Tests changed, move them to test-datasets (#167)

* PXD000001.sdrf.tsv removed from assets

* tests of ci moved to test-datasets

* PXD026600.sdrf.tsv removed

* first iteration of utils msstats_utils.R

.github/workflows/awsfulltest.yml

@@ -1,7 +1,7 @@
 name: nf-core AWS full size tests
 # This workflow is triggered on published releases.
 # It can be additionally triggered manually with GitHub actions workflow dispatch button.
-# It runs the -profile 'test_full' on AWS batch
+# It runs the -profile 'test_lfq' on AWS batch
 
 on:
   release:
@@ -17,7 +17,7 @@ jobs:
         uses: nf-core/tower-action@v3
         # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
-        # on the `test_full.config` test runs with only one set of parameters
+        # on the `test_lfq.config` test runs with only one set of parameters
 
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
@@ -28,7 +28,7 @@ jobs:
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/quantms/results-${{ github.sha }}"
             }
-          profiles: test_full,aws_tower
+          profiles: test_lfq,aws_tower
           nextflow_config: |
             process.errorStrategy = 'retry'
             process.maxRetries = 3

.github/workflows/awstest.yml

@@ -1,6 +1,6 @@
 name: nf-core AWS test
 # This workflow can be triggered manually with the GitHub actions workflow dispatch button.
-# It runs the -profile 'test' on AWS batch
+# It runs the -profile 'test_tmt' on AWS batch
 
 on:
   workflow_dispatch:
@@ -23,7 +23,7 @@ jobs:
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/quantms/results-test-${{ github.sha }}"
             }
-          profiles: test,aws_tower
+          profiles: test_tmt,aws_tower
           nextflow_config: |
             process.errorStrategy = 'retry'
             process.maxRetries = 3

.github/workflows/ci.yml

@@ -31,7 +31,7 @@ jobs:
           # Test latest edge release of Nextflow
           - NXF_VER: ""
             NXF_EDGE: "1"
-        test_profile: ["test", "test_lfq", "test_dia", "test_localize"]
+        test_profile: ["test_lfq", "test_dia", "test_localize", "test_tmt"]
         exec_profile: ["docker", "conda"]
         exclude:
           - test_profile: test_dia

.nf-core.yml

@@ -2,3 +2,5 @@ repository_type: pipeline
 lint:
   files_exist:
     - conf/igenomes.config
+    - conf/test_full.config
+    - conf/test.config