Introduction Usage Parameters Output Releases
  • Usage

FAQs

INPUT

Where can I find some example input data? Find some example input data here
What happens if I have the only PDBs and not the corresponding fasta files?

No problem, you can provide the PDBs as input (either via the samplesheet using the optional_data column or via the flag —pdbs_dir).

The flag —skip_pdbcoversion false will make sure that the fasta file is automatically extracted from the provided PDBs and subsequently used in the pipeline.

 nextflow run nf-core/multiplesequencealign \
      -profile easy_deploy,docker \
      --pdbs_dir YOUR_PDB_DIR \
      --aligner FAMSA \
      --tree CLUSTALO \
      --outdir results \
      --skip_pdbconversion false

USECASES

I want to deploy one tool on one dataset. I am not interested in any evaluation, report etc.

You should use the easy_deploy profile!

This will skip all the evaluation, reporting etc. step and keep the deployment to the minimum.

The following example: running FAMSA (with arguments -refine_mode on) using the guidetree built using CLUSTALO.

nextflow run nf-core/multiplesequencealign \
  -profile easy_deploy,docker \
  --seqs YOUR_FASTA \
  --aligner FAMSA \
  --args_aligner "-refine_mode on" \
  --tree CLUSTALO \
  --outdir results

You can leave the —tree and —args_aligner and —args_tree empty (just do not use the flags). Default values will be used.

Change the profile from docker to singularity or your preferred choice!

I want to deploy one tool on one dataset. I want to run a structural aligner.

The following example: running FOLDMASON (with arguments -refine_mode on) using the guidetree built using CLUSTALO.

nextflow run nf-core/multiplesequencealign \
  -profile easy_deploy,docker \
  --pdbs_dir YOUR_PDB_DIR\
  --aligner FOLDMASON \
  --tree CLUSTALO \
  --outdir results

You can leave the —tree and —args_aligner and —args_tree empty (just do not use the flags). Default values will be used. Foldmason is just an example, you can pick any other structural aligner.

One dataset, multiple tools. You should use the toolsheet to specify the tools use. 
nextflow run nf-core/multiplesequencealign \
  -profile easy_deploy,docker \
  --seqs YOUR_FASTA\
  --tools YOUR_TOOLSHEET\
  --outdir results

Your input dataset can be passed via the —seqs or —pdbs_dir, as explained in the examples above.

Can i run the same tool multiple times with different arguments? 
Absolutely yes! Create different rows in the toolsheet and add different arguments in the args_aligner column.
Can i run a structural evaluation on sequence-based aligners?

Yes, as long as you provide the structures, either via the samplesheet or via the —pdbs_dir flag.

You can also run proteinfold before to get your structures, in case you do not have them already. Here instructions on how to do it.