What's Changed

• essential fixes to make the embeded yaml parse by @marc-portier in #37
• Issues raised from the Arms project by @hariszaf in #57

New Contributors

• @marc-portier made their first contribution in #37

This new PEMA release:

• is based on a new pemabase Docker image (pemabase:v.2.1.1) which is now completely indepedent from any local resources and the user can build it through the Dockerfile.pemabase file
• a new marker gene, the 12S rRNA, is now also supported, by exploiting the 12S Vertebrate Classifier v2.0.0-ref database
• for the case of 18S rRNA marker gene, the PR2 database has been integrated so now the user may select between Silva and PR2
• thanks to the ncbi-taxonomist software, PEMA now provides an extended OTU/ASV table where in last column the NCBI Taxonomy Id
  for the taxonomic level closer to the species name rank for which there is one, is available

In addition, in this release:

• a sannity_check folder with datasets and parameters files for multiple combinations are now available, so tests can be performed to check whether pema runs properly after edits.
• bugs during the analysis of 18S data have been fixed
• the perSample outputs have been fixed
• convertion of non ena format raw data for multiple sequencers is supported

This new PEMA release (Docker image can be found here) has the following:

• it is based on this new pemabase (see Dockerfile.pemabase)
• this new pemabase (v.2.1.1) image is now available addressing issue #31
• the perSample outputs have been fixed (bug issue #25 )
• enhanced convertion of non ena format raw data (issue #19 )
• bugs during the analysis of 18S data have been fixed (issues #22 and #24 )
• a sannity_check folder with datasets and parameters files for multiple combinations are now available, so tests can be performed to check whether pema runs properly after edits.

This is the first PEMA release under its new architecture.

Custom reference databases are now supported too.

pema_v1_2.txt

pema_v1_1.txt