Merge pull request #143 from nf-core/ci-fixes

Get Singularity CI tests working

.github/filters.yml

@@ -3,7 +3,7 @@ bowtie_align:
   - software/bowtie/build/**
   - tests/software/bowtie/align/**
 
-bowtie_build:
+bowtie:
   - software/bowtie/build/**
   - tests/software/bowtie/build/**
 
@@ -12,7 +12,7 @@ bowtie2_align:
   - software/bowtie2/build/**
   - tests/software/bowtie2/align/**
 
-bowtie2_build:
+bowtie2:
   - software/bowtie2/build/**
   - tests/software/bowtie2/build/**
 

.github/workflows/pytest-workflow.yml

@@ -25,7 +25,7 @@ jobs:
       matrix:
         nxf_version: ['20.11.0-edge']
         tags: ['${{ fromJson(needs.changes.outputs.modules) }}']
-        profile: ['docker'] ## 'conda', 'singularity'
+        profile: ['docker', 'singularity'] ## 'conda'
     env:
       NXF_ANSI_LOG: false
     steps:
@@ -65,7 +65,7 @@ jobs:
         if: matrix.profile == 'singularity'
         uses: eWaterCycle/setup-singularity@v5
         with:
-          singularity-version: 3.5.3
+          singularity-version: 3.7.1
 
       - name: Setup miniconda
         if: matrix.profile == 'conda'
@@ -80,7 +80,7 @@ jobs:
 
       # Test the module
       - name: Run pytest-workflow
-        run: PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --wt 2 --kwdof
+        run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --wt 2 --kwdof
 
       - name: Upload logs on failure
         if: failure()

tests/config/nextflow.config

@@ -2,13 +2,12 @@ params {
     outdir = "output/"
     publish_dir_mode = "copy"
     enable_conda = false
-    singularity_pull_docker_container = true
+    singularity_pull_docker_container = false
 }
 
 if ("$PROFILE" == "singularity") {
     singularity.enabled = true
     singularity.autoMounts = true
-    singularity.runOptions = '-B /tmp/'
 } else if ("$PROFILE" == "conda") {
     params.enable_conda = true
 } else {

tests/software/bowtie/align/test.yml

@@ -42,6 +42,5 @@
     - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt
       md5sum: f3c398bba5158f4039334a932d79c051
     - path: output/bowtie/test.out
-      md5sum: a23e9a2a76e949aeb3693bcfae41a615
+      md5sum: a81cb18024616415a6cec3108a36fccd
     - path: output/bowtie/test.bam
-      should_exist: true

tests/software/bowtie/build/test.yml

@@ -15,4 +15,4 @@
     - path: output/bowtie/bowtie/NC_010473.rev.1.ebwt
       md5sum: 44f719c2fe42e1f35d54e798775846d1
     - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt
-      md5sum: f3c398bba5158f4039334a932d79c051
+      md5sum: f3c398bba5158f4039334a932d79c051

tests/software/bowtie2/build/test.yml

@@ -15,4 +15,4 @@
     - path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2
       md5sum: 4ccfee8857c3b1c69857e5ecdef597aa
     - path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2
-      md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72
+      md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72