Release 1.3.0

[will-rowe]

An issue to track progress on the next minor release. This is in response to the CLIMB/ARTIC workshop where there were some usability issues and improvement suggestions. Features to target for the next minor release (1.3.0):

QC report:

• [x] parameterise the coverage cutoff on the amplicon plot using the --depth flag provided to the artic_make_depth_mask. This is currently set to 50 on the plot but actually 20 is the minimum read depth used in the depth mask.
• [x] add more meaningful VCF fail output - include vars from the PASS and FAIL files
• [x] add some coverage stats from the alignment file (trimmed / primertrimmed)

Software:

• [x] update to the new medaka release on PyPi - test it and wait for conda recipe before releasing 1.3.0
• [x] optional - check the output of latest medaka vs longshot and evaluate if longshot can be replaced

Minion:

• [x] parameterise minimum read depth for masking, this will feed into the amplicon plotting
• [x] add the QC report to the core pipeline (remove requirement of --strict)
• [x] enforce full length amplicon alignment during align_trim when pipeline run with --strict

VCF report:

• [x] update the report to be more intuitive and informative (issue for artic-tools)

README/Tests:

• [x] looks like Travis is retiring/limiting free service plan? Try GitHub actions out instead
• [x] add the DOI to the readme, which has been minted since 1.2.0

[will-rowe]

Have updated [ARTIC tools]() to output more stats from VCF file and in TSV format, so we can parse those in this minion pipeline and add them to the MultiQC report.

New release is v0.3.0, updating conda now

[mattloose]

Which release is currently on conda?

[will-rowe]

Sorry - my earlier comment is in relation to artic-tools, which is a small utility program I'm maintaining for managing primer scheme tasks.

artic-tools == 0.3.0 artic == 1.2.1

[rpetit3]

Hello! Is there a timeline on v1.3.0? We've been using the dev branch for a while, but I'd like to get v1.3.0 into Bioconda. Thank you!