Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add nf-test sharding CI #1668

Open
wants to merge 53 commits into
base: dev
Choose a base branch
from
Open
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
53 commits
Select commit Hold shift + click to select a range
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
5e7f6f5
migrate pytest aligner tests to nf-test
maxulysse Oct 7, 2024
e9f0fb9
update CHANGELOG
maxulysse Oct 7, 2024
b3b16cf
Merge branch 'dev' into fresh-nf-test
maxulysse Oct 7, 2024
348fb34
4 shards for pipeline
maxulysse Oct 7, 2024
1d9a18e
install pdiff
maxulysse Oct 7, 2024
b7417ec
properly install pdiff
maxulysse Oct 7, 2024
89507f8
update nftignore and snapshots
maxulysse Oct 7, 2024
574047a
Merge branch 'dev' into fresh-nf-test
maxulysse Oct 7, 2024
7b7b9c1
update CHANGELOG
maxulysse Oct 8, 2024
1bfe04a
add tumor-normal-pair test
maxulysse Oct 8, 2024
c9b2f0d
update CHANGELOG
maxulysse Oct 8, 2024
0c5114f
add more tests, update to nft-utils 0.0.3, add nft-bam 0.4.0
maxulysse Oct 8, 2024
977389f
fix snapshots
maxulysse Oct 8, 2024
d31edb8
ignore bam files from snapshots
maxulysse Oct 8, 2024
1e82940
ignore bai files from snapshots
maxulysse Oct 8, 2024
4713bad
snapshot bam files
maxulysse Oct 8, 2024
56791a2
update nftignore - no files from multiqc_plots
maxulysse Oct 8, 2024
2c9d25b
update snapshots + snapshot bam files using nft-bam
maxulysse Oct 8, 2024
4db3c99
snapshot bam files
maxulysse Oct 8, 2024
5634713
properly update nftignore - no files from multiqc_plots
maxulysse Oct 8, 2024
6dd2fd6
snapshot cram files with nft-bam
maxulysse Oct 8, 2024
61f19fd
update snapshots
maxulysse Oct 8, 2024
ab16157
update nftignore
maxulysse Oct 8, 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
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
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"
Loading
Loading