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- added secondary channel to link dengue_typing reference genomes to mafft - dengue_typing now outputs original input fasta file (like seqtyping) - altered denim recipe to accomodate these changes
Co-Authored-By: cimendes <cimendes@users.noreply.github.com>
fix bug in momps
add skesa and process_skesa to the innuendo recipe
…e_typing multiple times.
fix flowcraft broadcast nf file path retrieval.
…es inside containers
fix flowcraft report nf file path retrieval.
DEN-IM recipe 2.0
set treeDag and forkTrre files paths from relative to absolute
Fix search for nextflow run command in .nextflow.log
* - added new utils file for commonly used functions - changed inspect and report modes to now used the get_nextflow_filepath function in utils * - add tests for get_nexflow_filepath Co-authored-by: bfrgoncalves <bfgoncalves@medicina.ulisboa.pt> Co-authored-by: cimendes <iines.mendes@gmail.com>
* Added manifest.config to define the pipeline mainScript and name meta-data information - Issue "186"
* added publish dir for mash_dist txt files * Fixed msh side channel * added to changelog * added to changelog * added -i to support multi fasta rather than whole fasta * Update changelog.md
- added kraken2 component and documentation - flowcraft build -l and flowcraft build -L prints an alphabetically ordered list of components - moved taxonomy results to `results/taxonomy/` - added support for maxbin2 reports (sample specific) - fix bug in megahit process when converting contigs to fastg files
* Move trimmomatic trimlog from mounted dir to /tmp due to severe performance hit in docker for mac due to I/O issues in the mounted dir. Co-authored-by: bfrgoncalves <bfgoncalves@medicina.ulisboa.pt> * remove rstrip for log_id retrieval * remove shell=True from trimmomatic's execution command * implemented the tempfile module to generate a temp dir for the trimmomatic log file (needed for compatibility with docker for macOS)
altered regex when parsing log file to allow any character in the path. added test
Codecov Report
@@ 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
Continue to review full report at Codecov.
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ODiogoSilva
approved these changes
Mar 2, 2019
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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/