sr320 · Oct 17, 2026 · Oct 12, 2026 · Oct 12, 2026 · Oct 12, 2026 · Oct 12, 2026
diff --git a/config/PAYTON2017_HAB_AMINUTUM.config b/config/PAYTON2017_HAB_AMINUTUM.config
@@ -0,0 +1,66 @@
+/*
+ * AREE :: run configuration for PAYTON2017_HAB_AMINUTUM (PRJEB18614)
+ *
+ * Payton et al. 2017, Sci Rep 7:3480 (doi:10.1038/s41598-017-03797-4);
+ * ArrayExpress E-MTAB-5345. Adult gill, 6 days on the paralytic-shellfish-
+ * toxin producer Alexandrium minutum (HAB, ~400 cells/mL) vs the non-toxic
+ * dinoflagellate Heterocapsa triquetra, 3 tanks per diet; gill of 6 oysters
+ * pooled per diet every 4 h for 52 h (13 libraries per diet), each library
+ * sequenced on two lanes (52 runs).
+ *
+ *   nextflow run workflows/rnaseq -config config/PAYTON2017_HAB_AMINUTUM.config \
+ *     -profile local,workstation
+ *
+ * Every run gets its own sample_id (the run accession), and
+ * replicate_unit = sample_accession sums each library's two lanes before
+ * DESeq2, so the replicates are the 13 libraries per diet, not 26 lanes.
+ *
+ *   aree fetch-samplesheet --bioproject PRJEB18614 --study PAYTON2017_HAB_AMINUTUM \
+ *     --label-field run_accession --label-pattern '^(?P<run>ERR\d+)$' \
+ *     --condition-attribute "growth condition" --attribute "organism part"
+ */
+
+includeConfig 'base.config'
+
+params {
+    mode = 'raw_reanalysis'
+
+    rnaseq {
+        study_id           = 'PAYTON2017_HAB_AMINUTUM'
+        // Null so --comparison_id on the command line takes effect.
+        comparison_id      = null
+        genome_assembly    = 'GCF_963853765.1'
+        annotation_version = 'GCF_963853765.1-RS_2024_06'
+        processed_results  = null
+    }
+
+    comparison_id = 'alexandrium_vs_heterocapsa_6d'
+
+    sample_sheet = 'data/studies/PAYTON2017_HAB_AMINUTUM/samplesheet.tsv'
+
+    control_level   = 'Heterocapsa_triquetra'
+    treatment_level = 'Alexandrium_minutum'
+
+    // Two sequencing lanes per library: sum them, so a library is one replicate.
+    replicate_unit  = 'sample_accession'
+
+    // FASTQ are not committed. Verify against ENA's MD5s:
+    //   awk -F'\t' 'NR>1 {print $4"  "$1"_"$2".fastq.gz"}' \
+    //     data/studies/PAYTON2017_HAB_AMINUTUM/fastq_manifest.tsv > md5sums.txt && md5sum -c md5sums.txt
+    reads = 'data/raw/PAYTON2017_HAB_AMINUTUM/ERR*_{1,2}.fastq.gz'
+
+    transcript_fasta = 'data/reference/GCF_963853765.1/rna.fna'
+    gtf              = 'data/reference/GCF_963853765.1/genomic.gtf'
+    tx2gene          = 'data/reference/GCF_963853765.1/tx2gene.tsv'
+    salmon_index     = null
+
+    outdir = 'results/rnaseq/PAYTON2017_HAB_AMINUTUM'
+}
+
+process {
+    // 52 HiSeq 2500 2x100 runs (26 libraries x 2 lanes). Sized for a 16 GB machine.
+    withName: 'SALMON_INDEX' { cpus = 8;  memory = '12 GB'; time = '4h'  }
+    withName: 'SALMON_QUANT' { cpus = 8;  memory = '12 GB'; time = '2h'  }
+    withName: 'TRIM_FASTP'   { cpus = 4;  memory = '8 GB';  time = '2h'  }
+    withName: 'FASTQC'       { cpus = 2;  memory = '4 GB';  time = '1h'  }
+}
diff --git a/data/studies/PAYTON2017_HAB_AMINUTUM/E-MTAB-5345.sdrf.txt b/data/studies/PAYTON2017_HAB_AMINUTUM/E-MTAB-5345.sdrf.txt
diff --git a/data/studies/PAYTON2017_HAB_AMINUTUM/ena_provenance.json b/data/studies/PAYTON2017_HAB_AMINUTUM/ena_provenance.json
@@ -0,0 +1,89 @@
+{
+  "study_id": "PAYTON2017_HAB_AMINUTUM",
+  "bioproject": "PRJEB18614",
+  "date_generated": "2026-10-11",
+  "generated_by": "src/intake/ena_samplesheet.py",
+  "queries": {
+    "run_report": "https://www.ebi.ac.uk/ena/portal/api/filereport?accession=PRJEB18614&result=read_run&fields=run_accession,sample_accession,sample_alias,experiment_accession,library_strategy,library_layout,library_selection,instrument_model,read_count,base_count,fastq_ftp,fastq_md5,fastq_bytes",
+    "sample_xml": "https://www.ebi.ac.uk/ena/browser/api/xml/<sample_accessions>"
+  },
+  "condition_attributes": [
+    "growth condition"
+  ],
+  "n_runs": 52,
+  "n_samples": 26,
+  "library_strategies": [
+    "RNA-Seq"
+  ],
+  "library_layouts": [
+    "PAIRED"
+  ],
+  "group_sizes": {
+    "Alexandrium_minutum": 26,
+    "Heterocapsa_triquetra": 26
+  },
+  "min_group_size": 26,
+  "total_fastq_bytes": 274235903248,
+  "outputs": {
+    "data/studies/PAYTON2017_HAB_AMINUTUM/samplesheet.tsv": "fa6584202b67c3afaf73047fb9b0fd4baed0b44d0ecda6a991ee7dae160a15ba",
+    "data/studies/PAYTON2017_HAB_AMINUTUM/fastq_manifest.tsv": "9ff5f98fa0c9bff25ca61624366bca783796e82046eafa0fdf8bf2feaf409be2"
+  },
+  "run_labels": {
+    "field": "run_accession",
+    "pattern": "^(?P<run>ERR\\d+)$",
+    "labels": {
+      "ERR1758942": "ERR1758942",
+      "ERR1758943": "ERR1758943",
+      "ERR1758944": "ERR1758944",
+      "ERR1758945": "ERR1758945",
+      "ERR1758946": "ERR1758946",
+      "ERR1758947": "ERR1758947",
+      "ERR1758948": "ERR1758948",
+      "ERR1758949": "ERR1758949",
+      "ERR1758950": "ERR1758950",
+      "ERR1758951": "ERR1758951",
+      "ERR1758952": "ERR1758952",
+      "ERR1758953": "ERR1758953",
+      "ERR1758954": "ERR1758954",
+      "ERR1758955": "ERR1758955",
+      "ERR1758956": "ERR1758956",
+      "ERR1758957": "ERR1758957",
+      "ERR1758958": "ERR1758958",
+      "ERR1758959": "ERR1758959",
+      "ERR1758960": "ERR1758960",
+      "ERR1758961": "ERR1758961",
+      "ERR1758962": "ERR1758962",
+      "ERR1758963": "ERR1758963",
+      "ERR1758964": "ERR1758964",
+      "ERR1758965": "ERR1758965",
+      "ERR1758966": "ERR1758966",
+      "ERR1758967": "ERR1758967",
+      "ERR1758968": "ERR1758968",
+      "ERR1758969": "ERR1758969",
+      "ERR1758970": "ERR1758970",
+      "ERR1758971": "ERR1758971",
+      "ERR1758972": "ERR1758972",
+      "ERR1758973": "ERR1758973",
+      "ERR1758974": "ERR1758974",
+      "ERR1758975": "ERR1758975",
+      "ERR1758976": "ERR1758976",
+      "ERR1758977": "ERR1758977",
+      "ERR1758978": "ERR1758978",
+      "ERR1758979": "ERR1758979",
+      "ERR1758980": "ERR1758980",
+      "ERR1758981": "ERR1758981",
+      "ERR1758982": "ERR1758982",
+      "ERR1758983": "ERR1758983",
+      "ERR1758984": "ERR1758984",
+      "ERR1758985": "ERR1758985",
+      "ERR1758986": "ERR1758986",
+      "ERR1758987": "ERR1758987",
+      "ERR1758988": "ERR1758988",
+      "ERR1758989": "ERR1758989",
+      "ERR1758990": "ERR1758990",
+      "ERR1758991": "ERR1758991",
+      "ERR1758992": "ERR1758992",
+      "ERR1758993": "ERR1758993"
+    }
+  }
+}
diff --git a/data/studies/PAYTON2017_HAB_AMINUTUM/fastq_manifest.tsv b/data/studies/PAYTON2017_HAB_AMINUTUM/fastq_manifest.tsv
@@ -0,0 +1,105 @@
+run_accession	mate	url	md5	bytes
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