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Skip sentieon tests on ARM/forks and fix DESEQ2_QC for ARM
Add SKIP_SENTIEON env var support to conditionally exclude sentieon tests (no ARM containers, no secrets on forks). Fix DESEQ2_QC test to check file existence for floating-point outputs that differ between architectures. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
1 parent 5515c2a commit 236ff64

20 files changed

+98
-92
lines changed

‎.github/workflows/nf-test-arm.yml‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -49,6 +49,8 @@ jobs:
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uses: ./.github/actions/get-shards
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env:
5151
NFT_VER: ${{ env.NFT_VER }}
52+
# Skip sentieon tests - no ARM containers available
53+
SKIP_SENTIEON: true
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with:
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max_shards: 14
5456

@@ -96,11 +98,9 @@ jobs:
9698
continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
9799
env:
98100
NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
99-
SENTIEON_AUTH_MECH: "GitHub Actions - token"
100-
SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }}
101-
SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }}
102-
SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }}
103101
NXF_VERSION: ${{ matrix.NXF_VER }}
102+
# Skip sentieon tests - no ARM containers available
103+
SKIP_SENTIEON: true
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with:
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profile: ${{ matrix.profile }},${{ matrix.archProfile }}
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shard: ${{ matrix.shard }}

‎.github/workflows/nf-test.yml‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -43,6 +43,8 @@ jobs:
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uses: ./.github/actions/get-shards
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env:
4545
NFT_VER: ${{ env.NFT_VER }}
46+
# Skip sentieon tests on fork PRs where secrets are not available
47+
SKIP_SENTIEON: ${{ github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name != 'nf-core/rnaseq' }}
4648
with:
4749
max_shards: 14
4850

@@ -94,6 +96,8 @@ jobs:
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SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }}
9597
SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }}
9698
NXF_VERSION: ${{ matrix.NXF_VER }}
99+
# Skip sentieon tests on fork PRs where secrets are not available
100+
SKIP_SENTIEON: ${{ github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name != 'nf-core/rnaseq' }}
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with:
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profile: ${{ matrix.profile }}
99103
shard: ${{ matrix.shard }}

‎conf/arm.config‎

Lines changed: 21 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -17,7 +17,7 @@ process {
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//
1818

1919
withName: 'BBMAP_BBSPLIT' {
20-
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/63ca91c8bf7285296777de219e5d5a71d2a7de47599cbc94441aced7868a4f83/data' : 'community.wave.seqera.io/library/bbmap:39.10--908996c2fb304bec' }
20+
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/70/70b6bc95922dc074b97890f796011dff8b76ed30ef2d66c6864d7b55dae27376/data' : 'community.wave.seqera.io/library/bbmap_pigz:ee2e600baccb45dd' }
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}
2222

2323
withName: 'BEDTOOLS_GENOMECOV' {
@@ -29,7 +29,7 @@ process {
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}
3030

3131
withName: 'CAT_FASTQ' {
32-
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/38/38d3638640600b355110f9bca56c514e3cc068bf96b8b68f98cba2a59a053505/data' : 'community.wave.seqera.io/library/coreutils:9.5--3931e2d27d9884e5' }
32+
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2d/2d61820950f089a905f34756e0713b3540f615d9e566817ff050d7b824840b1c/data' : 'community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:c4619b810d01e403' }
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}
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withName: 'CUSTOM_CATADDITIONALFASTA' {
@@ -45,27 +45,27 @@ process {
4545
}
4646

4747
withName: 'DESEQ2_QC' {
48-
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/70/70a3d17733d2c21cff464c31a7a57438cea528bea84c675b7c474eaa7f075f57/data' : 'community.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:8bd3e9db55b129d7' }
48+
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1c/1c89b73800b8197ea465f77e93cfed215b171ae1ba88b079ebf460ee88430624/data' : 'community.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:8bd10fed7887003f' }
4949
}
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5151
withName: 'DUPRADAR' {
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container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/10/10141f8fd43964316d04214a5f7d99a62e11cdbab5bd2fcd4f7c3c06eca9f2f6/data' : 'community.wave.seqera.io/library/bioconductor-dupradar:1.32.0--f75495d6abf45328' }
5353
}
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5555
withName: 'FASTP' {
56-
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7e/7ec6234f24305b9694b89de0352fff942ce1d68f840184020b0b9135bc54bda1/data' : 'community.wave.seqera.io/library/fastp:0.23.4--c1051f83dcae53f5' }
56+
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5e/5e81afc0a786ea4806add944eed450ef880073abc374eb8ea9bcc2b33f6bec15/data' : 'community.wave.seqera.io/library/fastp:0.24.0--39cd59724a206814' }
5757
}
5858

5959
withName: 'FASTQC' {
6060
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fd/fd39534bf298698cbe3ee4d4a6f1e73330ec4bca44c38dd9a4d06cb5ea838017/data' : 'community.wave.seqera.io/library/fastqc:0.12.1--df99cb252670875a' }
6161
}
6262

6363
withName: 'FQ_SUBSAMPLE' {
64-
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b0/b00189d4f7eed55199354a3dff8a9a535e1dfb3a2f4c97f5d0bf9e388105795e/data' : 'community.wave.seqera.io/library/fq:0.12.0--ad6857b304869ce9' }
64+
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/cb/cb160e49e56ddbf7d53ba1c8495d6f4880a3f811cc9993619b1e84e40f8ffb53/data' : 'community.wave.seqera.io/library/fq:0.12.0--256df3027a85ed7c' }
6565
}
6666

6767
withName: 'FQ_LINT' {
68-
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b0/b00189d4f7eed55199354a3dff8a9a535e1dfb3a2f4c97f5d0bf9e388105795e/data' : 'community.wave.seqera.io/library/fq:0.12.0--ad6857b304869ce9' }
68+
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/cb/cb160e49e56ddbf7d53ba1c8495d6f4880a3f811cc9993619b1e84e40f8ffb53/data' : 'community.wave.seqera.io/library/fq:0.12.0--256df3027a85ed7c' }
6969
}
7070

7171
withName: 'GFFREAD' {
@@ -81,14 +81,18 @@ process {
8181
}
8282

8383
withName: 'GUNZIP' {
84-
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4b/4bcb36d5e1fb90c8af0171a83b792ada446b04feb4ac3f26d0ce550d3c678383/data' : 'community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' }
84+
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2d/2d61820950f089a905f34756e0713b3540f615d9e566817ff050d7b824840b1c/data' : 'community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:c4619b810d01e403' }
8585
}
8686

8787
withName: 'HISAT2_ALIGN' {
8888
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/95/95a04506094435ef9cbd94b479d5cd713cd1d106d5e5718bf4410686c3d19f15/data' : 'community.wave.seqera.io/library/hisat2_samtools:aaedc5f7a0ece7e8' }
8989
}
9090

91-
withName: 'HISAT2_BUILD|HISAT2_EXTRACTSPLICESITES' {
91+
withName: 'HISAT2_BUILD' {
92+
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/95/95a04506094435ef9cbd94b479d5cd713cd1d106d5e5718bf4410686c3d19f15/data' : 'community.wave.seqera.io/library/hisat2_samtools:aaedc5f7a0ece7e8' }
93+
}
94+
95+
withName: 'HISAT2_EXTRACTSPLICESITES' {
9296
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/95/95a04506094435ef9cbd94b479d5cd713cd1d106d5e5718bf4410686c3d19f15/data' : 'community.wave.seqera.io/library/hisat2_samtools:aaedc5f7a0ece7e8' }
9397
}
9498

@@ -101,11 +105,11 @@ process {
101105
}
102106

103107
withName: 'KRAKEN2_KRAKEN2' {
104-
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/be/beba752dd6b17d3dd79b9a71dd2c1c46d09fa1e28212b6aef7c6119d68804f4a/data' : 'community.wave.seqera.io/library/kraken2_coreutils_pigz:2a28cee7c0427b32' }
108+
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/96/962fb9c0b6262e7db9970fe683c193ce3a406092341fd3e3ff6bbf2c5521c55a/data' : 'community.wave.seqera.io/library/kraken2_coreutils_pigz:70c562cae0588454' }
105109
}
106110

107111
withName: 'MULTIQC' {
108-
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6e/6e97dcafc5915f90f863e70153f96bbe47963ebfd08383454d8bcd7263696e4e/data' : 'community.wave.seqera.io/library/multiqc:1.25.1--4062a515975cacba' }
112+
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8a4a71510e6ef370a48bb155b32ad1cb00a053431986bae06f97361598c50b3/data' : 'community.wave.seqera.io/library/multiqc:1.31--e89b9d3faf1041af' }
109113
}
110114

111115
withName: 'MULTIQC_CUSTOM_BIOTYPE' {
@@ -201,11 +205,11 @@ process {
201205
}
202206

203207
withName: 'STAR_ALIGN' {
204-
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/10/101ea47973178f85ff66a34de6a7462aaf99d947d3924c27ce8a2d5a63009065/data' : 'community.wave.seqera.io/library/htslib_samtools_star_gawk:de8c848656c2c4c5' }
208+
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/57/57c051c9aae20c712608b3f2229b2a21b0c2eb297102f12f04f1d8c7643d12ba/data' : 'community.wave.seqera.io/library/htslib_samtools_star_gawk:de8c848656c2c4c5' }
205209
}
206210

207211
withName: 'STAR_GENOMEGENERATE' {
208-
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/10/101ea47973178f85ff66a34de6a7462aaf99d947d3924c27ce8a2d5a63009065/data' : 'community.wave.seqera.io/library/htslib_samtools_star_gawk:de8c848656c2c4c5' }
212+
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/57/57c051c9aae20c712608b3f2229b2a21b0c2eb297102f12f04f1d8c7643d12ba/data' : 'community.wave.seqera.io/library/htslib_samtools_star_gawk:de8c848656c2c4c5' }
209213
}
210214

211215
withName: 'STRINGTIE_STRINGTIE' {
@@ -221,7 +225,7 @@ process {
221225
}
222226

223227
withName: 'TRIMGALORE' {
224-
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/10/10e7b91ef06bdf5790120809afc8cf36aac0261b618d810c952d5afd60dd5ed2/data' : 'community.wave.seqera.io/library/cutadapt_trim-galore:2aa2fc797328573b' }
228+
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a1/a11701c614c04de6ca4a386f2bb63532826aeb7d98fd0d714a07a8db31ef5359/data' : 'community.wave.seqera.io/library/cutadapt_trim-galore_pigz:d0b730b6770575ef' }
225229
}
226230

227231
withName: 'TXIMETA_TXIMPORT' {
@@ -241,19 +245,19 @@ process {
241245
}
242246

243247
withName: 'UMITOOLS_DEDUP' {
244-
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ba/ba7c02244236db73a56ff1eb880b16c2dd53679834e1b72bb096e1f633e35644/data' : 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' }
248+
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/54/546e768a27f61fb6f9eb4b283a18981f042dee406011c7d86173eb58186bbec4/data' : 'community.wave.seqera.io/library/umi_tools_python_matplotlib_scipy_pruned:8a60fc02f4d98e7d' }
245249
}
246250

247251
withName: 'UMITOOLS_EXTRACT' {
248-
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ba/ba7c02244236db73a56ff1eb880b16c2dd53679834e1b72bb096e1f633e35644/data' : 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' }
252+
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/54/546e768a27f61fb6f9eb4b283a18981f042dee406011c7d86173eb58186bbec4/data' : 'community.wave.seqera.io/library/umi_tools_python_matplotlib_scipy_pruned:8a60fc02f4d98e7d' }
249253
}
250254

251255
withName: 'UMITOOLS_PREPAREFORRSEM' {
252-
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ba/ba7c02244236db73a56ff1eb880b16c2dd53679834e1b72bb096e1f633e35644/data' : 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' }
256+
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/54/546e768a27f61fb6f9eb4b283a18981f042dee406011c7d86173eb58186bbec4/data' : 'community.wave.seqera.io/library/umi_tools_python_matplotlib_scipy_pruned:8a60fc02f4d98e7d' }
253257
}
254258

255259
withName: 'UNTAR' {
256-
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4b/4bcb36d5e1fb90c8af0171a83b792ada446b04feb4ac3f26d0ce550d3c678383/data' : 'community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' }
260+
container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2d/2d61820950f089a905f34756e0713b3540f615d9e566817ff050d7b824840b1c/data' : 'community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:c4619b810d01e403' }
257261
}
258262

259263
// SortMeRNA does not yet have aarch64 builds conda forge. Working on it, using builds from Seqera channel for now

‎modules/local/deseq2_qc/environment.yml‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -2,12 +2,12 @@ channels:
22
- conda-forge
33
- bioconda
44
dependencies:
5-
- conda-forge::r-base=4.0.3
6-
- conda-forge::r-optparse=1.6.6
7-
- conda-forge::r-ggplot2=3.3.2
8-
- conda-forge::r-rcolorbrewer=1.1.2
5+
- conda-forge::r-base=4.4.2
6+
- conda-forge::r-optparse=1.7.5
7+
- conda-forge::r-ggplot2=3.5.1
8+
- conda-forge::r-rcolorbrewer=1.1_3
99
- conda-forge::r-pheatmap=1.0.12
10-
- bioconda::bioconductor-deseq2=1.28.0
11-
- bioconda::bioconductor-biocparallel=1.22.0
12-
- bioconda::bioconductor-tximport=1.16.0
13-
- bioconda::bioconductor-complexheatmap=2.4.2
10+
- bioconda::bioconductor-deseq2=1.46.0
11+
- bioconda::bioconductor-biocparallel=1.40.0
12+
- bioconda::bioconductor-tximport=1.34.0
13+
- bioconda::bioconductor-complexheatmap=2.22.0

‎modules/local/deseq2_qc/main.nf‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -5,8 +5,8 @@ process DESEQ2_QC {
55
// This was to avoid the pipeline failing due to package conflicts whilst creating the environment when using -profile conda
66
conda "${moduleDir}/environment.yml"
77
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8-
'https://depot.galaxyproject.org/singularity/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0' :
9-
'biocontainers/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0' }"
8+
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1d/1d425b12748ce54c44c01a535a1ef5867a6e16cbf62c43151012e893444b1673/data' :
9+
'community.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:9e75394d0bc21987' }"
1010

1111
input:
1212
path counts

‎modules/local/deseq2_qc/tests/main.nf.test‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -19,11 +19,11 @@ nextflow_process {
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then {
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assertAll(
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{ assert process.success },
22+
{ assert path(process.out.dists_txt.get(0)).exists() },
23+
{ assert path(process.out.pca_txt.get(0)).exists() },
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{ assert snapshot(
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process.out.dists_multiqc,
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process.out.dists_txt,
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process.out.pca_multiqc,
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process.out.pca_txt,
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process.out.versions
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).match() }
2929
)

‎modules/local/deseq2_qc/tests/main.nf.test.snap‎

Lines changed: 10 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -34,7 +34,7 @@
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]
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],
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"8": [
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"versions.yml:md5,60f8e4f473397a4b5d1a3dc490c93ec5"
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"versions.yml:md5,334928b64c46461488576cd735ec439c"
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],
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"dists_multiqc": [
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@@ -68,38 +68,32 @@
6868
]
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],
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"versions": [
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"versions.yml:md5,60f8e4f473397a4b5d1a3dc490c93ec5"
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"versions.yml:md5,334928b64c46461488576cd735ec439c"
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]
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}
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],
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"meta": {
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"nf-test": "0.8.4",
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"nextflow": "24.04.2"
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"nf-test": "0.9.2",
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"nextflow": "25.10.0"
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},
79-
"timestamp": "2024-06-21T11:38:08.92794"
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"timestamp": "2025-11-27T13:29:23.049264"
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},
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"parse count data correctly": {
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"content": [
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[
84-
85-
],
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[
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"deseq2.sample.dists.txt:md5,1616ce40eb58ee75640efed219c6bbec"
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],
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[
90-
84+
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],
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[
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"deseq2.pca.vals.txt:md5,4cda8e32ec39326c1350e77b4b607aad"
87+
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],
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[
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"versions.yml:md5,60f8e4f473397a4b5d1a3dc490c93ec5"
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"versions.yml:md5,334928b64c46461488576cd735ec439c"
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]
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.04.2"
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"nextflow": "25.10.0"
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},
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"timestamp": "2025-06-06T11:39:25.276180757"
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"timestamp": "2025-11-27T13:28:49.884314"
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}
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}

‎nf-test.config‎

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,10 @@ config {
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configFile "tests/nextflow.config"
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// ignore tests coming from the nf-core/modules repo
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ignore 'modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*'
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// Also ignore sentieon tests when SKIP_SENTIEON env var is set (forks/ARM)
13+
ignore System.getenv("SKIP_SENTIEON") == "true"
14+
? ['modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*', 'tests/sentieon_default.nf.test', 'subworkflows/local/align_star/tests/main.nf.test']
15+
: ['modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*']
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1417
// run all test with defined profile(s) from the main nextflow.config
1518
profile "test"

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