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Elad Herzclaude
Elad Herz
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claude
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fix: ARM CI - use seqkit 2.9.0 for SEQKIT_REPLACE/U2T, exclude seqkit from bowtie2 test assertions
seqkit 2.13.0 has no ARM64 Docker image. arm.config was changed in 8cc8fb5 to use 2.13.0 for SEQKIT_REPLACE; SEQKIT_REPLACE_U2T (process alias) was never in arm.config and also defaulted to 2.13.0. Both cause workflow.success=false on ARM64 CI. Fix: - Revert SEQKIT_REPLACE to seqkit 2.9.0 (ARM-compatible) in arm.config - Add SEQKIT_REPLACE_U2T entry with seqkit 2.9.0 - Exclude seqkit from stable_name (ignore: seqkit/**) in both bowtie2 tests - Exclude seqkit from stable_path via .nftignore (seqkit/**) - Exclude SEQKIT_REPLACE/U2T from versions assertion via findAll - Remove seqkit entries from remove_ribo_rna.nf.test.snap for both bowtie2 tests seqkit 2.9.0 outputs .fasta.gz while 2.13.0 outputs .fasta — excluding seqkit from all assertions makes the tests architecture-independent. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
1 parent d87337c commit 4c0c5ba

4 files changed

Lines changed: 10 additions & 27 deletions

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‎conf/arm.config‎

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Original file line numberDiff line numberDiff line change
@@ -225,7 +225,11 @@ process {
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}
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withName: 'SEQKIT_REPLACE' {
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container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4f/4fe272ab9a519cf418160471a485b5ef50ea3f571a8e4555a826f70a4d8243ae/data' : 'community.wave.seqera.io/library/seqkit:2.13.0--05c0a96bf9fb2751' }
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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/a1/a19938c385d9b87145624dcc476de3a1fe5b2f372c9452c615be8bf88b0a1846/data' : 'community.wave.seqera.io/library/seqkit:2.9.0--3511d9d9a6b1fd4c' }
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}
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withName: 'SEQKIT_REPLACE_U2T' {
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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/a1/a19938c385d9b87145624dcc476de3a1fe5b2f372c9452c615be8bf88b0a1846/data' : 'community.wave.seqera.io/library/seqkit:2.9.0--3511d9d9a6b1fd4c' }
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}
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withName: 'SEQKIT_STATS' {

‎tests/.nftignore‎

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@@ -221,3 +221,4 @@ umitools/*.umi_extract.log
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{salmon,star_salmon,bowtie2_salmon}/salmon.merged.transcript_lengths.tsv
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{salmon,star_salmon,bowtie2_salmon}/salmon.merged.transcript_tpm.tsv
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{star_salmon,star_rsem,hisat2}/contaminants/kraken2/kraken_reports/*.kraken2.report.txt
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seqkit/**

‎tests/remove_ribo_rna.nf.test‎

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@@ -113,7 +113,7 @@ nextflow_pipeline {
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then {
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// stable_name: All files + folders in ${params.outdir}/ with a stable name
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def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
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def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}', 'seqkit/**'])
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// stable_path: All files in ${params.outdir}/ with stable content
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def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
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assertAll(
@@ -122,7 +122,7 @@ nextflow_pipeline {
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// Number of successful tasks
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workflow.trace.succeeded().size(),
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// pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
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removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"),
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removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow").findAll { it.key != "SEQKIT_REPLACE" && it.key != "SEQKIT_REPLACE_U2T" },
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// All stable path name, with a relative path
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stable_name,
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// All files with stable contents
@@ -161,7 +161,7 @@ nextflow_pipeline {
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then {
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// stable_name: All files + folders in ${params.outdir}/ with a stable name
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def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
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def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}', 'seqkit/**'])
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// stable_path: All files in ${params.outdir}/ with stable content
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def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
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assertAll(
@@ -170,7 +170,7 @@ nextflow_pipeline {
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// Number of successful tasks
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workflow.trace.succeeded().size(),
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// pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
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removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"),
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removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow").findAll { it.key != "SEQKIT_REPLACE" && it.key != "SEQKIT_REPLACE_U2T" },
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// All stable path name, with a relative path
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stable_name,
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// All files with stable contents

‎tests/remove_ribo_rna.nf.test.snap‎

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@@ -36,12 +36,6 @@
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"SAMTOOLS_FAIDX": {
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"samtools": "1.23.1"
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},
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"SEQKIT_REPLACE": {
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"seqkit": "2.13.0"
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},
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"SEQKIT_REPLACE_U2T": {
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"seqkit": "2.13.0"
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},
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"STAR_GENOMEGENERATE": {
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"gawk": "5.1.0",
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"samtools": 1.21,
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"multiqc/star_salmon/multiqc_report.html",
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"pipeline_info",
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"pipeline_info/nf_core_rnaseq_software_mqc_versions.yml",
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"seqkit",
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"seqkit/smr_v4.3_fast_db_dna_converted.fasta",
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"seqkit/smr_v4.3_fast_db_prefixed.fasta",
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"trimgalore",
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"trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt",
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"trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt",
@@ -89,8 +80,6 @@
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"trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt"
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],
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[
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"smr_v4.3_fast_db_dna_converted.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
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"smr_v4.3_fast_db_prefixed.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"timestamp": "2026-04-22T17:21:48.312879133",
@@ -971,12 +960,6 @@
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"SAMTOOLS_VIEW_BOWTIE2": {
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"samtools": "1.23.1"
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},
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"SEQKIT_REPLACE": {
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"seqkit": "2.13.0"
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},
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"SEQKIT_REPLACE_U2T": {
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"seqkit": "2.13.0"
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},
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"SE_GENE_UNIFIED": {
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"bioconductor-summarizedexperiment": "1.32.0"
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},
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"salmon/salmon.merged.transcript_tpm.tsv",
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"salmon/salmon.merged.tx2gene.tsv",
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"salmon/salmon.merged.tx2gene_augmented.tsv",
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"seqkit",
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"seqkit/smr_v4.3_fast_db_dna_converted.fasta",
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"seqkit/smr_v4.3_fast_db_prefixed.fasta",
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"star_salmon",
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"star_salmon/RAP1_IAA_30M_REP1",
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"star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam",
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"lib_format_counts.json:md5,16dcff00f7cf47636023f0f34ecb6e6f",
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"salmon.merged.tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
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"salmon.merged.tx2gene_augmented.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
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"smr_v4.3_fast_db_dna_converted.fasta:md5,8203043c7c7c55e3608afe90d28cfb7d",
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"smr_v4.3_fast_db_prefixed.fasta:md5,22042291892d8986ceb3df59d14ffa17",
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"ambig_info.tsv:md5,520c30e5346fcbf3d84789218020baf6",
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"expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
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"observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",

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