databio/dnameth_pipelines issues and pull requests

#53 - MethylDackel

Issue - State: open - Opened by nsheff over 3 years ago
Labels: future

#53 - MethylDackel

Issue - State: open - Opened by nsheff over 3 years ago
Labels: future

#52 - Zipping files

Issue - State: closed - Opened by nsheff about 4 years ago - 1 comment

#52 - Zipping files

Issue - State: closed - Opened by nsheff about 4 years ago - 1 comment

#51 - what is bisulfiteReadConcordanceAnalysis.py ?

Issue - State: open - Opened by nsheff over 4 years ago - 1 comment

#51 - what is bisulfiteReadConcordanceAnalysis.py ?

Issue - State: open - Opened by nsheff over 4 years ago - 1 comment

#50 - 0.5.0 release

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

#50 - 0.5.0 release

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

#49 - Pep2

Pull Request - State: closed - Opened by nsheff over 4 years ago

#48 - Pep2

Pull Request - State: closed - Opened by stolarczyk over 4 years ago - 6 comments

#48 - Pep2

Pull Request - State: closed - Opened by stolarczyk over 4 years ago - 6 comments

#47 - trimmomatic_epignome

Issue - State: open - Opened by nsheff over 5 years ago

#47 - trimmomatic_epignome

Issue - State: open - Opened by nsheff over 5 years ago

#46 - use refgenie

Issue - State: open - Opened by nsheff over 5 years ago - 1 comment

#46 - use refgenie

Issue - State: open - Opened by nsheff over 5 years ago - 1 comment

#45 - Conditional spike-in processing; TrimGalore removal from RRBS

Pull Request - State: closed - Opened by vreuter almost 6 years ago

#45 - Conditional spike-in processing; TrimGalore removal from RRBS

Pull Request - State: closed - Opened by vreuter almost 6 years ago

#44 - Stage/checkpoint, mainly for start-point specification

Issue - State: open - Opened by vreuter almost 6 years ago - 4 comments
Labels: enhancement, priority-low

#44 - Stage/checkpoint, mainly for start-point specification

Issue - State: open - Opened by vreuter almost 6 years ago - 4 comments
Labels: enhancement, priority-low

#43 - Make spike-in failure non-fatal

Issue - State: open - Opened by vreuter almost 6 years ago

#43 - Make spike-in failure non-fatal

Issue - State: open - Opened by vreuter almost 6 years ago

#42 - Need monadic handling of input_to_fastq return type

Issue - State: open - Opened by vreuter almost 6 years ago - 1 comment

#42 - Need monadic handling of input_to_fastq return type

Issue - State: open - Opened by vreuter almost 6 years ago - 1 comment

#41 - release Version 0.4

Pull Request - State: closed - Opened by nsheff almost 6 years ago

#41 - release Version 0.4

Pull Request - State: closed - Opened by nsheff almost 6 years ago

#40 - Spike-in can skip epilog if needed

Pull Request - State: closed - Opened by vreuter almost 6 years ago - 12 comments

#40 - Spike-in can skip epilog if needed

Pull Request - State: closed - Opened by vreuter almost 6 years ago - 12 comments

#39 - Disregard spike-in errors

Issue - State: open - Opened by vreuter almost 6 years ago

#39 - Disregard spike-in errors

Issue - State: open - Opened by vreuter almost 6 years ago

#38 - use multicore samtools

Issue - State: open - Opened by nsheff almost 6 years ago

#37 - Mixed key case / naming convention

Issue - State: open - Opened by vreuter almost 6 years ago - 6 comments
Labels: question

#37 - Mixed key case / naming convention

Issue - State: open - Opened by vreuter almost 6 years ago - 6 comments
Labels: question

#36 - epilog error

Issue - State: closed - Opened by nsheff about 6 years ago - 7 comments

#36 - epilog error

Issue - State: closed - Opened by nsheff about 6 years ago - 7 comments

#35 - pass back filepaths to PM run call

Pull Request - State: closed - Opened by vreuter about 6 years ago

#35 - pass back filepaths to PM run call

Pull Request - State: closed - Opened by vreuter about 6 years ago

#34 - tests directory

Issue - State: closed - Opened by j-lawson about 6 years ago - 2 comments

#34 - tests directory

Issue - State: closed - Opened by j-lawson about 6 years ago - 2 comments

#33 - Explicitly specify output_dir for bismark deduplication; close #25

Pull Request - State: closed - Opened by vreuter about 6 years ago

#33 - Explicitly specify output_dir for bismark deduplication; close #25

Pull Request - State: closed - Opened by vreuter about 6 years ago

#32 - Modularized downstream processing

Pull Request - State: closed - Opened by vreuter about 6 years ago - 8 comments

#32 - Modularized downstream processing

Pull Request - State: closed - Opened by vreuter about 6 years ago - 8 comments

#31 - Modular use of epilog

Pull Request - State: closed - Opened by vreuter about 6 years ago

#31 - Modular use of epilog

Pull Request - State: closed - Opened by vreuter about 6 years ago

#30 - Once in place, use epilog downstream multicore

Issue - State: open - Opened by vreuter about 6 years ago - 3 comments
Labels: enhancement, future

#30 - Once in place, use epilog downstream multicore

Issue - State: open - Opened by vreuter about 6 years ago - 3 comments
Labels: enhancement, future

#29 - Make sure spike-in data strand specific flag matches main data

Issue - State: closed - Opened by vreuter about 6 years ago - 2 comments
Labels: question

#29 - Make sure spike-in data strand specific flag matches main data

Issue - State: closed - Opened by vreuter about 6 years ago - 2 comments
Labels: question

#28 - Get master into dev

Pull Request - State: closed - Opened by vreuter about 6 years ago

#28 - Get master into dev

Pull Request - State: closed - Opened by vreuter about 6 years ago

#27 - More granular targets for epilog

Issue - State: open - Opened by vreuter over 6 years ago - 2 comments
Labels: enhancement, priority-low, future

#26 - SAM tempfolder unused in WGBS?

Issue - State: open - Opened by vreuter over 6 years ago
Labels: question, priority-low

#25 - Bismark deduplication output destination error

Issue - State: closed - Opened by vreuter over 6 years ago - 3 comments

#25 - Bismark deduplication output destination error

Issue - State: closed - Opened by vreuter over 6 years ago - 3 comments

#24 - Add hook for epilog time limit

Issue - State: closed - Opened by vreuter over 6 years ago - 1 comment

#24 - Add hook for epilog time limit

Issue - State: closed - Opened by vreuter over 6 years ago - 1 comment

#23 - gzip / broken pipe errors in bismark methylation extractor

Issue - State: closed - Opened by vreuter over 6 years ago - 2 comments
Labels: question

#23 - gzip / broken pipe errors in bismark methylation extractor

Issue - State: closed - Opened by vreuter over 6 years ago - 2 comments
Labels: question

#22 - Tool naming

Issue - State: open - Opened by vreuter over 6 years ago - 5 comments
Labels: question

#22 - Tool naming

Issue - State: open - Opened by vreuter over 6 years ago - 5 comments
Labels: question

#21 - Dark sequencing, custom downstream analysis

Pull Request - State: closed - Opened by vreuter over 6 years ago - 6 comments

#20 - Epilog commands are run as targetless

Issue - State: closed - Opened by vreuter over 6 years ago
Labels: bug

#20 - Epilog commands are run as targetless

Issue - State: closed - Opened by vreuter over 6 years ago
Labels: bug

#19 - Epilog output to wrong folder

Issue - State: closed - Opened by vreuter over 6 years ago
Labels: bug

#19 - Epilog output to wrong folder

Issue - State: closed - Opened by vreuter over 6 years ago
Labels: bug

#18 - Sample subtype import

Issue - State: closed - Opened by vreuter over 6 years ago - 5 comments
Labels: bug, question

#18 - Sample subtype import

Issue - State: closed - Opened by vreuter over 6 years ago - 5 comments
Labels: bug, question

#17 - Consider transitioning custom methylation analysis from opt-in to opt-out

Issue - State: open - Opened by vreuter over 6 years ago - 1 comment
Labels: question

#16 - Monitor resource usage and adjust pipeline interface accordingly

Issue - State: open - Opened by vreuter over 6 years ago - 2 comments

#16 - Monitor resource usage and adjust pipeline interface accordingly

Issue - State: open - Opened by vreuter over 6 years ago - 2 comments

#15 - epilog uses only a single core

Issue - State: closed - Opened by nsheff over 6 years ago

#15 - epilog uses only a single core

Issue - State: closed - Opened by nsheff over 6 years ago

#14 - epilog cmd doesn't provide a target

Issue - State: closed - Opened by nsheff over 6 years ago - 2 comments

#14 - epilog cmd doesn't provide a target

Issue - State: closed - Opened by nsheff over 6 years ago - 2 comments

#13 - no context given in yaml file

Issue - State: closed - Opened by nsheff over 6 years ago

#13 - no context given in yaml file

Issue - State: closed - Opened by nsheff over 6 years ago

#12 - Python package dependencies

Issue - State: open - Opened by vreuter over 6 years ago - 2 comments
Labels: question

#12 - Python package dependencies

Issue - State: open - Opened by vreuter over 6 years ago - 2 comments
Labels: question

#11 - Master into dev

Pull Request - State: closed - Opened by vreuter over 6 years ago

#11 - Master into dev

Pull Request - State: closed - Opened by vreuter over 6 years ago

#10 - dark sequencing

Issue - State: open - Opened by nsheff over 6 years ago - 1 comment

#10 - dark sequencing

Issue - State: open - Opened by nsheff over 6 years ago - 1 comment

#9 - error with `get_epi_cmd`

Issue - State: closed - Opened by nsheff over 6 years ago

#9 - error with `get_epi_cmd`

Issue - State: closed - Opened by nsheff over 6 years ago

#8 - paired end bug

Issue - State: closed - Opened by nsheff over 6 years ago - 1 comment

#8 - paired end bug

Issue - State: closed - Opened by nsheff over 6 years ago - 1 comment

#7 - Main methods for pipelines, for Sample subtype import

Pull Request - State: closed - Opened by vreuter over 6 years ago - 1 comment

#6 - main

Issue - State: open - Opened by nsheff over 6 years ago

#6 - main

Issue - State: open - Opened by nsheff over 6 years ago

#5 - Setup for alternative base-level strategy

Pull Request - State: closed - Opened by vreuter over 6 years ago - 2 comments

#4 - Dev

Pull Request - State: closed - Opened by vreuter over 7 years ago

#3 - Standardize creation of tool commands

Issue - State: open - Opened by vreuter over 7 years ago

#2 - RRBS fill hook & more straightforward trimmer spec

Pull Request - State: closed - Opened by vreuter over 7 years ago - 1 comment

#1 - Pull master into dev

Pull Request - State: closed - Opened by vreuter over 7 years ago

GitHub / databio/dnameth_pipelines issues and pull requests