From 8ce628e33fe27bf4ab09a2381c2e8228d51c8c08 Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Mon, 20 May 2024 09:25:23 +0100 Subject: [PATCH] Nicer name, even for compressed files --- workflows/blobtoolkit.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/blobtoolkit.nf b/workflows/blobtoolkit.nf index 37f27f7b..3a66fe9f 100644 --- 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) { 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.fasta) { ch_fasta = Channel.value([ [ 'id': params.accession ?: file(params.fasta.replace(".gz", "")).baseName ], file(params.fasta) ]) } else { exit 1, 'Genome fasta file must be specified!' } if (params.taxon) { ch_taxon = Channel.value(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!' }