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Dev #65

Merged
merged 219 commits into from
Jan 13, 2019
Merged

Dev #65

merged 219 commits into from
Jan 13, 2019
+4,163,886 −1,475

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HendrikSchultheis
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HendrikSchultheis and others added 30 commits December 6, 2018 15:23
@HendrikSchultheis
print number of reduced kmer
3b4eb71
@renewiegandt
Merge pull request #8 from loosolab/master
2b99bb8 
merge master to dev
@JannikHamp
$workdir/merged.bed -> "$workdir"/merged.bed
e4256a9
@renewiegandt
Merge pull request #9 from loosolab/dev
58c8478 
Merge dev to motif_estimation to bring branch up to date
@renewiegandt
Bugfix in bed_to_fasta.R: Get last and second last instead of fixed i…
cc23250 
…ndices
@renewiegandt
bed_to_fasta.R: Improved documentation
62f6f3f
@renewiegandt
bed_to_fasta.R: Imporved parametercalling with optparse
cf9dcd8
@renewiegandt
adaption of pipeline.nf to changes in bed_to_fasta.R
6d5c604
@renewiegandt
Refactoring
ce52871
@renewiegandt
Merge pull request #13 from loosolab/dev
4ec60f7 
Dev
@anastasiia
changing the separator in the last line
b74af7f
@anastasiia
adding a column name strand containing always .
117ab50
@HendrikSchultheis
refactoring; renamed reduce_bed to reduce_sequence
98985d1
@renewiegandt
Merge pull request #15 from loosolab/peak_calling
8faf399 
Peak calling
@HendrikSchultheis
check whether jellyfish is installed
e0b9d38
@HendrikSchultheis
reduce_bed renamed to reduce_sequence
1730868
@renewiegandt
get_best_motif.py: fixed bug which caused to print motif header as la…
3c4f733 
…st line + improved documentation
@HendrikSchultheis
check whether jellyfish is installed
88fa298
@HendrikSchultheis
check whether cdhit is installed
e17d1db
@HendrikSchultheis
omit TODO
dcd185e
@HendrikSchultheis
check for header and forward it if provided
4c16f6f
@HendrikSchultheis
automatically detect and keep column names if provided
5a7c84e
@HendrikSchultheis
added author; better missing input error
97464ca
@HendrikSchultheis
added author
cc532bf
@renewiegandt
Fixed typos in get_best_motif.py
8389226
@renewiegandt
Reads BED-files with or without header
2fca158
@renewiegandt
Imporved description for installation in README.md
4dea8e4
@renewiegandt
Removed snakemake from yaml-file
1a7a812
@renewiegandt
Set parameter organism as required wihtout an default value
4844609
@HendrikSchultheis
spell check
d60faa7
anastasiia and others added 18 commits January 12, 2019 17:04
@anastasiia
Merge pull request #50 from loosolab/peak_calling
c398ce3 
Peak calling fixing the merging bug, changing the parameter name from max_bp_between to min_gap
@anastasiia
Update README.md
d644c07 
I think we needed the better explanation for the problem with MOODS
@HendrikSchultheis
Merge pull request #63 from loosolab/cluster
499206d 
Cluster
@renewiegandt
Update README.md
50214f0
@JannikHamp
fixed .bed.bed unconsitent output name
34a2830
@renewiegandt
Merge branch 'estimation_motifs' of https://github.molgen.mpg.de/loos…
f3c72c8 
…olab/masterJLU2018 into estimation_motifs
@renewiegandt
yml: fixed version of python and numpy to prevent bug in 1.1
f371e1d
@renewiegandt
remove personal path from nextflow.config
e3afe9f
@renewiegandt
renamed config files
0428556
@renewiegandt
Update README and help message in pipeline
5ea2f7a
@renewiegandt
pipeline.nf: added missing params.
d461966
@renewiegandt
Fixed typo
574881f
@renewiegandt
Updated configs to new parameteres
f1d0dc7
@renewiegandt
Merge pull request #64 from loosolab/JannikHamp-patch-3
c93ecaf 
fixed .bed.bed unconsitent output name
@renewiegandt
Added demo run files
5b201c0
@renewiegandt
Added demo command to README.md
1a740c2
@renewiegandt
Added missing letter in README.md
95edb00
@renewiegandt
Merge pull request #61 from loosolab/estimation_motifs
9b849f2 
Update README.md
@SebastianBeyvers SebastianBeyvers dismissed their stale review January 13, 2019 18:01

4 Mio lines changed, wtf ?

SebastianBeyvers
SebastianBeyvers approved these changes Jan 13, 2019
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Looks fine, don't bother my stupid comment from before. The 4 mio lines come from the original fasta file for chr1 of hg38.

@SebastianBeyvers
Merge pull request #66 from loosolab/estimation_motifs
62c362e 
Update README.md: Added step 4 of installation
renewiegandt
renewiegandt approved these changes Jan 13, 2019
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Pipeline runs. Approved.

@renewiegandt renewiegandt merged commit f6a7c27 into master Jan 13, 2019
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@renewiegandt renewiegandt renewiegandt approved these changes

@SebastianBeyvers SebastianBeyvers SebastianBeyvers approved these changes

@anastasiia anastasiia Awaiting requested review from anastasiia

@JannikHamp JannikHamp Awaiting requested review from JannikHamp

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6 participants
@HendrikSchultheis @renewiegandt @SebastianBeyvers @JannikHamp @anastasiia @msbentsen