assemblerflow/flowcraft issues and pull requests

#236 - Add more component

Issue - State: open - Opened by ayooluwaB over 1 year ago

#235 - bwa gatk not found

Issue - State: open - Opened by Rohit-Satyam over 1 year ago

#234 - Adding to Galaxy?

Issue - State: open - Opened by ajkarloss over 3 years ago

#233 - Errors with spades

Issue - State: open - Opened by drpturner about 4 years ago - 18 comments
Labels: bug

#232 - Errors when using option -m broadcast

Issue - State: closed - Opened by redbull05689 over 4 years ago - 1 comment

#231 - add ConFindr

Issue - State: open - Opened by cimendes over 4 years ago

#230 - New additions in flowcraft/templates not updated after build and inst…

Pull Request - State: open - Opened by parvsachdeva over 4 years ago - 1 comment

#229 - New additions in flowcraft/templates not included/updated after build and install

Issue - State: open - Opened by parvsachdeva over 4 years ago

#228 - Nextflow "set" input has been discontinued

Issue - State: open - Opened by cimendes almost 5 years ago
Labels: bug, engine, high priority

#227 - Hackathon

Pull Request - State: closed - Opened by ODiogoSilva almost 5 years ago - 1 comment

#226 - Update trimmomatic containers to version 0.39-1

Pull Request - State: open - Opened by cimendes about 5 years ago - 1 comment

#225 - using my own Docker from Gitlab

Issue - State: open - Opened by AKWB about 5 years ago - 9 comments

#224 - Fix for #219 - Bad python2 file lost in the bin folder

Pull Request - State: open - Opened by cimendes about 5 years ago - 1 comment

#223 - update with changes in dev

Pull Request - State: closed - Opened by cimendes about 5 years ago - 1 comment

#222 - Fix downsample

Pull Request - State: closed - Opened by cimendes about 5 years ago - 1 comment

#221 - Moved template file to proper location

Pull Request - State: closed - Opened by t0rrant about 5 years ago - 3 comments

#220 - Unable to obtain final report for simple assembly pipeline

Issue - State: open - Opened by rfm-targa about 5 years ago - 1 comment

#219 - Python3 syntax errors

Issue - State: open - Opened by t0rrant about 5 years ago - 3 comments
Labels: bug, mid/low priority

#218 - Integrity coverage fails

Issue - State: open - Opened by TheSequencingCenter about 5 years ago - 15 comments
Labels: bug, high priority

#217 - Bash errors when running nextflow with latest version (19.07.0)

Issue - State: open - Opened by cimendes about 5 years ago - 2 comments
Labels: bug, engine, high priority

#216 - add copyright information

Pull Request - State: open - Opened by cimendes about 5 years ago - 1 comment
Labels: documentation

#215 - Change docs instructions from using 'templates' as submodule

Issue - State: open - Opened by cometsong about 5 years ago - 1 comment
Labels: documentation, mid/low priority

#214 - Create CODE_OF_CONDUCT.md

Pull Request - State: closed - Opened by tiagofilipe12 about 5 years ago - 1 comment

#213 - Added hisat2 component

Pull Request - State: open - Opened by PhilPalmer about 5 years ago - 1 comment

#212 - Added hisat2 component

Pull Request - State: closed - Opened by PhilPalmer about 5 years ago - 1 comment

#211 - Set phred encoding when it fails to be determined - trimmomatic

Pull Request - State: closed - Opened by cimendes about 5 years ago - 2 comments

#210 - remove optional true

Pull Request - State: open - Opened by cimendes about 5 years ago - 1 comment

#209 - Dag files

Pull Request - State: closed - Opened by cimendes over 5 years ago - 2 comments
Labels: enhancement, engine, bufix

#208 - merge dev branch

Pull Request - State: closed - Opened by cimendes over 5 years ago

#207 - Update to version 1.4.2

Pull Request - State: closed - Opened by ODiogoSilva over 5 years ago - 1 comment

#206 - Added components for gatk

Pull Request - State: closed - Opened by PhilPalmer over 5 years ago - 1 comment

#205 - Lifebit

Pull Request - State: closed - Opened by PhilPalmer over 5 years ago - 1 comment

#204 - added manifest information to the `nextflow.config` file to allow for remote execution

Pull Request - State: closed - Opened by cimendes over 5 years ago - 2 comments
Labels: enhancement, engine

#203 - ectyper component

Issue - State: open - Opened by cimendes over 5 years ago
Labels: enhancement, Components

#202 - mobsuite component

Issue - State: open - Opened by cimendes over 5 years ago
Labels: enhancement, Components

#201 - Flowcraft report instructions

Issue - State: open - Opened by jacarrico over 5 years ago
Labels: enhancement

#200 - update den-im branch to the latest version of dev

Pull Request - State: closed - Opened by cimendes over 5 years ago

#199 - Update - version 1.4.1

Pull Request - State: closed - Opened by cimendes over 5 years ago - 1 comment

#198 - Update utils.py - fix regex

Pull Request - State: closed - Opened by cimendes over 5 years ago - 1 comment

#197 - Merge miguelpmachado dev branch with flowcraft innuendo branch

Pull Request - State: closed - Opened by bfrgoncalves over 5 years ago - 1 comment

#196 - momps and mlst: remove collect from report to avoid overwriting previous results when a pipeline is resumed

Pull Request - State: closed - Opened by cimendes over 5 years ago - 3 comments

#195 - momps, mlst results overwrite when pipeline is resumed

Issue - State: open - Opened by cimendes over 5 years ago - 1 comment
Labels: bug, help wanted

#194 - generated pipelines incompatible with nextflow's pipeline sharing

Issue - State: closed - Opened by cimendes over 5 years ago - 4 comments
Labels: enhancement, help wanted, discussion

#193 - true_coverage module in innuca recipe

Issue - State: open - Opened by cimendes over 5 years ago
Labels: bug, recipe

#192 - remove trimmomatic log

Issue - State: open - Opened by cimendes over 5 years ago - 1 comment
Labels: enhancement

#191 - Update to Innuca's recipe modules

Pull Request - State: open - Opened by cimendes over 5 years ago - 1 comment

#190 - Add SeqSero2 and stx subtyping

Pull Request - State: closed - Opened by miguelpmachado over 5 years ago - 5 comments

#189 - Automatically set local executor CPU limit

Issue - State: open - Opened by bfrgoncalves over 5 years ago - 1 comment
Labels: enhancement

#188 - Mash dist fixes

Pull Request - State: closed - Opened by tiagofilipe12 over 5 years ago - 2 comments
Labels: bug, Components

#187 - Add manifest scope to the pipeline config

Pull Request - State: closed - Opened by cimendes almost 6 years ago - 1 comment
Labels: enhancement

#186 - Add manifest to nextflow.config

Issue - State: closed - Opened by cimendes almost 6 years ago
Labels: enhancement

#185 - Add Kraken2 component

Pull Request - State: closed - Opened by cimendes almost 6 years ago - 1 comment

#184 - PR to accommodate comments on #183

Pull Request - State: closed - Opened by cimendes almost 6 years ago - 3 comments
Labels: enhancement, reports, inspect

#183 - Fix search for nextflow run command in .nextflow.log

Pull Request - State: closed - Opened by bfrgoncalves almost 6 years ago - 2 comments
Labels: bufix

#182 - Flowcraft reports and inspect fails when using proxies on nextflow run

Issue - State: closed - Opened by bfrgoncalves almost 6 years ago
Labels: bug

#181 - Merging inspect and report

Issue - State: open - Opened by jacarrico almost 6 years ago - 3 comments
Labels: enhancement, discussion

#180 - fix flowcraft report nf file path retrieval.

Pull Request - State: closed - Opened by bfrgoncalves almost 6 years ago - 2 comments

#179 - DEN-IM recipe 2.0

Pull Request - State: closed - Opened by cimendes almost 6 years ago - 1 comment
Labels: enhancement

#178 - Change on trimmomatic.py template

Pull Request - State: closed - Opened by jacarrico almost 6 years ago - 1 comment

#177 - set treeDag and forkTrre files paths from relative to absolute

Pull Request - State: closed - Opened by bfrgoncalves almost 6 years ago - 1 comment

#176 - fix flowcraft broadcast nf file path retrieval.

Pull Request - State: closed - Opened by bfrgoncalves almost 6 years ago - 1 comment

#175 - Changing nextflow run params order breaks flowcraft inspect broadcast mode

Issue - State: closed - Opened by bfrgoncalves almost 6 years ago - 1 comment
Labels: bug

#174 - Merging syntax with new operator

Issue - State: open - Opened by bfrgoncalves almost 6 years ago - 7 comments
Labels: enhancement, discussion

#173 - add skesa and process_skesa to the innuendo recipe

Pull Request - State: closed - Opened by bfrgoncalves almost 6 years ago - 1 comment

#172 - fix bug in momps

Pull Request - State: closed - Opened by cimendes almost 6 years ago - 3 comments
Labels: Components

#171 - fixed #170

Pull Request - State: closed - Opened by tiagofilipe12 almost 6 years ago - 1 comment
Labels: bug

#170 - Missing dockerhub tags for certain components

Issue - State: closed - Opened by ODiogoSilva almost 6 years ago
Labels: bug

#169 - Version 1.4.0 release

Pull Request - State: closed - Opened by ODiogoSilva almost 6 years ago - 1 comment

#168 - Singularity cache

Pull Request - State: closed - Opened by tiagofilipe12 almost 6 years ago - 2 comments
Labels: enhancement

#167 - Dockerhub tags

Pull Request - State: closed - Opened by tiagofilipe12 almost 6 years ago - 1 comment
Labels: enhancement

#166 - Skesa update

Pull Request - State: closed - Opened by tiagofilipe12 almost 6 years ago - 1 comment
Labels: Components

#165 - Container versioning

Pull Request - State: closed - Opened by tiagofilipe12 almost 6 years ago - 1 comment
Labels: enhancement

#164 - components version

Issue - State: closed - Opened by tiagofilipe12 almost 6 years ago
Labels: discussion

#163 - Template tests

Pull Request - State: open - Opened by tiagofilipe12 almost 6 years ago - 2 comments
Labels: tests

#162 - Automatic processes

Pull Request - State: closed - Opened by tiagofilipe12 almost 6 years ago - 1 comment
Labels: enhancement, engine

#161 - Diamond

Pull Request - State: closed - Opened by tiagofilipe12 almost 6 years ago - 1 comment
Labels: Components

#160 - added timestamp to report and inspect

Pull Request - State: closed - Opened by tiagofilipe12 almost 6 years ago - 2 comments
Labels: enhancement

#159 - Prokka

Pull Request - State: closed - Opened by tiagofilipe12 almost 6 years ago - 1 comment
Labels: Components

#158 - unicycler: Add parameter --long_reads

Pull Request - State: open - Opened by sjackman almost 6 years ago - 2 comments

#157 - Secondary channel for long reads

Issue - State: open - Opened by sjackman almost 6 years ago - 11 comments
Labels: enhancement

#156 - Add unicycler

Pull Request - State: closed - Opened by sjackman almost 6 years ago - 8 comments
Labels: Components

#155 - abyss, bandage, spades: Add GFA

Pull Request - State: closed - Opened by sjackman almost 6 years ago - 12 comments
Labels: Components

#154 - bandage: Fix output files

Pull Request - State: closed - Opened by sjackman almost 6 years ago - 2 comments

#153 - Added bacmet database to abricate

Pull Request - State: closed - Opened by tiagofilipe12 almost 6 years ago - 3 comments
Labels: Components

#152 - Recipes

Pull Request - State: closed - Opened by ODiogoSilva almost 6 years ago - 2 comments
Labels: enhancement

#151 - Default address change for flowcraft service

Pull Request - State: closed - Opened by tiagofilipe12 almost 6 years ago - 1 comment

#150 - Add bandage

Pull Request - State: closed - Opened by sjackman almost 6 years ago - 6 comments
Labels: Components

#149 - Add bcalm flowcraft

Pull Request - State: closed - Opened by natir almost 6 years ago - 3 comments
Labels: Components

#148 - unit tests for scripting templates

Issue - State: open - Opened by tiagofilipe12 almost 6 years ago - 2 comments
Labels: discussion

#147 - Add quast

Pull Request - State: closed - Opened by sjackman almost 6 years ago - 2 comments
Labels: Components

#146 - Added an abyss component to flowcraft, and added a new disableRR parameter to spades

Pull Request - State: closed - Opened by emreerhan almost 6 years ago - 7 comments
Labels: Components

#145 - Make component retrieval automatic

Issue - State: closed - Opened by ODiogoSilva almost 6 years ago - 4 comments
Labels: enhancement

#144 - merge specific params

Issue - State: open - Opened by tiagofilipe12 almost 6 years ago
Labels: enhancement, discussion

#142 - touch: cannot touch '.command.trace': Permission denied

Issue - State: closed - Opened by sjackman almost 6 years ago - 10 comments

#137 - Output assembly graph in GFA format [feature request]

Issue - State: closed - Opened by sjackman about 6 years ago - 14 comments
Labels: enhancement

#120 - Recipe rework to allow to redefine parameters and directives

Issue - State: closed - Opened by cimendes about 6 years ago - 5 comments
Labels: enhancement, recipe

#118 - Update processes directives to use selectors.

Issue - State: open - Opened by ODiogoSilva about 6 years ago - 3 comments
Labels: engine, high priority

#113 - Added Phenix, Public Health England SNP calling pipeline

Pull Request - State: closed - Opened by thanhleviet about 6 years ago - 2 comments

#78 - Allow merge

Issue - State: closed - Opened by cimendes over 6 years ago - 6 comments
Labels: enhancement, help wanted, discussion

#40 - Add unit tests for recipe creation

Issue - State: closed - Opened by ODiogoSilva over 6 years ago
Labels: tests

GitHub / assemblerflow/flowcraft issues and pull requests