nf-MaAsLin2

Acknowledgement

This pipeline is based on the original MaAsLin2 repo. Modifications have been made to make use of our infrastrucutre more readily. If you're here for details about the pipeline, please consider taking a look at the original repo.

Examples

====================

This is a MaAsLin2 pipeline for the Nextflow framework.

1. Four required parameters are an input merged metaphlan file, a metadata file, a project name and a base group name

2. An example input metadata file is 2-cloumn tsv file with headers

sample_name     group
AD8_10_1A       Tac_pre
AD8_10_3A       Jax_pre
AD8_10_1D       Tac_co
AD8_10_2D       Tac_co
AD8_10_3D       Tac_co
AD8_10_5D       Jax_co
AD8_11_1A       Tac_pre
AD8_11_1D       Tac_co
AD8_11_2D       Tac_co
AD8_11_3D       Jax_co
AD8_11_4A       Jax_pre
AD8_11_4D       Jax_co
AD8_11_5D       Jax_co

3. An example input metaphlan abundance profiles

sample_name	UNCLASSIFIED	Lactobacillus_johnsonii	GGB27876_SGB40310	Muribaculaceae_bacterium	Duncaniella_freteri	Ligilactobacillus_murinus	Adlercreutzia_muris	Adlercreutzia_caecimuris	Adlercreutzia_mucosicola
AD8_10_1A	12.42943	0.0	0.9643621890335738	0.0	2.7948849254256785	3.47154275066472	0.22291089609757747	0.7195498923805046	0.01243502150691652
(base) [ec2-user@ip-172-31-28-65 Maaslin]$ less  metaphlan_by_group2.tsv | cut -f1-10 | head -n 5
sample_name	UNCLASSIFIED	Lactobacillus_johnsonii	GGB27876_SGB40310	Muribaculaceae_bacterium	Duncaniella_freteri	Ligilactobacillus_murinus	Adlercreutzia_muris	Adlercreutzia_caecimuris	Adlercreutzia_mucosicola
AD8_10_1A	12.42943	0.0	0.9643621890335738	0.0	2.7948849254256785	3.47154275066472	0.22291089609757747	0.7195498923805046	0.01243502150691652
AD8_10_3A	19.04224	42.68327697691621	0.0	0.0	0.0	0.0	0.0	0.0	0.0
AD8_10_1D	6.65516	2.222596551686741	5.228421618666584	0.0	0.5258301300665145	3.9532844867036463	0.2390094525376891	0.03543369973962381	0.0005974069502992425
AD8_10_2D	14.100220000000002	9.299011762878296	3.6592790089581535	0.0	0.272534226109324	2.563172069940028	0.3113952857405082	0.011759679627562157	0.0

4. An example batch job

aws batch submit-job \
  --job-name nf-maaslin2 \
  --job-queue priority-maf-pipelines \
  --job-definition nextflow-production \
  --container-overrides command="FischbachLab/nf-maaslin2 \
"--profiles", "awsbatch", \
"--project", "TEST", \
"--group_name", "Tac_pre", \
"--input_path", "s3://nextflow-pipelines/nf-maaslin2/data/metaphlan_abundance_profiles.tsv", \
"--metadata", "s3://nextflow-pipelines/nf-maaslin2/data/metadata.tsv", \
"--output_path", "s3://genomics-workflow-core/Results/maaslin2" "

5. Command line to run on a local machine

nextflow run main.nf \
--profiles local \
--project TEST \
--group_name Tac_pre \
--input_path "s3://nextflow-pipelines/nf-maaslin2/data/metaphlan_abundance_profiles.tsv" \
--metadata "s3://nextflow-pipelines/nf-maaslin2/data/metadata.tsv" \
--output_path "s3://genomics-workflow-core/Results/maaslin2" 

6. The final output files:

s3://genomics-workflow-core/Results/maaslin2/TEST/Maaslin2_outputs/