diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index a4000ee67b..9703584f2c 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -26,28 +26,63 @@ jobs:
           - "latest-everything"
         test:
           - "default"
-        profile: ["docker"]
+        profile: ["docker", "singularity", "conda"]
+        exclude:
+          - NXF_VER: "latest-everything"
+            profile: "conda"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+
+      - uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Install Python dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
+
+      - uses: actions/cache@v2
+        with:
+          path: /usr/local/bin/nextflow
+          key: ${{ runner.os }}
+          restore-keys: |
+            ${{ runner.os }}-nextflow-
+
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Set up Python
-        uses: actions/setup-python@v2
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-singularity@v5
         with:
-          python-version: "3.x"
+          singularity-version: 3.7.1
 
-      - name: Install dependencies
-        run: python -m pip install --upgrade pip pytest-workflow
+      - name: Set up miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          channels: conda-forge,bioconda,defaults
+          python-version: ${{ matrix.python-version }}
+
+      - name: Conda clean
+        if: matrix.profile == 'conda'
+        run: conda clean -a
 
       - name: Run pipeline with tests settings
         uses: Wandalen/wretry.action@v1.0.11
         with:
-          command: PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.test }} --symlink --kwdof --git-aware --color=yes
+          command: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.test }} --symlink --kwdof --git-aware --color=yes
           attempt_limit: 3
 
       - name: Output log on failure
@@ -91,6 +126,7 @@ jobs:
           - "freebayes"
           - "gatk4_spark"
           - "haplotypecaller"
+          - "intervals"
           - "manta"
           - "markduplicates"
           - "mpileup"
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 073331b0d9..ff8dbf746c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -27,6 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#731](https://github.com/nf-core/sarek/pull/731) - Run the somatic test as default on `-profile test_full`, the germline can be tested with `-profile test_full_somatic`
 - [#733](https://github.com/nf-core/sarek/pull/733) - Add description for params.cf_chrom_len
 - [#734](https://github.com/nf-core/sarek/pull/734) - nf-core modules update -a
+- [#736](https://github.com/nf-core/sarek/pull/736) - More extensive CI for default test
 
 ### Fixed
 
diff --git a/conf/test.config b/conf/test.config
index 0089be490b..3ec92dfe1e 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -253,29 +253,32 @@ process {
     }
 }
 
-// ENABLE CI containers for testing
+// Enable container engines/virtualisation envs for CI testing
+// only works when specified with the profile ENV
+// otherwise tests can be done with the regular provided profiles
 if (System.getenv('PROFILE')) {
     if ("$PROFILE" == "conda") {
-            params.enable_conda    = true
-            docker.enabled         = false
-            singularity.enabled    = false
-            podman.enabled         = false
-            shifter.enabled        = false
-            charliecloud.enabled   = false
+        conda.createTimeout                      = "120 min"
+        params.enable_conda                      = true
+        charliecloud.enabled                     = false
+        docker.enabled                           = false
+        podman.enabled                           = false
+        shifter.enabled                          = false
+        singularity.enabled                      = false
     } else if ("$PROFILE" == "docker") {
-            docker.enabled         = true
-            docker.userEmulation   = { params.use_gatk_spark ? false : true }.call()
-            singularity.enabled    = false
-            podman.enabled         = false
-            shifter.enabled        = false
-            charliecloud.enabled   = false
-            fixOwnership = true
+        docker.enabled                           = true
+        docker.userEmulation                     = { params.use_gatk_spark ? false : true }.call()
+        charliecloud.enabled                     = false
+        podman.enabled                           = false
+        shifter.enabled                          = false
+        singularity.enabled                      = false
     } else if ("$PROFILE" == "singularity") {
-            singularity.enabled    = true
-            singularity.autoMounts = true
-            docker.enabled         = false
-            podman.enabled         = false
-            shifter.enabled        = false
-            charliecloud.enabled   = false
+        params.singularity_pull_docker_container = false
+        singularity.autoMounts                   = true
+        singularity.enabled                      = true
+        charliecloud.enabled                     = false
+        docker.enabled                           = false
+        podman.enabled                           = false
+        shifter.enabled                          = false
     }
 }
diff --git a/nextflow.config b/nextflow.config
index 5ec00cd60e..a3fe349c1b 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -143,63 +143,62 @@ profiles {
     debug { process.beforeScript = 'echo $HOSTNAME' }
     conda {
         params.enable_conda    = true
+        charliecloud.enabled   = false
         docker.enabled         = false
-        singularity.enabled    = false
         podman.enabled         = false
         shifter.enabled        = false
-        charliecloud.enabled   = false
+        singularity.enabled    = false
     }
     mamba {
-        params.enable_conda    = true
         conda.useMamba         = true
+        params.enable_conda    = true
+        charliecloud.enabled   = false
         docker.enabled         = false
-        singularity.enabled    = false
         podman.enabled         = false
         shifter.enabled        = false
-        charliecloud.enabled   = false
+        singularity.enabled    = false
     }
     docker {
         docker.enabled         = true
         docker.userEmulation   = { params.use_gatk_spark ? false : true }.call()
-        singularity.enabled    = false
+        charliecloud.enabled   = false
         podman.enabled         = false
         shifter.enabled        = false
-        charliecloud.enabled   = false
-        fixOwnership = true
+        singularity.enabled    = false
     }
     singularity {
-        singularity.enabled    = true
         singularity.autoMounts = true
+        singularity.enabled    = true
+        charliecloud.enabled   = false
         docker.enabled         = false
         podman.enabled         = false
         shifter.enabled        = false
-        charliecloud.enabled   = false
     }
     podman {
         podman.enabled         = true
+        charliecloud.enabled   = false
         docker.enabled         = false
-        singularity.enabled    = false
         shifter.enabled        = false
-        charliecloud.enabled   = false
+        singularity.enabled    = false
     }
     shifter {
         shifter.enabled        = true
+        charliecloud.enabled   = false
         docker.enabled         = false
-        singularity.enabled    = false
         podman.enabled         = false
-        charliecloud.enabled   = false
+        singularity.enabled    = false
     }
     charliecloud {
         charliecloud.enabled   = true
         docker.enabled         = false
-        singularity.enabled    = false
         podman.enabled         = false
         shifter.enabled        = false
+        singularity.enabled    = false
     }
     gitpod {
-        executor.name          = 'local'
         executor.cpus          = 16
         executor.memory        = 60.GB
+        executor.name          = 'local'
     }
     test               { includeConfig 'conf/test.config' }
     test_full          { includeConfig 'conf/test_full.config' }
diff --git a/tests/test_default.yml b/tests/test_default.yml
index 80794a291b..6d1a6e73d6 100644
--- a/tests/test_default.yml
+++ b/tests/test_default.yml
@@ -24,7 +24,7 @@
     - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
     # binary changes md5sums on reruns.
     - path: results/reports/bcftools/strelka/test/test.strelka.variants.bcftools_stats.txt
-      md5sum: 28d99fd4fa63e24e6805f1d12c3b71d3
+    # conda changes md5sums for test.
     - path: results/reports/fastqc/test-test_L1
     - path: results/reports/markduplicates/test/test.md.metrics
       contains: ["test	8547	767	84	523391	3882	0	0	0.385081", "1.0	767	767"]
@@ -49,9 +49,9 @@
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
       md5sum: b1c2a861f64e20a94108a6de3b76c582
     - path: results/reports/samtools/test/test.md.cram.stats
-      md5sum: 52411f93d9b5382342b40a351c2e313c
+    # conda changes md5sums for test.
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: 811d834ff8849e69e7c5925dc2a34257
+    # conda changes md5sums for test.
     - path: results/reports/vcftools/strelka/test/test.strelka.variants.FILTER.summary
       md5sum: dd87f507da7de20d5318841af312493b
     - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.count
@@ -67,60 +67,3 @@
     - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi
     - path: results/strelka
       should_exist: false
-- name: Run default pipeline without intervals
-  command: nextflow run main.nf -profile test,no_intervals
-  tags:
-    - default
-    - no_intervals
-    - preprocessing
-  files:
-    - path: results/csv/markduplicates.csv
-      md5sum: 0d6120bb99e92f6810343270711ca53e
-    - path: results/csv/markduplicates_no_table.csv
-      md5sum: 2a2d3d4842befd4def39156463859ee3
-    - path: results/csv/recalibrated.csv
-      md5sum: 42628ec994c16f565e5407b40a9c1ac3
-    - path: results/multiqc
-    - path: results/no_intervals.bed
-      md5sum: f3dac01ea66b95fe477446fde2d31489
-    - path: results/no_intervals.bed.gz
-      md5sum: f3dac01ea66b95fe477446fde2d31489
-    - path: results/no_intervals.bed.gz.tbi
-      md5sum: f3dac01ea66b95fe477446fde2d31489
-    - path: results/preprocessing/markduplicates/test/test.md.cram
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/recal_table/test/test.recal.table
-      md5sum: 4ac774bf5f1157e77426fd82f5ac0fbe
-    - path: results/preprocessing/recalibrated/test/test.recal.cram
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
-    # binary changes md5sums on reruns.
-    - path: results/reports/fastqc/test-test_L1
-    - path: results/reports/markduplicates/test/test.md.metrics
-      contains: ["test	8547	767	84	523391	3882	0	0	0.385081", "1.0	767	767"]
-    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
-      md5sum: 76fa71922a3f748e507c2364c531dfcb
-    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
-      md5sum: abc5df85e302b79985627888870882da
-    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
-      md5sum: d536456436eb275159b8c6af83213d80
-    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
-      md5sum: 38fe39894abe62e38f8ac214cba64f2b
-    - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
-      md5sum: b1c2a861f64e20a94108a6de3b76c582
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
-      md5sum: 76fa71922a3f748e507c2364c531dfcb
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
-      md5sum: abc5df85e302b79985627888870882da
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
-      md5sum: d536456436eb275159b8c6af83213d80
-    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
-      md5sum: 38fe39894abe62e38f8ac214cba64f2b
-    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
-      md5sum: b1c2a861f64e20a94108a6de3b76c582
-    - path: results/reports/samtools/test/test.md.cram.stats
-      md5sum: 52411f93d9b5382342b40a351c2e313c
-    - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: d80ad11b8e308a3d5b1fb6f8e13cef38
diff --git a/tests/test_intervals.yml b/tests/test_intervals.yml
new file mode 100644
index 0000000000..8f24169243
--- /dev/null
+++ b/tests/test_intervals.yml
@@ -0,0 +1,105 @@
+- name: Run intervals false pipeline
+  command: nextflow run main.nf -profile test --intervals false
+  tags:
+    - intervals
+    - intervals_false
+    - preprocessing
+  files:
+    - path: results/csv/markduplicates.csv
+      md5sum: 0d6120bb99e92f6810343270711ca53e
+    - path: results/csv/markduplicates_no_table.csv
+      md5sum: 2a2d3d4842befd4def39156463859ee3
+    - path: results/csv/recalibrated.csv
+      md5sum: 42628ec994c16f565e5407b40a9c1ac3
+    - path: results/multiqc
+    - path: results/preprocessing/markduplicates/test/test.md.cram
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/recal_table/test/test.recal.table
+      md5sum: 4ac774bf5f1157e77426fd82f5ac0fbe
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
+    # binary changes md5sums on reruns.
+    - path: results/reports/fastqc/test-test_L1
+    - path: results/reports/markduplicates/test/test.md.metrics
+      contains: ["test	8547	767	84	523391	3882	0	0	0.385081", "1.0	767	767"]
+    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
+      md5sum: 76fa71922a3f748e507c2364c531dfcb
+    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
+      md5sum: abc5df85e302b79985627888870882da
+    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
+      md5sum: d536456436eb275159b8c6af83213d80
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
+      md5sum: 38fe39894abe62e38f8ac214cba64f2b
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      md5sum: 76fa71922a3f748e507c2364c531dfcb
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+      md5sum: abc5df85e302b79985627888870882da
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      md5sum: d536456436eb275159b8c6af83213d80
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
+      md5sum: 38fe39894abe62e38f8ac214cba64f2b
+    - path: results/reports/samtools/test/test.md.cram.stats
+      md5sum: 52411f93d9b5382342b40a351c2e313c
+    - path: results/reports/samtools/test/test.recal.cram.stats
+      md5sum: 811d834ff8849e69e7c5925dc2a34257
+
+- name: Run default pipeline without intervals
+  command: nextflow run main.nf -profile test,no_intervals
+  tags:
+    - intervals
+    - no_intervals
+    - preprocessing
+  files:
+    - path: results/csv/markduplicates.csv
+      md5sum: 0d6120bb99e92f6810343270711ca53e
+    - path: results/csv/markduplicates_no_table.csv
+      md5sum: 2a2d3d4842befd4def39156463859ee3
+    - path: results/csv/recalibrated.csv
+      md5sum: 42628ec994c16f565e5407b40a9c1ac3
+    - path: results/multiqc
+    - path: results/no_intervals.bed
+      md5sum: f3dac01ea66b95fe477446fde2d31489
+    - path: results/no_intervals.bed.gz
+      md5sum: f3dac01ea66b95fe477446fde2d31489
+    - path: results/no_intervals.bed.gz.tbi
+      md5sum: f3dac01ea66b95fe477446fde2d31489
+    - path: results/preprocessing/markduplicates/test/test.md.cram
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/recal_table/test/test.recal.table
+      md5sum: 4ac774bf5f1157e77426fd82f5ac0fbe
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
+    # binary changes md5sums on reruns.
+    - path: results/reports/fastqc/test-test_L1
+    - path: results/reports/markduplicates/test/test.md.metrics
+      contains: ["test	8547	767	84	523391	3882	0	0	0.385081", "1.0	767	767"]
+    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
+      md5sum: 76fa71922a3f748e507c2364c531dfcb
+    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
+      md5sum: abc5df85e302b79985627888870882da
+    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
+      md5sum: d536456436eb275159b8c6af83213d80
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
+      md5sum: 38fe39894abe62e38f8ac214cba64f2b
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
+      md5sum: b1c2a861f64e20a94108a6de3b76c582
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      md5sum: 76fa71922a3f748e507c2364c531dfcb
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+      md5sum: abc5df85e302b79985627888870882da
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      md5sum: d536456436eb275159b8c6af83213d80
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
+      md5sum: 38fe39894abe62e38f8ac214cba64f2b
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
+      md5sum: b1c2a861f64e20a94108a6de3b76c582
+    - path: results/reports/samtools/test/test.md.cram.stats
+      md5sum: 52411f93d9b5382342b40a351c2e313c
+    - path: results/reports/samtools/test/test.recal.cram.stats
+      md5sum: d80ad11b8e308a3d5b1fb6f8e13cef38
diff --git a/tests/test_targeted.yml b/tests/test_targeted.yml
index ce1e3b36eb..a1638dec7b 100644
--- a/tests/test_targeted.yml
+++ b/tests/test_targeted.yml
@@ -56,50 +56,3 @@
       md5sum: 52411f93d9b5382342b40a351c2e313c
     - path: results/reports/samtools/test/test.recal.cram.stats
       md5sum: 5ed26e702d5c2238a1f3cdc5e5b44f98
-
-- name: Run intervals false pipeline
-  command: nextflow run main.nf -profile test --intervals false
-  tags:
-    - default
-    - preprocessing
-  files:
-    - path: results/csv/markduplicates.csv
-      md5sum: 0d6120bb99e92f6810343270711ca53e
-    - path: results/csv/markduplicates_no_table.csv
-      md5sum: 2a2d3d4842befd4def39156463859ee3
-    - path: results/csv/recalibrated.csv
-      md5sum: 42628ec994c16f565e5407b40a9c1ac3
-    - path: results/multiqc
-    - path: results/preprocessing/markduplicates/test/test.md.cram
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/recal_table/test/test.recal.table
-      md5sum: 4ac774bf5f1157e77426fd82f5ac0fbe
-    - path: results/preprocessing/recalibrated/test/test.recal.cram
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
-    # binary changes md5sums on reruns.
-    - path: results/reports/fastqc/test-test_L1
-    - path: results/reports/markduplicates/test/test.md.metrics
-      contains: ["test	8547	767	84	523391	3882	0	0	0.385081", "1.0	767	767"]
-    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
-      md5sum: 76fa71922a3f748e507c2364c531dfcb
-    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
-      md5sum: abc5df85e302b79985627888870882da
-    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
-      md5sum: d536456436eb275159b8c6af83213d80
-    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
-      md5sum: 38fe39894abe62e38f8ac214cba64f2b
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
-      md5sum: 76fa71922a3f748e507c2364c531dfcb
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
-      md5sum: abc5df85e302b79985627888870882da
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
-      md5sum: d536456436eb275159b8c6af83213d80
-    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
-      md5sum: 38fe39894abe62e38f8ac214cba64f2b
-    - path: results/reports/samtools/test/test.md.cram.stats
-      md5sum: 52411f93d9b5382342b40a351c2e313c
-    - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: 811d834ff8849e69e7c5925dc2a34257
diff --git a/tests/test_tools.yml b/tests/test_tools.yml
index 9d3c289be1..7d8d4619f8 100644
--- a/tests/test_tools.yml
+++ b/tests/test_tools.yml
@@ -298,7 +298,7 @@
     - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.g.vcf.gz
     # binary changes md5sums on reruns.
     - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.g.vcf.gz.tbi
-      md5sum: 9870fcf1afbf7cbccc3b63d75acf1f4f
+    # binary changes md5sums on reruns.
     - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.vcf.gz
     # binary changes md5sums on reruns.
     - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.vcf.gz.tbi