Feature: co-assemblies submission with --mode metagenomic_assembly

assets/samplesheet_assembly_coassembly_no_coverage.csv

@@ -0,0 +1,2 @@
+id,fasta,fastq_1,fastq_2,coverage,run_accession,assembler,assembler_version
+no_coverage_paired_reads,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz;https://github.com/nf-core/test-datasets/raw/modules/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_1.fastq.gz,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz;https://github.com/nf-core/test-datasets/raw/modules/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_2.fastq.gz,,SRR3183850;SRR3183951,SPAdes,3.15

assets/samplesheet_assembly_coassembly_with_coverage.csv

@@ -0,0 +1,2 @@
+id,fasta,fastq_1,fastq_2,coverage,run_accession,assembler,assembler_version
+coassembly_sample,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz,,,45.5,SRR3183850;SRR3183951,SPAdes,3.15

assets/schema_input_assembly.json

@@ -26,9 +26,7 @@
                 "anyOf": [
                     {
                         "type": "string",
-                        "format": "file-path",
-                        "exists": true,
-                        "pattern": "^\\S+\\.(fq|fastq)(\\.gz)?$"
+                        "pattern": "^\\S+\\.(fq|fastq)(\\.gz)?(;\\S+\\.(fq|fastq)(\\.gz)?)*$"
                     },
                     {
                         "type": "string",
@@ -37,15 +35,13 @@
                 ],
                 "default": null,
                 "errorMessage": "FASTQ file must have extension '.fq' or '.fastq' (optionally gzipped)",
-                "description": "Path to single-end/paired-end forward reads in FASTQ format (optionally gzipped). Required if coverage is not provided"
+                "description": "Path to single-end/paired-end forward reads in FASTQ format (optionally gzipped). Required if coverage is not provided. For co-assemblies, semicolon-separated paths (e.g. run1_R1.fq.gz;run2_R1.fq.gz)"
             },
             "fastq_2": {
                 "anyOf": [
                     {
                         "type": "string",
-                        "format": "file-path",
-                        "exists": true,
-                        "pattern": "^\\S+\\.(fq|fastq)(\\.gz)?$"
+                        "pattern": "^\\S+\\.(fq|fastq)(\\.gz)?(;\\S+\\.(fq|fastq)(\\.gz)?)*$"
                     },
                     {
                         "type": "string",
@@ -54,7 +50,7 @@
                 ],
                 "default": null,
                 "errorMessage": "FASTQ file for reverse reads must have extension '.fq' or '.fastq' (optionally gzipped)",
-                "description": "Path to reverse reads in FASTQ format for paired-end data (optionally gzipped). Leave empty for single-end reads"
+                "description": "Path to reverse reads in FASTQ format for paired-end data (optionally gzipped). Leave empty for single-end reads. For co-assemblies, use semicolon-separated paths (e.g. run1_R2.fq.gz;run2_R2.fq.gz)"
             },
             "coverage": {
                 "anyOf": [
@@ -76,7 +72,7 @@
                 "type": "string",
                 "pattern": "^\\S+$",
                 "errorMessage": "Accession must be provided and cannot contain spaces",
-                "description": "ENA run accession for the reads used to generate the metagenomic assembly. Reads must already be submitted to ENA",
+                "description": "ENA run accession(s) for the reads used to generate the metagenomic assembly. Reads must already be submitted to ENA. For co-assemblies, use semicolon-separated values (e.g. ERR000001;ERR000002)",
                 "meta": ["run_accession"]
             },
             "assembler": {