ci: Remove skipped tests

Idk what we're going to do about these...

.github/workflows/nf-test.yml

@@ -35,138 +35,6 @@ jobs:
         shard: [1, 2, 3]
         profile: [conda, docker_self_hosted, singularity]
         filter: [module, workflow]
-        exclude:
-          - path: modules/nf-core/nf-test
-          - profile: conda
-            path: modules/nf-core/angsd/gl
-          - profile: conda
-            path: modules/nf-core/annotsv/installannotations
-          - profile: conda
-            path: modules/nf-core/happy/sompy
-          - profile: conda
-            path: modules/nf-core/backsub
-          - profile: conda
-            path: modules/nf-core/bakta/bakta
-          - profile: conda
-            path: modules/nf-core/bakta/baktadbdownload
-          - profile: conda
-            path: modules/nf-core/bases2fastq
-          - profile: conda
-            path: modules/nf-core/bcl2fastq
-          - profile: conda
-            path: modules/nf-core/bclconvert
-          - profile: conda
-            path: modules/nf-core/celesta
-          - profile: conda
-            path: modules/nf-core/cellpose
-          - profile: conda
-            path: modules/nf-core/cellranger/count
-          - profile: conda
-            path: modules/nf-core/cellranger/mkfastq
-          - profile: conda
-            path: modules/nf-core/cellranger/mkgtf
-          - profile: conda
-            path: modules/nf-core/cellranger/mkref
-          - profile: conda
-            path: modules/nf-core/cellranger/mkvdjref
-          - profile: conda
-            path: modules/nf-core/cellranger/multi
-          - profile: conda
-            path: modules/nf-core/cellranger/vdj
-          - profile: conda
-            path: modules/nf-core/checkqc
-          - profile: conda
-            path: modules/nf-core/custom/dumpsoftwareversions
-          - profile: conda
-            path: modules/nf-core/deepcell/mesmer
-          - profile: conda
-            path: modules/nf-core/deepvariant
-          - profile: conda
-            path: modules/nf-core/ensemblvep/vep
-          - profile: conda
-            path: modules/nf-core/fastk/fastk
-          - profile: conda
-            path: modules/nf-core/fastk/histex
-          - profile: conda
-            path: modules/nf-core/fastk/merge
-          - profile: conda
-            path: modules/nf-core/fcs/fcsadaptor
-          - profile: conda
-            path: modules/nf-core/fcs/fcsgx
-          - profile: conda
-            path: modules/nf-core/ganon/buildcustom
-          - profile: conda
-            path: modules/nf-core/ganon/classify
-          - profile: conda
-            path: modules/nf-core/ganon/report
-          - profile: conda
-            path: modules/nf-core/ganon/table
-          - profile: conda
-            path: modules/nf-core/gatk4/cnnscorevariants
-          - profile: conda
-            path: modules/nf-core/gatk4/determinegermlinecontigploidy
-          - profile: conda
-            path: modules/nf-core/genescopefk
-          - profile: conda
-            path: modules/nf-core/ilastik/multicut
-          - profile: conda
-            path: modules/nf-core/ilastik/pixelclassification
-          - profile: conda
-            path: modules/nf-core/imputeme/vcftoprs
-          - profile: conda
-            path: modules/nf-core/mcquant
-          - profile: conda
-            path: modules/nf-core/merquryfk/katcomp
-          - profile: conda
-            path: modules/nf-core/merquryfk/katgc
-          - profile: conda
-            path: modules/nf-core/merquryfk/merquryfk
-          - profile: conda
-            path: modules/nf-core/merquryfk/ploidyplot
-          - profile: conda
-            path: modules/nf-core/molkartgarage/clahe
-          - profile: conda
-            path: modules/nf-core/quartonotebook
-          - profile: conda
-            path: modules/nf-core/scimap/spatiallda
-          - profile: conda
-            path: modules/nf-core/sentieon/bwaindex
-          - profile: conda
-            path: modules/nf-core/sentieon/bwamem
-          - profile: conda
-            path: modules/nf-core/sentieon/dedup
-          - profile: conda
-            path: modules/nf-core/sentieon/qualcal
-          - profile: conda
-            path: modules/nf-core/spaceranger/mkgtf
-          - profile: conda
-            path: modules/nf-core/spaceranger/mkref
-          - profile: conda
-            path: modules/nf-core/spaceranger/count
-          - profile: conda
-            path: modules/nf-core/spotiflow
-          - profile: conda
-            path: modules/nf-core/svanalyzer/svbenchmark
-          - profile: conda
-            path: modules/nf-core/universc
-          - profile: singularity
-            path: modules/nf-core/universc
-          - profile: conda
-            path: modules/nf-core/vt/decompose
-          - profile: singularity
-            path: modules/nf-core/bases2fastq
-          - profile: conda
-            path: modules/nf-core/wittyer
-          - profile: conda
-            path: modules/nf-core/islandpath
-          - profile: conda
-            path: subworkflows/nf-core/vcf_annotate_ensemblvep
-          - profile: conda
-            path: subworkflows/nf-core/bcl_demultiplex
-          - profile: conda
-            path: subworkflows/nf-core/fastq_align_bamcmp_bwa
-          - profile: conda
-            path: subworkflows/nf-core/fastq_align_bwa
     env:
       NXF_ANSI_LOG: false
       NFTEST_VER: "0.9.0"
@@ -275,3 +143,136 @@ jobs:
         if: always()
         run: |
           sudo rm -rf /home/ubuntu/tests/
+
+# TODO What do we do with these?
+# - path: modules/nf-core/nf-test
+# - profile: conda
+#   path: modules/nf-core/angsd/gl
+# - profile: conda
+#   path: modules/nf-core/annotsv/installannotations
+# - profile: conda
+#   path: modules/nf-core/happy/sompy
+# - profile: conda
+#   path: modules/nf-core/backsub
+# - profile: conda
+#   path: modules/nf-core/bakta/bakta
+# - profile: conda
+#   path: modules/nf-core/bakta/baktadbdownload
+# - profile: conda
+#   path: modules/nf-core/bases2fastq
+# - profile: conda
+#   path: modules/nf-core/bcl2fastq
+# - profile: conda
+#   path: modules/nf-core/bclconvert
+# - profile: conda
+#   path: modules/nf-core/celesta
+# - profile: conda
+#   path: modules/nf-core/cellpose
+# - profile: conda
+#   path: modules/nf-core/cellranger/count
+# - profile: conda
+#   path: modules/nf-core/cellranger/mkfastq
+# - profile: conda
+#   path: modules/nf-core/cellranger/mkgtf
+# - profile: conda
+#   path: modules/nf-core/cellranger/mkref
+# - profile: conda
+#   path: modules/nf-core/cellranger/mkvdjref
+# - profile: conda
+#   path: modules/nf-core/cellranger/multi
+# - profile: conda
+#   path: modules/nf-core/cellranger/vdj
+# - profile: conda
+#   path: modules/nf-core/checkqc
+# - profile: conda
+#   path: modules/nf-core/custom/dumpsoftwareversions
+# - profile: conda
+#   path: modules/nf-core/deepcell/mesmer
+# - profile: conda
+#   path: modules/nf-core/deepvariant
+# - profile: conda
+#   path: modules/nf-core/ensemblvep/vep
+# - profile: conda
+#   path: modules/nf-core/fastk/fastk
+# - profile: conda
+#   path: modules/nf-core/fastk/histex
+# - profile: conda
+#   path: modules/nf-core/fastk/merge
+# - profile: conda
+#   path: modules/nf-core/fcs/fcsadaptor
+# - profile: conda
+#   path: modules/nf-core/fcs/fcsgx
+# - profile: conda
+#   path: modules/nf-core/ganon/buildcustom
+# - profile: conda
+#   path: modules/nf-core/ganon/classify
+# - profile: conda
+#   path: modules/nf-core/ganon/report
+# - profile: conda
+#   path: modules/nf-core/ganon/table
+# - profile: conda
+#   path: modules/nf-core/gatk4/cnnscorevariants
+# - profile: conda
+#   path: modules/nf-core/gatk4/determinegermlinecontigploidy
+# - profile: conda
+#   path: modules/nf-core/genescopefk
+# - profile: conda
+#   path: modules/nf-core/ilastik/multicut
+# - profile: conda
+#   path: modules/nf-core/ilastik/pixelclassification
+# - profile: conda
+#   path: modules/nf-core/imputeme/vcftoprs
+# - profile: conda
+#   path: modules/nf-core/mcquant
+# - profile: conda
+#   path: modules/nf-core/merquryfk/katcomp
+# - profile: conda
+#   path: modules/nf-core/merquryfk/katgc
+# - profile: conda
+#   path: modules/nf-core/merquryfk/merquryfk
+# - profile: conda
+#   path: modules/nf-core/merquryfk/ploidyplot
+# - profile: conda
+#   path: modules/nf-core/molkartgarage/clahe
+# - profile: conda
+#   path: modules/nf-core/quartonotebook
+# - profile: conda
+#   path: modules/nf-core/scimap/spatiallda
+# - profile: conda
+#   path: modules/nf-core/sentieon/bwaindex
+# - profile: conda
+#   path: modules/nf-core/sentieon/bwamem
+# - profile: conda
+#   path: modules/nf-core/sentieon/dedup
+# - profile: conda
+#   path: modules/nf-core/sentieon/qualcal
+# - profile: conda
+#   path: modules/nf-core/spaceranger/mkgtf
+# - profile: conda
+#   path: modules/nf-core/spaceranger/mkref
+# - profile: conda
+#   path: modules/nf-core/spaceranger/count
+# - profile: conda
+#   path: modules/nf-core/spotiflow
+# - profile: conda
+#   path: modules/nf-core/svanalyzer/svbenchmark
+# - profile: conda
+#   path: modules/nf-core/universc
+# - profile: singularity
+#   path: modules/nf-core/universc
+# - profile: conda
+#   path: modules/nf-core/vt/decompose
+# - profile: singularity
+#   path: modules/nf-core/bases2fastq
+# - profile: conda
+#   path: modules/nf-core/wittyer
+# - profile: conda
+#   path: modules/nf-core/islandpath
+# - profile: conda
+#   path: subworkflows/nf-core/vcf_annotate_ensemblvep
+# - profile: conda
+#   path: subworkflows/nf-core/bcl_demultiplex
+# - profile: conda
+#   path: subworkflows/nf-core/fastq_align_bamcmp_bwa
+# - profile: conda
+#   path: subworkflows/nf-core/fastq_align_bwa