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[do not merge] stress testing PR #6286 #6716

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c2f20e4
ci: Attempt to split everything out
edmundmiller Aug 23, 2024
8897f68
ci: Add changed since, sharding, and ci
edmundmiller Aug 23, 2024
2e20ff4
ci: Add filter to try to get jobs split up
edmundmiller Aug 23, 2024
ea0de23
ci: Switch to only-changed
edmundmiller Aug 23, 2024
2c5b4bd
ci: See if follow-dependencies works without "related-tests"
edmundmiller Aug 23, 2024
6322086
ci: Remove skipped tests
edmundmiller Aug 23, 2024
71d9e5a
ci: Actually use the nf-test version
edmundmiller Aug 23, 2024
afd049d
ci: module => process
edmundmiller Aug 23, 2024
a823ee3
ci: Clean up job names
edmundmiller Aug 23, 2024
0d2c26c
dummy: Make a change
edmundmiller Aug 23, 2024
97f6406
ci: Skip test.tap
edmundmiller Aug 23, 2024
c486922
ci: Add fetch-depth
edmundmiller Aug 23, 2024
d58ecdb
ci: Clean up name
edmundmiller Aug 23, 2024
52a826d
ci: Lint everything
edmundmiller Aug 23, 2024
1043d64
ci: Get the job names clean
edmundmiller Aug 23, 2024
94c2453
ci: Add hide-progress on linting
edmundmiller Aug 23, 2024
ab5194b
ci: Add psuedocode for conda-fail.yml
edmundmiller Aug 24, 2024
2a218e3
test: Snapshot the versions contents, not the hash
edmundmiller Sep 10, 2024
e833cd5
ci: Keep running nf-core lint the way it was
Sep 18, 2024
392ffe7
ci: Move conda skips out
edmundmiller Sep 24, 2024
af2d917
ci: Address a comment
edmundmiller Sep 24, 2024
372625e
style: Move prettier and editorconfig to pre-commit
edmundmiller Sep 24, 2024
1670c52
ci: Add note about nf-core lint pre-commit
edmundmiller Sep 24, 2024
adf6658
chore: Copy over conda skips
edmundmiller Sep 24, 2024
d0caf9e
ci: only-changed => changed-since
edmundmiller Sep 30, 2024
164498a
Add samtools sort and unzip to stress test
adamrtalbot Sep 30, 2024
fed0e6c
dummy: Add changes to actual module files not tests
edmundmiller Sep 30, 2024
0b8d4e4
dummy: Remove comment because malt build is borked
edmundmiller Sep 30, 2024
d7eb610
dummy: Touch untar
edmundmiller Sep 30, 2024
c9f1ed0
yolo
adamrtalbot Oct 1, 2024
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ci: Remove skipped tests
Idk what we're going to do about these...
edmundmiller committed Sep 30, 2024

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commit 6322086e54dd63ed8328cc0d7234010babd212f0
265 changes: 133 additions & 132 deletions .github/workflows/nf-test.yml
Original file line number Diff line number Diff line change
@@ -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"
@@ -272,3 +140,136 @@ 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