From d36b980c57d29c5bd64fc8be6b59da82f06b06e6 Mon Sep 17 00:00:00 2001 From: Peter Kruczkiewicz Date: Fri, 7 Jul 2023 13:51:17 -0500 Subject: [PATCH] Remove/replace references to GUNZIP_NCBI_FLU_FASTA --- workflows/illumina.nf | 1 - workflows/nanopore.nf | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/workflows/illumina.nf b/workflows/illumina.nf index 34f51f9..663bf4d 100644 --- a/workflows/illumina.nf +++ b/workflows/illumina.nf @@ -16,7 +16,6 @@ ch_influenza_metadata = file(params.ncbi_influenza_metadata) include { IRMA } from '../modules/local/irma' include { CHECK_SAMPLE_SHEET } from '../modules/local/check_sample_sheet' include { SUBTYPING_REPORT } from '../modules/local/subtyping_report' -include { GUNZIP_NCBI_FLU_FASTA } from '../modules/local/misc' include { BLAST_MAKEBLASTDB } from '../modules/local/blast_makeblastdb' include { BLAST_BLASTN } from '../modules/local/blastn' include { CAT_ILLUMINA_FASTQ } from '../modules/local/cat_illumina_fastq' diff --git a/workflows/nanopore.nf b/workflows/nanopore.nf index 2dd21bd..be3f1e9 100644 --- a/workflows/nanopore.nf +++ b/workflows/nanopore.nf @@ -142,7 +142,7 @@ workflow NANOPORE { ch_ref_fasta = file(params.ref_db, type: 'file') CHECK_REF_FASTA(ch_ref_fasta) ch_versions = ch_versions.mix(CHECK_REF_FASTA.out.versions) - CAT_DB(GUNZIP_NCBI_FLU_FASTA.out.fna, CHECK_REF_FASTA.out.fasta) + CAT_DB(ZSTD_DECOMPRESS_FASTA.out.file, CHECK_REF_FASTA.out.fasta) ch_input_ref_db = CAT_DB.out.fasta }