* Updated MetaPhlAn2 command to be compatible with the latest version. * Fix executable search to allow for folders in $PATH to have the same names as executables (ie, bowtie2). * Fix error in header format for humann2_unpack_pathways tool.
0.11.1
* Fix the write table function to allow the tools with optional output arguments (renorm, rename, regroup, infer_taxonomy) to write to stdout if an output path is not provided.
0.11.0
* Add a check and remove of spaces if present in fastq/fasta input files to address new illumina casava v1.8 format.
0.10.0
* The query threshold filtering computation was updated so strand directionality does not affect results (ie reverse was two percent less than forward equivalent).
0.9.10
* The query threshold filtering computation was updated to allow for query starts that are larger than query end indexes.
0.9.9
Other Changes
* HUMAnN submitted as of this release. * Renamed executable humann2_merge_abundance_tables to humann2_unpack_pathways. * Removed executable blastx_coverage because only module is currently used. * humann2_associate is now more robust to user-provided/misspecified/missing metadata. * Descriptions of HUMAnN utility scripts and "tutorials" in the manual have been standardized as "Guides to HUMAnN utility scripts" and "Other HUMAnN guides." These include several new guides for previously available scripts, e.g. humann2_barplot.