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Support auto-download/build of --metaeuk_db, matching KofamScan's pattern

Status: Open.

#485 In nf-core/metatdenovo;

· erikrikarddaniel opened on Aug 29, 2026

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metatdenovo 2.0

Adopt typed parameters so booleans can be set from the command line

Status: Open.

#478 In nf-core/metatdenovo;

· erikrikarddaniel opened on Aug 26, 2026

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metatdenovo 2.0

TRANSDECODER_PREDICT breaks -resume and fails on every re-execution

Status: Open.

#477 In nf-core/metatdenovo;

· erikrikarddaniel opened on Aug 26, 2026

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metatdenovo 2.0

Add a stub-mode pipeline test to cover channel wiring without databases

Status: Open.

#476 In nf-core/metatdenovo;

· erikrikarddaniel opened on Aug 26, 2026

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metatdenovo 2.0

EUKulele's raw DIAMOND alignments are published although nothing consumes them

Status: Open.

#475 In nf-core/metatdenovo;

· erikrikarddaniel opened on Aug 26, 2026

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metatdenovo 2.0

Sorted BAM files and their indexes are published regardless of --save_bam

Status: Open.

#474 In nf-core/metatdenovo;

· erikrikarddaniel opened on Aug 26, 2026

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metatdenovo 2.0

Also write summary tables as Parquet

Status: Open.

#473 In nf-core/metatdenovo;

· erikrikarddaniel opened on Aug 25, 2026

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metatdenovo 2.0

Option to annotate only the protein-consolidated representatives

Status: Open.

#472 In nf-core/metatdenovo;

· erikrikarddaniel opened on Aug 25, 2026

test_full: writing a downloaded database to an s3:// storeDir fails, aws: command not found

Status: Open.

#471 In nf-core/metatdenovo;

· erikrikarddaniel opened on Aug 25, 2026

·  

metatdenovo 2.0

test_full cannot stage S3 database directories: aws: command not found

Status: Open.

#470 In nf-core/metatdenovo;

· erikrikarddaniel opened on Aug 25, 2026

Consolidate ORF/protein calls across multiple gene callers in mixed prokaryote/eukaryote projects

enhancementNew feature or requestNew feature or request

Status: Open.

#460 In nf-core/metatdenovo;

· erikrikarddaniel opened on Aug 12, 2026

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metatdenovo 2.0

Record featureCounts' Unassigned_NoFeatures counts in overall_stats.tsv.gz

enhancementNew feature or requestNew feature or request

Status: Open.

#451 In nf-core/metatdenovo;

· erikrikarddaniel opened on Jul 31, 2026

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metatdenovo 2.0