From 424dd1ad89b9020efe4551c6c710b792b8265f14 Mon Sep 17 00:00:00 2001 From: Mike Lee Date: Sun, 7 Apr 2024 07:00:32 -0700 Subject: [PATCH] Update Snakefile - fix to single-end humann3 run where the ref db needs to be explicitly specified - this wasn't always necessary, but it became so a little while back. a fix was already implemented for paired-end, but apparently i didn't catch it for single-end (and it wouldn't cause a problem unless it was the first time a workflow was run on a new system) --- .../SW_MGIllumina/workflow_code/Snakefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Metagenomics/Illumina/Workflow_Documentation/SW_MGIllumina/workflow_code/Snakefile b/Metagenomics/Illumina/Workflow_Documentation/SW_MGIllumina/workflow_code/Snakefile index 8340ab25..835638e4 100644 --- a/Metagenomics/Illumina/Workflow_Documentation/SW_MGIllumina/workflow_code/Snakefile +++ b/Metagenomics/Illumina/Workflow_Documentation/SW_MGIllumina/workflow_code/Snakefile @@ -905,7 +905,7 @@ else: humann_config --update database_folders nucleotide {params.humann_nucleotide_db_path} > /dev/null 2>&1 humann_config --update database_folders protein {params.humann_protein_db_path} > /dev/null 2>&1 - humann --input {input.R1} --output {params.output_dir} --threads {resources.cpus} --output-basename {wildcards.ID} --metaphlan-options "--bowtie2db {params.metaphlan_dir} --unclassified_estimation --add_viruses --sample_id {wildcards.ID}" --bowtie-options "--sensitive --mm" > {log} 2>&1 + humann --input {input.R1} --output {params.output_dir} --threads {resources.cpus} --output-basename {wildcards.ID} --metaphlan-options "--index mpa_vJan21_CHOCOPhlAnSGB_202103 --bowtie2db {params.metaphlan_dir} --unclassified_estimation --add_viruses --sample_id {wildcards.ID}" --bowtie-options "--sensitive --mm" > {log} 2>&1 mv {params.tmp_metaphlan} {output[3]} rm -rf {params.tmp_dir} """