he accession number is in fact mutually exclusive of the yaml file

sanger-tol · May 17, 2024 · 052be1c · 052be1c
1 parent 51bf1b1
commit 052be1c
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diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -75,7 +75,7 @@
             "type": "object",
             "fa_icon": "fas fa-dna",
             "description": "Reference genome related files and options required for the workflow.",
-            "required": ["taxon", "accession", "fasta"],
+            "required": ["taxon", "fasta"],
             "properties": {
                 "taxon": {
                     "type": ["string", "integer"],

diff --git a/workflows/blobtoolkit.nf b/workflows/blobtoolkit.nf
@@ -22,7 +22,7 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
 
 // Check mandatory parameters
 if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
-if (params.fasta && params.accession) { ch_fasta = Channel.value([ [ 'id': params.accession ], params.fasta ]) } else { exit 1, 'Genome fasta file and accession must be specified!' }
+if (params.fasta) { ch_fasta = Channel.value([ [ 'id': params.accession ?: file(params.fasta).baseName ], file(params.fasta) ]) } else { exit 1, 'Genome fasta file must be specified!' }
 if (params.taxon) { ch_taxon = Channel.of(params.taxon) } else { exit 1, 'NCBI Taxon ID not specified!' }
 if (params.blastp) { ch_blastp = Channel.value([ [ 'id': file(params.blastp).baseName ], params.blastp ]) } else { exit 1, 'Diamond BLASTp database must be specified!' }
 if (params.blastx) { ch_blastx = Channel.value([ [ 'id': file(params.blastx).baseName ], params.blastx ]) } else { exit 1, 'Diamond BLASTx database must be specified!' }
@@ -32,7 +32,9 @@ if (params.fetchngs_samplesheet && !params.align) { exit 1, '--align not specifi
 
 // Create channel for optional parameters
 if (params.busco_db) { ch_busco_db = Channel.fromPath(params.busco_db) } else { ch_busco_db = Channel.empty() }
-if (params.yaml && params.accession) { ch_yaml = Channel.of([ [ 'id': params.accession ], params.yaml ]) } else { ch_yaml = Channel.empty() }
+if (params.yaml) { ch_yaml = Channel.fromPath(file(params.yaml)) } else { ch_yaml = Channel.empty() }
+if (params.yaml && params.accession) { exit 1, '--yaml cannot be provided at the same time as --accession !' }
+if (!params.yaml && !params.accession) { exit 1, '--yaml and --accession are both mising. Pick one !' }
 
 /*
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