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Chunk SanntiS - and "sync" inputs for this
This is an attempt to make reduce SanntiS runtime and memory more manageable. The input contigs, their proteins and interproscan annotations are "synced" not with a bespoke script. This should make SanntiS resource usage more predictable.
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‎tests/assembly_erz101.fasta.gz‎

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‎tests/default.nf.test.snap‎

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{
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"-profile test": {
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"content": [
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{
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"ANTISMASH_ANTISMASH": {
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"antismash": "8.0.1",
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"CONCATENATE_INTERPROSCAN_TSV": {
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"pigz": "2.3.4"
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},
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"CONCATENATE_SANNTIS_GFFS": {
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"python": "3.13.1"
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},
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"CREATE_GFF_SUMMARY": {
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"mgnify-pipelines-toolkit": "1.4.9"
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},
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"seqkit": "v2.10.0",
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"samtools": "1.22.1+htslib-1.22.1"
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},
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"FILTER_IPS_AND_FAA_BY_CONTIGS": {
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"seqkit": "2.13.0",
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"python": "3.14.3"
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},
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"FIND_UNPIGZ": {
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"find": "4.6.0",
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"pigz": 2.8
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"qc_failed_assemblies.csv"
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],
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[
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"ERZ101_annotation_summary.gff.gz:md5,76972e908b4d8272614fbe079d1b106d",
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"ERZ101_annotation_summary.gff.gz.csi:md5,6373535e5e29235e1a74919d299cd730",
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"ERZ101_annotation_summary.gff.gz:md5,1dfb47ffc087a1f40c77afe955027a9e",
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"ERZ101_annotation_summary.gff.gz.csi:md5,d87619e95adab1761233f9ba24ca7f80",
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"ERZ101_annotation_summary.gff.gz.gzi:md5,ae516cdccf54e18c35d9d77c7aae27f4",
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"ERZ101_predicted_cds.gff.gz:md5,8449d2fa579a5c8d188b2d13a09439c4",
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"ERZ101_dbcan_cgc.gff.gz:md5,e14511869398914ec5ec9037ae60f7b0",
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"ERZ101_predicted_cds.gff.gz:md5,aa149f822f5c05de1c63674a22f911d4",
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"ERZ101_dbcan_cgc.gff.gz:md5,83e22b309e638d71766423f3cc7ad498",
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"ERZ101_dbcan_overview.tsv.gz:md5,71857c4ba58ecf8345838f2f2aef11cb",
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"ERZ101_dbcan_standard_out.tsv.gz:md5,6be9ab29b289ff46cc6e4b6fe48dc3d7",
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"ERZ101_dbcan_sub_hmm.tsv.gz:md5,b9813dc2c2c30d062597f6ff81807706",
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"ERZ101_dbcan_sub_hmm.tsv.gz:md5,05bc3a17c1ffcd562352bf10cc4d8da9",
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"ERZ101_dbcan_substrates.tsv.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
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"ERZ101_emapper_annotations.tsv.gz:md5,acf16652adebcb33083edd74c5ec6e5f",
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"ERZ101_emapper_seed_orthologs.tsv.gz:md5,57c36dd24cfd371f6a183fcd8cc85619",
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"ERZ101_pfam_summary.tsv.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474",
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"ERZ101_proteins2rhea.tsv.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
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"ERZ101_proteins2rhea.tsv.gz.gzi:md5,c2cb56f4c5bf656faca0986e7eba0308",
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"ERZ101_antismash_summary.tsv.gz:md5,6ad987c8844dc8cf1ef764afca708c12",
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"ERZ101_antismash_summary.tsv.gz:md5,0fd7d1a0e04f0a25a8e49a697c986a4f",
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"ERZ101_antismash_summary.tsv.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474",
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"ERZ101_dram.html.gz:md5,65198bf5083e96a1e00861290586a0c4",
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"ERZ101_dram.tsv.gz:md5,b913fe1ba596ac43f9a38058c3aae645",
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"ERZ101_kegg_modules_summary.tsv.gz:md5,9d9859bfbbfac5b1708b6472f7eb74bb",
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"ERZ101_kegg_modules_summary.tsv.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474",
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"ERZ101_sanntis.gff.gz:md5,df19e1b84ba6f691d20c72b397c88abf",
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"ERZ101_filtered_contigs.fasta.gz:md5,6499031bc92e9dd14320dc30de65b438",
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"ERZ101_filtered_contigs.fasta.gz.fai:md5,7a69e27810bebf9e31e84bc9b6d62206",
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"ERZ101_filtered_contigs.fasta.gz.gzi:md5,4e8f724db1539b04d8cde5564f0b471c",
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"ERZ101_quast_stats.tsv.gz:md5,94b537397fa8207f31e84d798eca4f67",
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"ERZ101_filtered_contigs.fasta.gz:md5,010fd0b578bdd9629e9a9b41e8b5bbd6",
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"ERZ101_filtered_contigs.fasta.gz.fai:md5,57034897e5827c1dba986c70145a1d63",
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"ERZ101_filtered_contigs.fasta.gz.gzi:md5,5737309e5668e4669c50a0a7f3c7ff0b",
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"ERZ101_quast_stats.tsv.gz:md5,f1c11d01769d2f12c567067c0f732864",
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"ERZ101_aligned_to_contaminant.tsv.gz:md5,bf678dade1ff3067918b61ce0d4225e6",
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"ERZ101_aligned_to_human.tsv.gz:md5,515849d5bcd7dfbdb518539785d47f50",
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"ERZ101.html:md5,e56d9f9358ef11fc76a5c4d95bcea909",
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"ERZ101.krona.txt.gz:md5,e8f24f3ddbf7289920fae9f28ab185c8",
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"ERZ101_contigs_taxonomy.tsv.gz:md5,79cd8563ff9bca613332d1a516f0ef3e",
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"ERZ101_contigs_taxonomy.tsv.gz:md5,3f110e2b35b9b2c79be1607c51b27ecf",
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"ERZ102_annotation_summary.gff.gz:md5,fbbaf2729dc18319f9ee628c28202b24",
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"ERZ102_annotation_summary.gff.gz.csi:md5,227cc48ce8973f38f00dd7bd67365899",
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"ERZ102_annotation_summary.gff.gz.gzi:md5,ae516cdccf54e18c35d9d77c7aae27f4",
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"analysed_assemblies.csv:md5,333c3997aa4621cf3a644719e9021296",
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"samplesheet_dram.tsv.gz:md5,d9509874f9f6bbc2ab165106655fbce1",
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"multiqc_citations.txt:md5,2d1a8ef8ba06c7eada06ab3e96552ea4",
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"multiqc_general_stats.txt:md5,214026c97163f61612fc28449b589f97",
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"multiqc_general_stats.txt:md5,8b5ca1d9ddb8883eac63fffefd2ae6b8",
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"multiqc_host_decontamination_table.txt:md5,b8d06985826c0451c759e08382db2347",
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"multiqc_host_decontamination_table_table.txt:md5,b8d06985826c0451c759e08382db2347",
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"multiqc_human_decontamination_table.txt:md5,f8bc5f4b45b46d49826e5d8207a3b8f2",
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"multiqc_human_decontamination_table_table.txt:md5,f8bc5f4b45b46d49826e5d8207a3b8f2",
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"multiqc_quast.txt:md5,d8600bbb835979a7817be9827ff85be2",
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"multiqc_quast.txt:md5,dc380d5fca13b91b7c21552ba8cd9f70",
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"quast_num_contigs.txt:md5,a078f48987914adbb249f0d8382f31f1",
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"quast_table.txt:md5,be0aea9b4cf84382aa6dc71787f4203a",
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"quast_table.txt:md5,4dfa7d5c1a3715c24c29d1fe8c458319",
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"qc_failed_assemblies.csv:md5,3292564aa6122920901d9bb724447ad4"
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]
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],
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"timestamp": "2026-03-09T09:26:09.063484904",
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.10.3"
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},
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"timestamp": "2026-02-25T22:19:26.921976"
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"nf-test": "0.9.4",
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"nextflow": "25.10.0"
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}
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}
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}

‎tests/test_samplesheet.csv‎

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sample,assembly_fasta,contaminant_reference,human_reference,phix_reference
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ERZ101,https://github.com/EBI-Metagenomics/assembly-analysis-pipeline/raw/refs/heads/main/tests/assembly_erz101.fasta.gz,contamination,human,
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ERZ102,https://github.com/EBI-Metagenomics/assembly-analysis-pipeline/raw/refs/heads/main/tests/assembly_erz102.fasta.gz,,,
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ERZ666,https://github.com/EBI-Metagenomics/assembly-analysis-pipeline/raw/refs/heads/main/tests/assembly_qc_fail_length_filtered.fasta.gz,,,
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ERZ999,https://github.com/EBI-Metagenomics/assembly-analysis-pipeline/raw/refs/heads/main/tests/assembly_qc_fail_n_bases.fasta.gz,,,
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ERZ101,https://github.com/EBI-Metagenomics/assembly-analysis-pipeline/raw/refs/heads/feature/chunk-contigs-and-ips/tests/assembly_erz101.fasta.gz,contamination,human,
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ERZ102,https://github.com/EBI-Metagenomics/assembly-analysis-pipeline/raw/refs/heads/feature/chunk-contigs-and-ips/tests/assembly_erz102.fasta.gz,,,
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ERZ666,https://github.com/EBI-Metagenomics/assembly-analysis-pipeline/raw/refs/heads/feature/chunk-contigs-and-ips/tests/assembly_qc_fail_length_filtered.fasta.gz,,,
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ERZ999,https://github.com/EBI-Metagenomics/assembly-analysis-pipeline/raw/refs/heads/feature/chunk-contigs-and-ips/tests/assembly_qc_fail_n_bases.fasta.gz,,,

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