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[Metagenomics Illumina] fix to single-end problem when running with new setup #79

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[Metagenomics Illumina] fix to single-end problem when running with new setup #79

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2 changes: 1 addition & 1 deletion Metagenomics/Illumina/Workflow_Documentation/SW_MGIllumina/workflow_code/Snakefile
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Expand Up @@ -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}
"""
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