From b146852fe0230c628d1eab5c3d70b8aceadee53b Mon Sep 17 00:00:00 2001 From: FrancescoSantini Date: Wed, 21 Aug 2024 16:47:05 +0200 Subject: [PATCH] added resource request for AWS --- snakefile.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/snakefile.py b/snakefile.py index e6e146c..b02766f 100644 --- a/snakefile.py +++ b/snakefile.py @@ -256,6 +256,8 @@ def lookup(column, predicate, fields=[]): gtf = GTF_FILE output: os.path.join(OUTPUT_DIR, 'input_annotation_stats.tsv') + resources: + mem_mb = config['execution']['rules']['check_annotation_files']['memory'] log: os.path.join(LOG_DIR, 'check_annotation_files.log') shell: "{RSCRIPT_EXEC} {SCRIPTS_DIR}/validate_input_annotation.R {input.gtf} {input.cdna} {input.dna} {OUTPUT_DIR} >> {log} 2>&1" @@ -417,7 +419,8 @@ def hisat2_file_arguments(args): output: os.path.join(MAPPED_READS_DIR, 'hisat2', '{sample}_Aligned.sortedByCoord.out.bam') resources: - mem_mb = config['execution']['rules']['hisat2_map']['memory'] + mem_mb = config['execution']['rules']['hisat2_map']['memory'], + disk_mb=lambda wc, input: max(3 * input.size_mb, config['execution']['rules']['hisat2_map']['disk_mb']) params: samfile = lambda wildcards: os.path.join(MAPPED_READS_DIR, 'hisat2', "_".join([wildcards.sample, 'Aligned.out.sam'])), index_dir = rules.hisat2_index.params.index_directory,