nf-core
Export distance matrix files
Description of feature
While ampliseq outputs beta diversity results by metadata feature to results/qiime2/diversity/beta_diversity/DISTANCE-METRIC_distance_matrix_METADATA-FEATURE, it does not include the raw distance matrix. I see that these matrices are saved within the work directory within a directory called diversity_core (ex. work/57/ce33c441419c48f56572c9f137f2b8/diversity_core/weighted_unifrac_distance_matrix.qza). It would be great to export these raw distance matrix qiime artifacts to results/qiime2/diversity/beta_diversity/.
This may be as simples as adding distance = QIIME2_DIVERSITY_CORE.out.distance to emit in https://github.com/nf-core/ampliseq/blob/master/subworkflows/local/qiime2_diversity.nf?
Hi there,
I think thats covered with --save_intermediates that affects https://github.com/nf-core/ampliseq/blob/d8dd15d5e7760752691357c177bed2e35a2e413f/conf/modules.config#L947-L950
Could you append to you command --save_intermediates -resume and see if that yields what you need?
If thats indeed what you were looking for, maybe its not documented properly?
Hi Daniel, thank you for the prompt response! Yes, this flag works, but, obviously, includes other intermediate files. I'd personally prefer not to output those because many are redundant with those already included in the results folder. I figured users would like the full distance matrices as apart of the standard output without also including these other intermediate files.
Fair point. That could be changed indeed that distance matrix files are by default in the results folder.