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Dev #67

Merged
merged 148 commits into from
Jan 14, 2019
Merged

Dev #67

merged 148 commits into from
Jan 14, 2019

Commits on Dec 6, 2018

  1. print number of reduced kmer

    @HendrikSchultheis
    HendrikSchultheis committed Dec 6, 2018
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Commits on Jan 3, 2019

  1. Added more comments and author / mail description

    basti committed Jan 3, 2019
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  2. Added functionality to Fix #19

    basti committed Jan 3, 2019
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  3. Tries to Fix #18

    basti committed Jan 3, 2019
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  4. renamed ID field to gene_id in response to: #29

    basti committed Jan 3, 2019
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  5. added "_" separation in the third gtf-column in response to #29

    basti committed Jan 3, 2019
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  6. Commented every function / method to resolve #29

    basti committed Jan 3, 2019
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  7. Commented every function / method to resolve #29

    basti committed Jan 3, 2019
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  8. Removed data_files

    basti committed Jan 3, 2019
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  9. Merge remote-tracking branch 'origin/dev' into gtf_creation

    basti committed Jan 3, 2019
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Commits on Jan 4, 2019

  1. updated script. Now the path of subscripts is automatically aquired. … 

    …Fixed error which wrote output to the path of subscripts instead of the working directory
    @JannikHamp
    JannikHamp committed Jan 4, 2019
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  2. added some documentation

    @JannikHamp
    JannikHamp committed Jan 4, 2019
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  3. added collumn for strand information

    @JannikHamp
    JannikHamp committed Jan 4, 2019
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  4. added column "strand"

    @JannikHamp
    JannikHamp committed Jan 4, 2019
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  5. documentation

    @JannikHamp
    JannikHamp committed Jan 4, 2019
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  6. documentation

    @JannikHamp
    JannikHamp committed Jan 4, 2019
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  7. Merge pull request #38 from loosolab/peak_calling 

    Peak calling to dev
    @anastasiia
    anastasiia committed Jan 4, 2019
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  8. documentation

    @JannikHamp
    JannikHamp committed Jan 4, 2019
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  9. documentation

    @JannikHamp
    JannikHamp committed Jan 4, 2019
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  10. Added check for optparse to bed_to_fasta.R

    @renewiegandt
    renewiegandt committed Jan 4, 2019
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  11. Merge branch 'dev' into estimation_motifs

    @renewiegandt
    renewiegandt committed Jan 4, 2019
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  12. improved motif clustering

    @renewiegandt
    renewiegandt committed Jan 4, 2019
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Commits on Jan 5, 2019

  1. imporved structure of merge_similar_clusters.R

    @renewiegandt
    renewiegandt committed Jan 5, 2019
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  2. Update compareBed.sh

    @JannikHamp
    JannikHamp committed Jan 5, 2019
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Commits on Jan 6, 2019

  1. bed_to_fasta.R: improved syntax; fixed typos

    @renewiegandt
    renewiegandt committed Jan 6, 2019
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  2. label_cluster.R: improved syntax and documentation; fixed typos

    @renewiegandt
    renewiegandt committed Jan 6, 2019
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  3. merge_similar_clusters.R: improved syntax and documentation; fixed typos

    @renewiegandt
    renewiegandt committed Jan 6, 2019
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  4. Added ";" in attributes (last) field -> fix #29

    basti committed Jan 6, 2019
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  5. Added Validator -> Fix #32

    basti committed Jan 6, 2019
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  6. Added check for \t at the end of lines in BED-file

    @renewiegandt
    renewiegandt committed Jan 6, 2019
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  7. Remove header = false from fread

    @renewiegandt
    renewiegandt committed Jan 6, 2019
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  8. Added Validator

    basti committed Jan 6, 2019
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  9. Merge pull request #39 from loosolab/estimation_motifs 

    Improved: Motif clustering
    @renewiegandt
    renewiegandt committed Jan 6, 2019
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  10. Changed comments for pullrequest

    basti committed Jan 6, 2019
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  11. Changed comments for pullrequest

    basti committed Jan 6, 2019
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  12. Changed comments for pullrequest

    basti committed Jan 6, 2019
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  13. Changed comments activity categorizer

    basti committed Jan 6, 2019
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  14. Changed comments activity table generator

    basti committed Jan 6, 2019
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  15. Merge remote-tracking branch 'origin/dev' into gtf_creation

    basti committed Jan 6, 2019
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  16. Added gitignore !

    basti committed Jan 6, 2019
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  17. removed pycache files

    basti committed Jan 6, 2019
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  18. Specified statement in GTFGen

    basti committed Jan 6, 2019
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  19. merge.R: Set separator from auto to '\t' in fread

    @renewiegandt
    renewiegandt committed Jan 6, 2019
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Commits on Jan 7, 2019

  1. Merge branch 'cluster' of https://github.molgen.mpg.de/loosolab/maste… 

    …rJLU2018 into cluster
    @HendrikSchultheis
    HendrikSchultheis committed Jan 7, 2019
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  2. Merge remote-tracking branch 'origin/dev' into cluster

    @HendrikSchultheis
    HendrikSchultheis committed Jan 7, 2019
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  3. show help if called without arguments; require = quiet

    @HendrikSchultheis
    HendrikSchultheis committed Jan 7, 2019
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  4. show help if called without arguments; require = quiet

    @HendrikSchultheis
    HendrikSchultheis committed Jan 7, 2019
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Commits on Jan 8, 2019

  1. Basic parameter checks added

    @HendrikSchultheis
    HendrikSchultheis committed Jan 8, 2019
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  2. Merge pull request #40 from loosolab/gtf_creation 

    Gtf creation
    @SebastianBeyvers
    SebastianBeyvers committed Jan 8, 2019
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  3. Update yaml; removed debug code from pipeline; update README

    @renewiegandt
    renewiegandt committed Jan 8, 2019
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  4. Merge pull request #41 from loosolab/peak_calling 

    Peak calling to dev after resolving overlaps
    @anastasiia
    anastasiia committed Jan 8, 2019
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  5. Merge branch 'dev' into estimation_motifs

    @renewiegandt
    renewiegandt committed Jan 8, 2019
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  6. this r script is no more necessary, the other does its job

    @JannikHamp
    JannikHamp committed Jan 8, 2019
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  7. New updated version. Faster and more robust

    @JannikHamp
    JannikHamp committed Jan 8, 2019
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  8. updated version.. make unique updated, more robust in general

    @JannikHamp
    JannikHamp committed Jan 8, 2019
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  9. Added basic parameter checks.

    @HendrikSchultheis
    HendrikSchultheis committed Jan 8, 2019
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  10. get_best_motif.py: Added alternative name to best_motif file

    @renewiegandt
    renewiegandt committed Jan 8, 2019
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  11. Add shebang to tfbsscan

    @msbentsen
    msbentsen committed Jan 8, 2019
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  12. added information for logfile

    @JannikHamp
    JannikHamp committed Jan 8, 2019
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  13. added dicumentation and parameter for .stats output file

    @JannikHamp
    JannikHamp committed Jan 8, 2019
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  14. Merge pull request #42 from loosolab/estimation_motifs 

    Update yaml; removed debug code from pipeline; update README
    @renewiegandt
    renewiegandt committed Jan 8, 2019
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  15. get_best_motif.py: removed whitespace from motif header

    @renewiegandt
    renewiegandt committed Jan 8, 2019
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  16. added script get_motif_seq.R

    @renewiegandt
    renewiegandt committed Jan 8, 2019
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  17. pipeline.nf: implemented get_motif_seq.R

    @renewiegandt
    renewiegandt committed Jan 8, 2019
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  18. added r packages: RJSONIO, varhandle to masterenv.yml

    @renewiegandt
    renewiegandt committed Jan 8, 2019
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  19. Merge branch 'dev' into estimation_motifs

    @renewiegandt
    renewiegandt committed Jan 8, 2019
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Commits on Jan 9, 2019

  1. documentation changes

    @JannikHamp
    JannikHamp committed Jan 9, 2019
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  2. Merge pull request #45 from loosolab/peak_calling 

    added the shebang line
    @anastasiia
    anastasiia committed Jan 9, 2019
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  3. Fixed naming scheme for 3rd column

    basti committed Jan 9, 2019
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  4. get_best_motif.py: added parameter cluster id

    @renewiegandt
    renewiegandt committed Jan 9, 2019
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  5. get_motif_seq.R: added parameter tmp_path and cluster_id

    @renewiegandt
    renewiegandt committed Jan 9, 2019
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  6. pipeline.nf: adjusting to new parameters required by get_best_motif; … 

    …get_motif_seq
    @renewiegandt
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  7. Parameter summary added; fixed wrong default for threads parameter

    @HendrikSchultheis
    HendrikSchultheis committed Jan 9, 2019
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  8. updated check for trailing tabs in motiffiles

    @JannikHamp
    JannikHamp committed Jan 9, 2019
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  9. removed echo from testing

    @JannikHamp
    JannikHamp committed Jan 9, 2019
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  10. Added log file for part 2.2_motif_estimation

    @renewiegandt
    renewiegandt committed Jan 9, 2019
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  11. more documentation, replce =, <-

    @JannikHamp
    JannikHamp committed Jan 9, 2019
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  12. Parameter summary added

    @HendrikSchultheis
    HendrikSchultheis committed Jan 9, 2019
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  13. Added Shebang in response to #44

    basti committed Jan 9, 2019
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  14. Merge pull request #33 from loosolab/JannikHamp-patch-1 

    updated script. Now the path of subscripts is automatically aquired. …
    @renewiegandt
    renewiegandt committed Jan 9, 2019
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  15. Merge pull request #43 from loosolab/cluster 

    Cluster
    @renewiegandt
    renewiegandt committed Jan 9, 2019
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  16. Merge branch 'dev' into estimation_motifs

    @renewiegandt
    renewiegandt committed Jan 9, 2019
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  17. added missing shebangs to 2.2 scripts #44

    @renewiegandt
    renewiegandt committed Jan 9, 2019
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  18. pipeline.nf: adjusting to new parameter required by 2.1 scripts

    @renewiegandt
    renewiegandt committed Jan 9, 2019
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Commits on Jan 10, 2019

  1. Merge pull request #49 from loosolab/gtf_creation 

    Gtf creation
    @SebastianBeyvers
    SebastianBeyvers committed Jan 10, 2019
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  2. pipeline.nf: fixed typos

    @renewiegandt
    renewiegandt committed Jan 10, 2019
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  3. Updated config, updated skript for changes in Ensembl Release 95 temp… 

    …orary fix for #51. needs more improvement of config handling
    basti committed Jan 10, 2019
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  4. get_best_motif.py: Removed additional whitespace in motif header

    @renewiegandt
    renewiegandt committed Jan 10, 2019
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  5. pipeline.nf: removed code for debuging

    @renewiegandt
    renewiegandt committed Jan 10, 2019
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  6. fixed max_pos calculation

    @JannikHamp
    JannikHamp committed Jan 10, 2019
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  7. correct maxpos calculation

    @JannikHamp
    JannikHamp committed Jan 10, 2019
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  8. fixed for correct contains_maxpos calculation

    @JannikHamp
    JannikHamp committed Jan 10, 2019
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  9. Merge pull request #53 from loosolab/JannikHamp-patch-2 

    correct maxpos calculation
    @renewiegandt
    renewiegandt committed Jan 10, 2019
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  10. bed_to_fasta.R: changes lapply to vapply

    @renewiegandt
    renewiegandt committed Jan 10, 2019
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  11. Merge branch 'dev' into estimation_motifs

    @renewiegandt
    renewiegandt committed Jan 10, 2019
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  12. Removed import os from get_best_motif.py

    @renewiegandt
    renewiegandt committed Jan 10, 2019
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  13. Removed newline from get_motif_seq

    @renewiegandt
    renewiegandt committed Jan 10, 2019
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  14. script for calculation of absolute max_pos values at start

    @JannikHamp
    JannikHamp committed Jan 10, 2019
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  15. added Rscript for maxpos calculation

    @JannikHamp
    JannikHamp committed Jan 10, 2019
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  16. Merge pull request #47 from loosolab/estimation_motifs 

    2.2 creates json file containing motif sequences
    @HendrikSchultheis
    HendrikSchultheis committed Jan 10, 2019
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  17. fixed for correct max_pos calculation after possible splitting 

    a new R script has been added, which calculates the absolut positions first. Here the relative positions are calculated again, after the column with contains_maxpos flags has been created.
    @JannikHamp
    JannikHamp committed Jan 10, 2019
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  18. Merge branch 'estimation_motifs' of https://github.molgen.mpg.de/loos… 

    …olab/masterJLU2018 into estimation_motifs
    @renewiegandt
    renewiegandt committed Jan 10, 2019
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  19. Merge branch 'dev' into tfbsscan-shebang

    @HendrikSchultheis
    HendrikSchultheis committed Jan 10, 2019
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  20. Merge pull request #46 from loosolab/tfbsscan-shebang 

    Add shebang to tfbsscan
    @HendrikSchultheis
    HendrikSchultheis committed Jan 10, 2019
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  21. forgot $path to start the new Rscript. now fixed

    @JannikHamp
    JannikHamp committed Jan 10, 2019
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  22. Fix for #51

    basti committed Jan 10, 2019
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Commits on Jan 11, 2019

  1. Fixed 1 output value of FilterMotifs.stats output. Flag 1 ratio was n… 

    …ot correct, due to variable naming issue
    @JannikHamp
    JannikHamp committed Jan 11, 2019
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  2. check if output ends with .bed

    @JannikHamp
    JannikHamp committed Jan 11, 2019
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  3. Delete abs_max_score.R

    @JannikHamp
    JannikHamp committed Jan 11, 2019
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  4. max_pos calculation is done in one Rscript

    @JannikHamp
    JannikHamp committed Jan 11, 2019
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  5. documentation

    @JannikHamp
    JannikHamp committed Jan 11, 2019
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  6. changed stats file name to compareBed.stats

    @JannikHamp
    JannikHamp committed Jan 11, 2019
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  7. changed name of output compareBed.stats in description

    @JannikHamp
    JannikHamp committed Jan 11, 2019
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  8. Merge pull request #54 from loosolab/JannikHamp-patch-1 

    Jannik hamp patch 1
    @JannikHamp
    JannikHamp committed Jan 11, 2019
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  9. added info, that file_paths must not contain the "|" pipe symbol

    @JannikHamp
    JannikHamp committed Jan 11, 2019
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  10. Added sorted outputs to improve handling in IGV 

    -> Fix #55
    basti committed Jan 11, 2019
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  11. Removed some typos in Readme

    basti committed Jan 11, 2019
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  12. Merge pull request #59 from loosolab/JannikHamp-patch-1 

    added info, that file_paths must not contain the "|" pipe symbol
    @renewiegandt
    renewiegandt committed Jan 11, 2019
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  13. Merge pull request #56 from loosolab/gtf_creation 

    Gtf creation
    @SebastianBeyvers
    SebastianBeyvers committed Jan 11, 2019
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Commits on Jan 12, 2019

  1. Update README.md

    @renewiegandt
    renewiegandt committed Jan 12, 2019
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  2. Merge branch 'dev' into estimation_motifs

    @renewiegandt
    renewiegandt committed Jan 12, 2019
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  3. pipeline.nf: Default of parameter max_size_fp is set to 200

    @renewiegandt
    renewiegandt committed Jan 12, 2019
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  4. README.md: fixed typos

    @renewiegandt
    renewiegandt committed Jan 12, 2019
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  5. add r package bit64 to environment

    @HendrikSchultheis
    HendrikSchultheis committed Jan 12, 2019
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  6. cast start and end column to integer64 to prevent scientific notation

    @HendrikSchultheis
    HendrikSchultheis committed Jan 12, 2019
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  7. cast start and end column to integer64 to prevent scientific notation

    @HendrikSchultheis
    HendrikSchultheis committed Jan 12, 2019
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  8. fixed missing point

    @HendrikSchultheis
    HendrikSchultheis committed Jan 12, 2019
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  9. Update README.md

    @renewiegandt
    renewiegandt committed Jan 12, 2019
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  10. Merge pull request #50 from loosolab/peak_calling 

    Peak calling fixing the merging bug, changing the parameter name from max_bp_between to min_gap
    @anastasiia
    anastasiia committed Jan 12, 2019
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  11. Update README.md 

    I think we needed the better explanation for the problem with MOODS
    @anastasiia
    anastasiia committed Jan 12, 2019
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  12. Merge pull request #63 from loosolab/cluster 

    Cluster
    @HendrikSchultheis
    HendrikSchultheis committed Jan 12, 2019
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  13. Update README.md

    @renewiegandt
    renewiegandt committed Jan 12, 2019
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  14. fixed .bed.bed unconsitent output name

    @JannikHamp
    JannikHamp committed Jan 12, 2019
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  15. Merge branch 'estimation_motifs' of https://github.molgen.mpg.de/loos… 

    …olab/masterJLU2018 into estimation_motifs
    @renewiegandt
    renewiegandt committed Jan 12, 2019
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  16. yml: fixed version of python and numpy to prevent bug in 1.1

    @renewiegandt
    renewiegandt committed Jan 12, 2019
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  17. remove personal path from nextflow.config

    @renewiegandt
    renewiegandt committed Jan 12, 2019
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  18. renamed config files

    @renewiegandt
    renewiegandt committed Jan 12, 2019
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  19. Update README and help message in pipeline

    @renewiegandt
    renewiegandt committed Jan 12, 2019
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  20. pipeline.nf: added missing params.

    @renewiegandt
    renewiegandt committed Jan 12, 2019
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  21. Fixed typo

    @renewiegandt
    renewiegandt committed Jan 12, 2019
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  22. Updated configs to new parameteres

    @renewiegandt
    renewiegandt committed Jan 12, 2019
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Commits on Jan 13, 2019

  1. Merge pull request #64 from loosolab/JannikHamp-patch-3 

    fixed .bed.bed unconsitent output name
    @renewiegandt
    renewiegandt committed Jan 13, 2019
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  2. Added demo run files

    @renewiegandt
    renewiegandt committed Jan 13, 2019
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  3. Added demo command to README.md

    @renewiegandt
    renewiegandt committed Jan 13, 2019
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  4. Added missing letter in README.md

    @renewiegandt
    renewiegandt committed Jan 13, 2019
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  5. Merge pull request #61 from loosolab/estimation_motifs 

    Update README.md
    @renewiegandt
    renewiegandt committed Jan 13, 2019
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  6. Update README.md: Added step 4 of installation

    @renewiegandt
    renewiegandt committed Jan 13, 2019
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  7. Merge pull request #66 from loosolab/estimation_motifs 

    Update README.md: Added step 4 of installation
    @SebastianBeyvers
    SebastianBeyvers committed Jan 13, 2019
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