From 147084570414029e607d12a0fc58401827adfbcb Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Thu, 28 Sep 2023 13:51:39 +0100 Subject: [PATCH 1/3] Fix for schema --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index a3c4e77..6a3b80d 100755 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -15,7 +15,7 @@ "input": { "type": "string", "format": "file-path", - "pattern": "^\\S+\\.fa$", + "pattern": "^\\S+\\.fa?sta$", "description": "Input fasta file", "help_text": "You need the input fasta file", "fa_icon": "fas fa-file-fasta" From 64ce40aa91c71b0e2b852f09f0d65a15fc17fc2e Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Thu, 28 Sep 2023 13:58:50 +0100 Subject: [PATCH 2/3] Fixes --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 6a3b80d..fecc160 100755 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -15,7 +15,7 @@ "input": { "type": "string", "format": "file-path", - "pattern": "^\\S+\\.fa?sta$", + "pattern": "^\\S+\\.fn?a(sta)?$", "description": "Input fasta file", "help_text": "You need the input fasta file", "fa_icon": "fas fa-file-fasta" From e9609f91bdd2fb4fb02c1adc7dbec01bd58bd179 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Thu, 28 Sep 2023 14:12:16 +0100 Subject: [PATCH 3/3] Fixes for LSF --- conf/test_full.config | 1 - nextflow.config | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/conf/test_full.config b/conf/test_full.config index 71fc824..3608708 100755 --- 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 index a1ec9d8..325ab59 100755 --- 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