Update - version 1.4.1

[cimendes]

This PR merges the latest updates to flowcraft in the dev branch.

Changes:

• New features Added support for the report system to: maxbin2 Added new manifest.config with the pipeline metadata

• New components Kraken2: Taxonomic identification on FastQ files

• Bug fixes Fix bug in mompscomponent related to added in the introduction of the clear input parameter Fixed bug with the -ft parameters not retrieving the dockerhub tags for all the components. Fixed bug in the megahit process where the fastg mode would break the process Fix inspect and report mode to fetch the nextflow file independently of its position in the nextflow run command inside the .nextflow.log file. Fix parsing of .nextflow.log file when searching for nextflow run command. Fixed bug between mash_sketch_fasta and mash_dist.

• Minor/Other changes Added option to dengue_typing to retrive closest referece sequence and link it with a secondary channel into mafft New version of DEN-IM recipe Now prints an ordered list of components Moved taxonomy results from results/annotation/ to results/taxonomy/

[codecov-io]

Codecov Report

Merging #199 into master will increase coverage by 0.29%. The diff coverage is 47.05%.

@@            Coverage Diff             @@
##           master     #199      +/-   ##
==========================================
+ Coverage   43.67%   43.97%   +0.29%     
==========================================
  Files          64       67       +3     
  Lines        5946     6042      +96     
==========================================
+ Hits         2597     2657      +60     
- Misses       3349     3385      +36

Impacted Files	Coverage Δ
flowcraft/generator/recipes/denim.py	100% <ø> (ø)	:arrow_up:
flowcraft/tests/test_assemblerflow.py	100% <ø> (ø)	:arrow_up:
flowcraft/generator/recipe.py	85.71% <ø> (+0.46%)	:arrow_up:
flowcraft/flowcraft.py	60.82% <0%> (-1.95%)	:arrow_down:
flowcraft/templates/trimmomatic.py	0% <0%> (ø)	:arrow_up:
flowcraft/templates/process_tsv.py	0% <0%> (ø)
flowcraft/generator/components/alignment.py	100% <100%> (ø)	:arrow_up:
flowcraft/generator/utils.py	100% <100%> (ø)
flowcraft/__init__.py	100% <100%> (ø)	:arrow_up:
flowcraft/generator/components/metagenomics.py	100% <100%> (ø)	:arrow_up:
... and 11 more

---

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 38a0fbf...a797482. Read the comment docs.