From 633026cfd8983af75568e2879a966f56b0e74a53 Mon Sep 17 00:00:00 2001 From: Jakub Vasicek Date: Thu, 16 May 2024 15:29:18 +0200 Subject: [PATCH] option: keep only MANE select transcripts --- Snakefile | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/Snakefile b/Snakefile index 17db45d..82f6c6a 100644 --- a/Snakefile +++ b/Snakefile @@ -74,9 +74,9 @@ rule download_reference_proteome: rule reference_filter_format: input: fasta="data/fasta/Homo_sapiens.GRCh38.pep.all.fa", - tr=expand('{proxy}', proxy=["data/transcripts_reference_" + str(config['ensembl_release']) + '_MANE_Select.csv'] if config['only_MANE_select'] else []) + tr=expand('{proxy}', proxy=["data/transcripts_reference_" + str(config['ensembl_release']) + '.csv'] if config['only_MANE_select'] else []) output: - "data/fasta/ensembl_reference_proteinDB_" + str(config['ensembl_release']) + "_tagged.fa" + "data/fasta/ensembl_reference_proteinDB_" + str(config['ensembl_release']) + "_tagged" + ('_MANE_Select' if config['only_MANE_select'] else '') + ".fa" conda: "envs/prohap.yaml" params: tr_filter=('-tr data/transcripts_reference_' + str(config['ensembl_release']) + '_MANE_Select.csv') if config['only_MANE_select'] else '' @@ -88,7 +88,7 @@ rule default_transcript_list: ref_fasta="data/fasta/ensembl_reference_proteinDB_" + str(config['ensembl_release']) + "_tagged.fa", annot="data/gtf/" + config['annotationFilename'] + ".db" output: - "data/transcripts_reference_" + str(config['ensembl_release']) + ('_MANE_Select' if config['only_MANE_select'] else '') + ".csv" + temp("data/transcripts_reference_" + str(config['ensembl_release']) + ".csv") params: MANE=int(config['only_MANE_select']) shell: @@ -96,7 +96,7 @@ rule default_transcript_list: rule reference_remove_stop: input: - "data/fasta/ensembl_reference_proteinDB_" + str(config['ensembl_release']) + "_tagged.fa" + "data/fasta/ensembl_reference_proteinDB_" + str(config['ensembl_release']) + "_tagged" + ('_MANE_Select' if config['only_MANE_select'] else '') + ".fa" output: temp("data/fasta/ensembl_reference_proteinDB_" + str(config['ensembl_release']) + "_clean.fa") conda: "envs/prohap.yaml"