SciLifeLab NGI-ChIPseq issues

SciLifeLab / NGI-ChIPseq

Nextflow ChIP-seq data analysis pipeline, National Genomics Infrastructure, Science for Life Laboratory in Stockholm

MIT License

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issues

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Azure changes

#66 TChan92 closed 6 years ago
3
Validate macsconfig inputs before starting

#65 ewels closed 6 years ago
0
Change the method for annotating peaks

#64 chuan-wang closed 6 years ago
0
Fix the installation of ChIPpeakAnno in Dockerfile; Reduce the required memory for get_software_versions and multiqc

#63 chuan-wang closed 6 years ago
1
Peak annotation requires internet access

#62 orzechoj closed 6 years ago
3
To high memory requirement for local jobs

#61 orzechoj closed 6 years ago
1
Include statistics about unmapped reads; Fix bug about container in nextflow.config

#60 chuan-wang closed 6 years ago
4
workflow config not available when parsing config

#59 ewels closed 6 years ago
2
Change the method for counting mapped reads

#58 chuan-wang closed 6 years ago
0
Remove subpaths from docker mkdir

#57 ewels closed 6 years ago
1
Tool updates, more docker mount points

#56 ewels closed 6 years ago
2
Adding primary alignment filtering; Adding new plotting functions in deepTools

#55 chuan-wang closed 6 years ago
2
deepTools - bamPEFragmentSize, plotPCA

#54 ewels closed 6 years ago
4
Remove multimapping reads

#53 ewels closed 6 years ago
3
Use Singularity instead of environment modules

#52 ewels closed 7 years ago
3
Samtools stats for alignment metrics in MultiQC

#51 ewels closed 7 years ago
1
Fix uppmax testing config order bug

#50 ewels closed 7 years ago
0
v1.4 Updates: Adding post peak calling filtering and annotations; generating coverage bw file in deepTools

#49 chuan-wang closed 7 years ago
3
Optional filtering blacklist regions

#48 orzechoj closed 7 years ago
8
v1.3 config refactor and new options added

#47 chuan-wang closed 7 years ago
4
Refactored configs

#46 ewels closed 7 years ago
3
Put phantompeaktools results in MultiQC report

#45 orzechoj closed 6 years ago
2
Add samtools stats for mapping stats

#44 orzechoj closed 7 years ago
2
Collect software versions, help message

#43 ewels closed 7 years ago
1
Use input channel for output docs rendering.

#42 ewels closed 7 years ago
1
Adding installation of R packages requird by markdown_to_html.r

#41 chuan-wang closed 7 years ago
0
Strand cross-correlation analysis before, or after de-duplication?

#40 sifakise closed 6 years ago
2
Check NF version, always run trace + timeline

#39 ewels closed 7 years ago
0
Added docs about -resume.

#38 ewels closed 7 years ago
0
Proper multipart HTML email.

#37 ewels closed 7 years ago
4
Add genome files for ngsplot

#36 chuan-wang closed 7 years ago
5
Add --broad option for MACS

#35 chuan-wang closed 7 years ago
1
Minor docs tweak

#34 ewels closed 7 years ago
0
Picard fix. Bunch of updates ported from NGI-RNAseq

#33 ewels closed 7 years ago
2
Docker version failed to carry out BWA process and exit. Any suggestions?

#32 zhenyisong closed 7 years ago
42
Add blacklist region filtering

#31 ewels closed 7 years ago
3
Don't save intermediate files by default

#30 ewels closed 7 years ago
3
Hotfix: uppmax config file - samtools process name

#29 ewels closed 7 years ago
0
Fix error about REF definitions

#28 chuan-wang closed 7 years ago
0
Fix error about REF for ngsplot, and specify supported genome in README.md

#27 chuan-wang closed 7 years ago
1
Refactor BAM count for deepTools. Remove 'testing' NF profile.

#26 ewels closed 7 years ago
1
Fix issue that deepTools give error when handling single-file input

#25 chuan-wang closed 7 years ago
4
Add specifications of pipeline output

#24 chuan-wang closed 7 years ago
1
Massive update - cleanup and Docker implementation

#23 ewels closed 7 years ago
8
Write documentation describing output

#22 ewels closed 7 years ago
1
Make scripts stand-alone

#21 ewels closed 7 years ago
1
Config + readme updates

#20 ewels closed 7 years ago
4
Modules revised for phantompeakqualtools and ngsplot in config file; Code revised for ngsplot in main.nf

#19 chuan-wang closed 8 years ago
1
Allow single end input as well as paired end.

#18 ewels closed 8 years ago
0
line 111 .fromFilePairs revised to .fromPath

#17 chuan-wang closed 8 years ago
2