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Add nf-test sharding CI #1668

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merged 61 commits into from
Oct 28, 2024
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6839ad2
ci: Copy over from methylseq
edmundmiller Oct 1, 2024
6fdf037
ci: Move Sarek specific settings to ci
edmundmiller Oct 1, 2024
ac87c35
ci: tap => xml
edmundmiller Oct 1, 2024
50b9c88
build: Add triggers
edmundmiller Oct 1, 2024
277c7fa
ci: Add clean up
edmundmiller Oct 1, 2024
fb36aa8
ci: Give jobs a name
edmundmiller Oct 1, 2024
ca0cfc3
ci: job-total => 5
edmundmiller Oct 1, 2024
06f22b6
ci: Follow dependencies
edmundmiller Oct 1, 2024
fcec8fa
ci: Wondering if we can combine proccesses and functions
edmundmiller Oct 1, 2024
f44ffa3
test: Manually nump software versions txt
edmundmiller Oct 2, 2024
5187cc1
ci: Run processes and functions seperately
edmundmiller Oct 2, 2024
ee7107f
ci(#1672): Remove latest-everything
edmundmiller Oct 2, 2024
0f4c1ed
Merge branch 'dev' into fresh-nf-test
maxulysse Oct 4, 2024
89d1b07
Update .github/workflows/ci.yml
maxulysse Oct 4, 2024
9edd171
Update .github/nf-test-tags.yml
maxulysse Oct 4, 2024
bf661f4
no need for tags
maxulysse Oct 4, 2024
8386f98
just 1 shard for pipeline as we have just 1 test currently
maxulysse Oct 4, 2024
6924616
just 1 shard for pipeline as we have just 1 test currently
maxulysse Oct 4, 2024
304198c
just 1 shard for pipeline as we have just 1 test currently
maxulysse Oct 4, 2024
bea4da6
fix samplesheet_to_channel test
maxulysse Oct 4, 2024
1304a7c
update all modules/subworkflows
maxulysse Oct 4, 2024
0afb9fc
update nf-core/utils_nfcore_pipeline subworkflow
maxulysse Oct 4, 2024
a87503c
update nf-core/utils_nfvalidation_plugin subworkflow
maxulysse Oct 4, 2024
b3b16cf
Merge branch 'dev' into fresh-nf-test
maxulysse Oct 7, 2024
348fb34
4 shards for pipeline
maxulysse Oct 7, 2024
574047a
Merge branch 'dev' into fresh-nf-test
maxulysse Oct 7, 2024
d42727b
Merge branch 'nft-utils-0-0-3' into fresh-nf-test
maxulysse Oct 8, 2024
cba29dd
no need to exclude pipeline shards anymore
maxulysse Oct 8, 2024
0dd1d41
Merge branch 'dev' into fresh-nf-test
maxulysse Oct 11, 2024
44d8f3b
remove filter process for now
maxulysse Oct 11, 2024
4ba50b2
bump minimum NXF_VER
maxulysse Oct 11, 2024
f470227
no status is 0
maxulysse Oct 11, 2024
245d355
Merge branch 'dev' into fresh-nf-test
maxulysse Oct 15, 2024
acb7cb9
Merge branch 'dev' into fresh-nf-test
maxulysse Oct 23, 2024
016377c
Merge branch 'dev' into fresh-nf-test
maxulysse Oct 24, 2024
7e7b66c
Merge branch 'fresh-nf-test' of github.com:nf-core/sarek into fresh-n…
maxulysse Oct 24, 2024
038c2ec
print tests run
maxulysse Oct 24, 2024
b182313
Typo
maxulysse Oct 24, 2024
5500193
echo the results
maxulysse Oct 24, 2024
6beaace
print to GITHUB_OUTPUT
maxulysse Oct 24, 2024
d1f531a
print to GITHUB_SUMMARY
maxulysse Oct 24, 2024
5c92608
Better summary
maxulysse Oct 24, 2024
5b4827c
Better summary
maxulysse Oct 24, 2024
8d876af
Better summary
maxulysse Oct 24, 2024
e03627e
update to python v5
maxulysse Oct 24, 2024
1370581
nicer summary
maxulysse Oct 24, 2024
9815858
escape single quote
maxulysse Oct 24, 2024
105821f
polish
maxulysse Oct 24, 2024
2fab5f9
try concatenate reports
maxulysse Oct 24, 2024
2b6b408
fix path
maxulysse Oct 24, 2024
36cedb3
add needs
maxulysse Oct 24, 2024
a1cb1c4
update actions
maxulysse Oct 24, 2024
bfb3a38
update action
maxulysse Oct 24, 2024
2d094ee
update path
maxulysse Oct 24, 2024
0ddea42
update path
maxulysse Oct 24, 2024
2de9bf1
update path
maxulysse Oct 24, 2024
67269a9
update path
maxulysse Oct 24, 2024
1c06bab
revert to v3
maxulysse Oct 24, 2024
04dca87
revert to a working state
maxulysse Oct 25, 2024
acfec84
Merge branch 'dev' into fresh-nf-test
maxulysse Oct 28, 2024
f3b96aa
Apply suggestions from code review
maxulysse Oct 28, 2024
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50 changes: 50 additions & 0 deletions .github/nf-test-tags.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,50 @@
exclude:
- tags: "bcftools/annotate"
- tags: "bcftools/concat"
- tags: "bcftools/mpileup"
- tags: "bcftools/sort"
- tags: "bwa/index"
- tags: "bwa/mem"
- tags: "bwamem2/index"
- tags: "bwamem2/mem"
- tags: "cat/cat"
- tags: "cat/fastq"
- tags: "cnvkit/antitarget"
- tags: "cnvkit/batch"
- tags: "cnvkit/reference"
- tags: "deepvariant"
- tags: "dragmap/align"
- tags: "dragmap/hashtable"
- tags: "ensemblvep/download"
- tags: "ensemblvep/vep"
- tags: "fastp"
- tags: "fastqc"
- tags: "fgbio/fastqtobam"
- tags: "freebayes"
- tags: "gatk4/applybqsr"
- tags: "gatk4/baserecalibrator"
- tags: "gatk4/estimatelibrarycomplexity"
- tags: "gatk4/genomicsdbimport"
- tags: "gatk4/haplotypecaller"
- tags: "gatk4/markduplicates"
- tags: "gatk4/mergevcfs"
- tags: "gatk4/mutect2"
- tags: "gatk4spark/applybqsr"
- tags: "gatk4spark/markduplicates"
- tags: "gawk"
- tags: "lofreq/callparallel"
- tags: "mosdepth"
- tags: "multiqc"
- tags: "ngscheckmate/ncm"
- tags: "samblaster"
- tags: "samtools/convert"
- tags: "samtools/mpileup"
- tags: "samtools/stats"
- tags: "snpeff/snpeff"
- tags: "strelka/germline"
- tags: "strelka/somatic"
- tags: "subworkflows/utils_nfvalidation_plugin"
- tags: "tabix/bgziptabix"
- tags: "tabix/tabix"
- tags: "tiddit/sv"
- tags: "untar"
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