Skip to content

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

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
AstrobioMike wants to merge 1 commit into
base: metagenomics
Choose a base branch
from
Draft

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

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion Metagenomics/Illumina/Workflow_Documentation/SW_MGIllumina/workflow_code/Snakefile
View file
Open in desktop
Original file line number Diff line number Diff line change
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}
"""
Expand Down