Fix nf-test snapshot failures for ARM/amd64 compatibility and seqkit 2.13.0

- Exclude KRAKEN2 from versions snapshot in raw input stub test to fix
  ARM vs amd64 version mismatch (kraken2 2.1.5 vs 2.1.6)
- Update remove_ribo_rna snap for seqkit/replace 2.13.0 which outputs
  .fasta (uncompressed) instead of .fasta.gz

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: Elad Herz

tests/contaminant_screening_input.nf.test

@@ -139,7 +139,7 @@ nextflow_pipeline {
                 { assert workflow.success },
                 { assert snapshot(
                     workflow.trace.succeeded().size(),
-                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"),
+                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow").findAll { it.key != "KRAKEN2" },
                     stable_name,
                     stable_path
                 ).match() }

tests/contaminant_screening_input.nf.test.snap

@@ -30,10 +30,6 @@
                 "GUNZIP_GTF": {
                     "gunzip": 1.13
                 },
-                "KRAKEN2": {
-                    "kraken2": "2.1.6",
-                    "pigz": 2.8
-                },
                 "SAMTOOLS_FAIDX": {
                     "samtools": "1.23.1"
                 },

tests/remove_ribo_rna.nf.test.snap

@@ -76,8 +76,8 @@
                 "pipeline_info",
                 "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml",
                 "seqkit",
-                "seqkit/smr_v4.3_fast_db_dna_converted.fasta.gz",
-                "seqkit/smr_v4.3_fast_db_prefixed.fasta.gz",
+                "seqkit/smr_v4.3_fast_db_dna_converted.fasta",
+                "seqkit/smr_v4.3_fast_db_prefixed.fasta",
                 "trimgalore",
                 "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt",
                 "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt",
@@ -89,8 +89,8 @@
                 "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt"
             ],
             [
-                "smr_v4.3_fast_db_dna_converted.fasta.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
-                "smr_v4.3_fast_db_prefixed.fasta.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                "smr_v4.3_fast_db_dna_converted.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "smr_v4.3_fast_db_prefixed.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "timestamp": "2026-04-22T17:21:48.312879133",