Merge pull request #13 from sanger-tol/DLBPointon-patch-1

Fix for schema
sanger-tol · Sep 28, 2023 · 083e047 · 083e047
2 parents f170ae3 + e9609f9
commit 083e047
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Showing 3 changed files with 2 additions and 3 deletions.
diff --git a/conf/test_full.config b/conf/test_full.config
@@ -22,7 +22,6 @@ params {
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
 
     input       = "/lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_DF5033/assembly/draft/DF5033.hifiasm.noTelos.20211120/DF5033.noTelos.hifiasm.purged.noCont.noMito.fasta"
-    outdir      = "./results"
     pacbio      = "/lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_DF5033/genomic_data/nxOscSpes1/pacbio/fasta/"
     cram        = "/lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_DF5033/genomic_data/nxOscSpes1/hic-arima2/full/"
     sample      = "CurationPretextTest"

diff --git a/nextflow.config b/nextflow.config
@@ -17,7 +17,7 @@ params {
     cram                       = null
 
     // Boilerplate options
-    outdir                     = null
+    outdir                     = "results"
     tracedir                   = "${params.outdir}/pipeline_info"
     publish_dir_mode           = 'copy'
     email                      = null

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -15,7 +15,7 @@
                 "input": {
                     "type": "string",
                     "format": "file-path",
-                    "pattern": "^\\S+\\.fa$",
+                    "pattern": "^\\S+\\.fn?a(sta)?$",
                     "description": "Input fasta file",
                     "help_text": "You need the input fasta file",
                     "fa_icon": "fas fa-file-fasta"