Update to version 1.4.2 #207

ODiogoSilva · 2019-06-18T08:19:59Z

No description provided.

…le, it will try to type using the read data.

Moved reads side channel from split_assembly to dengue_typing updated dengue_typing container

typing from reads and another for typing from assembly

typing from reads and another for typing from assembly - code cleanup and bug fixes

code cleanup corrected issue with side channel on dengue_typing

# Conflicts: # changelog.md

…hen it's not

fix bug

… remote execution (#204) - Partial solve to #194 issue - Deprecation of the `manifest.config´ file - Add the manifest information to the `nextflow.config` file

Added components for gatk

codecov-io · 2019-06-18T08:20:33Z

Codecov Report

Merging #207 into master will decrease coverage by 2.01%.
The diff coverage is 15.5%.

@@            Coverage Diff             @@
##           master     #207      +/-   ##
==========================================
- Coverage   43.97%   41.95%   -2.02%     
==========================================
  Files          67       72       +5     
  Lines        6042     6461     +419     
==========================================
+ Hits         2657     2711      +54     
- Misses       3385     3750     +365

Impacted Files	Coverage Δ
flowcraft/generator/components/phylogeny.py	`100% <ø> (ø)`	⬆️
flowcraft/generator/components/assembly.py	`100% <ø> (ø)`	⬆️
flowcraft/flowcraft.py	`60.62% <ø> (-0.21%)`	⬇️
flowcraft/generator/recipes/denim.py	`100% <ø> (ø)`	⬆️
flowcraft/tests/test_assemblerflow.py	`100% <ø> (ø)`	⬆️
flowcraft/templates/process_newick.py	`0% <0%> (ø)`	⬆️
flowcraft/templates/dengue_typing_reads.py	`0% <0%> (ø)`
flowcraft/templates/process_metabat.py	`0% <0%> (ø)`
flowcraft/templates/dengue_typing_assembly.py	`0% <0%> (ø)`
flowcraft/templates/split_fasta.py	`0% <0%> (ø)`	⬆️
... and 12 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 fc3f4bd...890d54d. Read the comment docs.

cimendes and others added 30 commits December 27, 2018 11:32

Dengue typing requires reads in input - when a sample fails to assemb…

bc8f42c

…le, it will try to type using the read data.

add option to raxml process to simplify labels in newick tree

36a44d1

cleanup

c968000

moved dengue_typing script into template.

bd640ce

Moved reads side channel from split_assembly to dengue_typing updated dengue_typing container

devided dengue_typing into two components with two templates, one for

ba17696

typing from reads and another for typing from assembly

devided dengue_typing into two components with two templates, one for

42a2ac8

typing from reads and another for typing from assembly - code cleanup and bug fixes

add custom exit code. code cleanup and commenting

8fb4be6

fix bug and code cleanup

40d0be6

add check_coverage to denim recipe

268fff2

code cleanup corrected issue with side channel on dengue_typing

fix database location

2e06f3e

fix bug in the add label option

9dde95c

add identity and coverage to dengue_typing report.json

fd675c1

latest update to den-im recipe components - dengue_typing

bd5f7c2

Merge branch 'den-im' into dev

d65d1ba

fix typo

d6b3fbd

Update spades container to the 3.13.0 version

705d209

Add seroba component

1a22f0e

Merge remote-tracking branch 'origin/dev' into dev

99e7e1c

# Conflicts: # changelog.md

fix typo

5d2da64

remove temporary folder when a seroba run is successful, as well as w…

a308341

…hen it's not

remove temporary folder when a seroba run is successful, as well as w…

7bababb

…hen it's not

renames input files to avoid filename matching errors

2056dc0

fix bug

added concoct component for metagenomic binning

c3f7f14

added concoct report (workaround issue)

2f35cbe

fixed script for concoct

dc4caa6

add metabat2 component

bca3be0

remove submodule from dev install

33845b4

fix typo

e9ea39f

Added bwa component

260ff85

Added cpus to bwa command

a4db6b1

cimendes and others added 15 commits June 11, 2019 12:53

added manifest information to the nextflow.config file to allow for…

a50e0ae

… remote execution (#204) - Partial solve to #194 issue - Deprecation of the `manifest.config´ file - Add the manifest information to the `nextflow.config` file

Added component for haplotypecaller

58e8cc7

Added merge vcfs to haplotypecaller component

b823897

Added mark duplicates component

6fcc1e6

Added bam index to mark duplicates

1e13999

Added base_recalibrator component

6d43c7d

Removed publishDir for haplotypecaller

54dd4de

Added apply_bqsr process to base_recalibrator component

46fab6d

Updated changelog

5392202

Added description to haplotypecaller

83f1328

Rebase with dev

804bca3

Add check for the location of specific dot files

492df2e

Merge pull request #206 from assemblerflow/lifebit

0527009

Added components for gatk

Updated changelog

e0bc4d8

Updated version

890d54d

cimendes approved these changes Jun 18, 2019

View reviewed changes

bfrgoncalves approved these changes Jun 18, 2019

View reviewed changes

ODiogoSilva merged commit d6c6a3c into master Jun 18, 2019

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Update to version 1.4.2 #207

Update to version 1.4.2 #207

ODiogoSilva commented Jun 18, 2019

codecov-io commented Jun 18, 2019 •

edited

Loading

Update to version 1.4.2 #207

Update to version 1.4.2 #207

Conversation

ODiogoSilva commented Jun 18, 2019

codecov-io commented Jun 18, 2019 • edited Loading

Codecov Report

codecov-io commented Jun 18, 2019 •

edited

Loading