Taxprofiler.md

nf-core/taxprofiler is a Nextflow workflow to run multiple profiling tools at once.

To run it you will need:

• To be able to run Nextflow
• A set of databases for the tools you want to run, and a corresponding CSV file to run the pipeline

tool,db_name,db_params,db_path
kraken2,db1,--quick,/qib/platforms/Informatics/transfer/outgoing/databases/kraken2/benlangmead/k2_standard_20230314/
centrifuge,2019,,/qib/platforms/Informatics/transfer/outgoing/databases/centrifuge/centrigufe_2019
kaiju,2021-nr-euk,,/qib/platforms/Informatics/transfer/outgoing/databases/kaiju/2021-nr-euk
metaphlan,Jan21,,/qib/platforms/Informatics/transfer/outgoing/databases/metaphlan4/mpa_vJan21

• The FASTQ files to be profiled, and a corresponding samplesheet:

sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta
Sample1,ERR5766176,ILLUMINA,Sample1_R1.fastq.gz,Sample1_R2.fastq.gz,
Sample2,ERR5766179,ILLUMINA,Sample2_R1.fastq.gz,Sample2_R2.fastq.gz,

Running

Depending on your premises (see how to run Nextflow pipeline first), you will run a command like:

nextflow run nf-core/taxprofiler \
  -profile singularity \
  --input samplesheet.csv \
  --databases databases.csv \
  --outdir test \
  --run_centrifuge --run_kaiju --run_kraken2 --run_metaphlan

[-        ] process > NFCORE_TAXPROFILER:TAXPROFILER:UNTAR                                                          -
[ea/5f48b1] process > NFCORE_TAXPROFILER:TAXPROFILER:FASTQC (ERX5474932)                                            [100%] 2 of 2, cached: 2 ✔
[d4/907387] process > NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:KRAKEN2_KRAKEN2 (db1|kraken2|ERX5474932_pe)          [100%] 2 of 2, cached: 2 ✔
[19/3e5d6f] process > NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:CENTRIFUGE_CENTRIFUGE (2019|ERX5474932_pe)           [100%] 2 of 2, cached: 2 ✔
[5c/fe67f8] process > NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:CENTRIFUGE_KREPORT (2019|ERX5474932_pe)              [100%] 2 of 2, cached: 2 ✔
[79/bfeb67] process > NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:METAPHLAN_METAPHLAN (Jan21|ERX5474932_pe)            [100%] 2 of 2, cached: 2 ✔
[64/be1222] process > NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:KAIJU_KAIJU (2021-nr-euk|ERX5474932_pe)              [100%] 2 of 2, cached: 2 ✔
[00/6b0c69] process > NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:KAIJU_KAIJU2TABLE_SINGLE (2021-nr-euk|ERX5474932_pe) [100%] 2 of 2, cached: 2 ✔
[-        ] process > NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:MOTUS_PROFILE                                        -
[06/5aeb40] process > NFCORE_TAXPROFILER:TAXPROFILER:MULTIQC                                                        [100%] 1 of 1 ✔
-[nf-core/taxprofiler] Pipeline completed successfully-