_pedigree_file: v1.0
+        create_pedigree_file: 1.0
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """
@@ -47,7 +47,7 @@ process CREATE_PEDIGREE_FILE {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        create_pedigree_file: v1.0
+        create_pedigree_file: 1.0
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """

modules/local/trgt/main.nf

@@ -42,7 +42,7 @@ process TRGT {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        trgt: \$(echo \$(trgt -V) | sed 's/TRGT //' )
+        trgt: \$(echo \$(trgt -V) | sed 's/trgt //' )
     END_VERSIONS
     """
 }

nf-test.config

@@ -1,11 +1,16 @@
 config {
+    // location for all nf-tests
+    testsDir "."
+    // nf-test directory including temporary files for each test
+    workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"
+    // location of an optional nextflow.config file specific for executing tests
+    configFile "conf/test.config"
+    // run all test with defined profile(s) from the main nextflow.config
+    profile "test"
+    // Include plugins
     plugins {
-        load "[email protected]"
+        load "[email protected]"
+        load "[email protected]"
         load "[email protected]"
     }
-    testsDir "."
-    workDir ".nf-test"
-    configFile "tests/nextflow.config"
-    profile "docker"
-
 }