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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

Commits on Dec 6, 2018

  1. print number of reduced kmer

    @HendrikSchultheis
    HendrikSchultheis committed Dec 6, 2018
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Commits on Dec 17, 2018

  1. Merge pull request #8 from loosolab/master 

    merge master to dev
    @renewiegandt
    renewiegandt committed Dec 17, 2018
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  2. $workdir/merged.bed -> "$workdir"/merged.bed

    @JannikHamp
    JannikHamp committed Dec 17, 2018
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Commits on Dec 18, 2018

  1. Merge pull request #9 from loosolab/dev 

    Merge dev to motif_estimation to bring branch up to date
    @renewiegandt
    renewiegandt committed Dec 18, 2018
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  2. Bugfix in bed_to_fasta.R: Get last and second last instead of fixed i… 

    …ndices
    @renewiegandt
    renewiegandt committed Dec 18, 2018
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  3. bed_to_fasta.R: Improved documentation

    @renewiegandt
    renewiegandt committed Dec 18, 2018
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Commits on Dec 19, 2018

  1. bed_to_fasta.R: Imporved parametercalling with optparse

    @renewiegandt
    renewiegandt committed Dec 19, 2018
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  2. adaption of pipeline.nf to changes in bed_to_fasta.R

    @renewiegandt
    renewiegandt committed Dec 19, 2018
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  3. Refactoring

    @renewiegandt
    renewiegandt committed Dec 19, 2018
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  4. Merge pull request #13 from loosolab/dev 

    Dev
    @renewiegandt
    renewiegandt committed Dec 19, 2018
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  5. changing the separator in the last line

    @anastasiia
    anastasiia committed Dec 19, 2018
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  6. adding a column name strand containing always .

    @anastasiia
    anastasiia committed Dec 19, 2018
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  7. refactoring; renamed reduce_bed to reduce_sequence

    @HendrikSchultheis
    HendrikSchultheis committed Dec 19, 2018
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  8. Merge pull request #15 from loosolab/peak_calling 

    Peak calling
    @renewiegandt
    renewiegandt committed Dec 19, 2018
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  9. check whether jellyfish is installed

    @HendrikSchultheis
    HendrikSchultheis committed Dec 19, 2018
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  10. reduce_bed renamed to reduce_sequence

    @HendrikSchultheis
    HendrikSchultheis committed Dec 19, 2018
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  11. get_best_motif.py: fixed bug which caused to print motif header as la… 

    …st line + improved documentation
    @renewiegandt
    renewiegandt committed Dec 19, 2018
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  12. check whether jellyfish is installed

    @HendrikSchultheis
    HendrikSchultheis committed Dec 19, 2018
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  13. check whether cdhit is installed

    @HendrikSchultheis
    HendrikSchultheis committed Dec 19, 2018
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  14. omit TODO

    @HendrikSchultheis
    HendrikSchultheis committed Dec 19, 2018
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  15. check for header and forward it if provided

    @HendrikSchultheis
    HendrikSchultheis committed Dec 19, 2018
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  16. automatically detect and keep column names if provided

    @HendrikSchultheis
    HendrikSchultheis committed Dec 19, 2018
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  17. added author; better missing input error

    @HendrikSchultheis
    HendrikSchultheis committed Dec 19, 2018
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  18. added author

    @HendrikSchultheis
    HendrikSchultheis committed Dec 19, 2018
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  19. Fixed typos in get_best_motif.py

    @renewiegandt
    renewiegandt committed Dec 19, 2018
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  20. Reads BED-files with or without header

    @renewiegandt
    renewiegandt committed Dec 19, 2018
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Commits on Dec 20, 2018

  1. Imporved description for installation in README.md

    @renewiegandt
    renewiegandt committed Dec 20, 2018
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  2. Removed snakemake from yaml-file

    @renewiegandt
    renewiegandt committed Dec 20, 2018
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  3. Set parameter organism as required wihtout an default value

    @renewiegandt
    renewiegandt committed Dec 20, 2018
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  4. spell check

    @HendrikSchultheis
    HendrikSchultheis committed Dec 20, 2018
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  5. Added Parameter gtf_path. If path is set process create_gtf will be s… 

    …kipped
    @renewiegandt
    renewiegandt committed Dec 20, 2018
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  6. spell check

    @HendrikSchultheis
    HendrikSchultheis committed Dec 20, 2018
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  7. fixed more typos

    @HendrikSchultheis
    HendrikSchultheis committed Dec 20, 2018
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  8. process description for reduce_sequence and clustering

    @HendrikSchultheis
    HendrikSchultheis committed Dec 20, 2018
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  9. Fixed typo in bed_to_fasta.R

    @renewiegandt
    renewiegandt committed Dec 20, 2018
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  10. Merge pull request #12 from loosolab/motif_estiamtion 

    Motif estiamtion
    @renewiegandt
    renewiegandt committed Dec 20, 2018
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  11. Added new parameter list to README.mf

    @renewiegandt
    renewiegandt committed Dec 20, 2018
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  12. Merge branch 'motif_estiamtion' of https://github.molgen.mpg.de/looso… 

    …lab/masterJLU2018 into motif_estiamtion
    @renewiegandt
    renewiegandt committed Dec 20, 2018
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Commits on Dec 21, 2018

  1. Merge pull request #17 from loosolab/cluster 

    Cluster
    @HendrikSchultheis
    HendrikSchultheis committed Dec 21, 2018
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  2. Fixed bug in pipeline.nf: parameter gtf_path is now working

    @renewiegandt
    renewiegandt committed Dec 21, 2018
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Commits on Dec 22, 2018

  1. Merge pull request #21 from loosolab/motif_estiamtion 

    Fixed bug caused by paramterer gtf_path
    @renewiegandt
    renewiegandt committed Dec 22, 2018
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Commits on Dec 27, 2018

  1. Improving comments 

    Answer for the issue #22
    @anastasiia
    anastasiia committed Dec 27, 2018
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Commits on Jan 2, 2019

  1. fix for the help message called using -h

    @anastasiia
    anastasiia committed Jan 2, 2019
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  2. fixing the bug with the output directory name

    @anastasiia
    anastasiia committed Jan 2, 2019
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Commits on Jan 3, 2019

  1. Merge pull request #24 from loosolab/peak_calling 

    Improving comments in the footprints_extraction.py script
    @renewiegandt
    renewiegandt committed Jan 3, 2019
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  2. sorting scripts depending on their function

    @renewiegandt
    renewiegandt committed Jan 3, 2019
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  3. Renaming output paths

    @renewiegandt
    renewiegandt committed Jan 3, 2019
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  4. install optparse if not yet installed; added missing author to docume… 

    …ntation
    @HendrikSchultheis
    HendrikSchultheis committed Jan 3, 2019
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  5. Merge pull request #30 from loosolab/cluster 

    Clustering
    @HendrikSchultheis
    HendrikSchultheis committed Jan 3, 2019
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  6. Merge branch 'dev' into estimation_motifs

    @renewiegandt
    renewiegandt committed Jan 3, 2019
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  7. Merge pull request #28 from loosolab/estimation_motifs 

     sorting scripts depending on their function
    @renewiegandt
    renewiegandt committed Jan 3, 2019
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  8. Added more comments and author / mail description

    basti committed Jan 3, 2019
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  9. missing points in readme 

    Have noticed that there are some missing points at the end of sentences.
    @anastasiia
    anastasiia committed Jan 3, 2019
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  10. Added functionality to Fix #19

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

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

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

    basti committed Jan 3, 2019
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  14. Merge pull request #31 from loosolab/anastasiia-patch-1 

    missing points in readme
    @renewiegandt
    renewiegandt committed Jan 3, 2019
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  15. Commented every function / method to resolve #29

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

    basti committed Jan 3, 2019
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  17. Removed data_files

    basti committed Jan 3, 2019
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  18. 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. Merge pull request #37 from loosolab/dev 

    Dev to my branch
    @anastasiia
    anastasiia committed Jan 4, 2019
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  3. if there is no additional information provided by the original input … 

    …bed file. the point will be printed to the last column in the output bed file
    @anastasiia
    anastasiia committed Jan 4, 2019
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  4. checking for the directory the user wants to save the file in, and cr… 

    …eating one if it does not exist
    @anastasiia
    anastasiia committed Jan 4, 2019
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  5. adding a check if the directory was passed by the user

    @anastasiia
    anastasiia committed Jan 4, 2019
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  6. added some documentation

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

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

    @JannikHamp
    JannikHamp committed Jan 4, 2019
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  9. documentation

    @JannikHamp
    JannikHamp committed Jan 4, 2019
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  10. documentation

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

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

    @JannikHamp
    JannikHamp committed Jan 4, 2019
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  13. documentation

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

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

    @renewiegandt
    renewiegandt committed Jan 4, 2019
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  16. 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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  5. fixing the bug with footprint length

    @anastasiia
    anastasiia committed Jan 7, 2019
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  6. fixing the bug with overlaps + adding a merging function if the footp… 

    …rints have small ammount of bp in between
    @anastasiia
    anastasiia committed Jan 7, 2019
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  7. allowing user to set the parameter for max bp allowed in between the … 

    …footprints; also adding some comments
    @anastasiia
    anastasiia 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. changing the name of footprints from footprint_ to f_ to make sure th… 

    …e script of René works well
    @anastasiia
    anastasiia committed Jan 8, 2019
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  3. Merge pull request #40 from loosolab/gtf_creation 

    Gtf creation
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  4. Update yaml; removed debug code from pipeline; update README

    @renewiegandt
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  5. Merge pull request #41 from loosolab/peak_calling 

    Peak calling to dev after resolving overlaps
    @anastasiia
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  6. Merge branch 'dev' into estimation_motifs

    @renewiegandt
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  7. this r script is no more necessary, the other does its job

    @JannikHamp
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  8. New updated version. Faster and more robust

    @JannikHamp
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  9. updated version.. make unique updated, more robust in general

    @JannikHamp
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  10. Added basic parameter checks.

    @HendrikSchultheis
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  11. get_best_motif.py: Added alternative name to best_motif file

    @renewiegandt
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  12. added the shebang line 

    Answer to #44
    @anastasiia
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  13. Add shebang to tfbsscan

    @msbentsen
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  14. added information for logfile

    @JannikHamp
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  15. added dicumentation and parameter for .stats output file

    @JannikHamp
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  16. Merge pull request #42 from loosolab/estimation_motifs 

    Update yaml; removed debug code from pipeline; update README
    @renewiegandt
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  17. get_best_motif.py: removed whitespace from motif header

    @renewiegandt
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  18. added script get_motif_seq.R

    @renewiegandt
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  19. pipeline.nf: implemented get_motif_seq.R

    @renewiegandt
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  20. added r packages: RJSONIO, varhandle to masterenv.yml

    @renewiegandt
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  21. Merge branch 'dev' into estimation_motifs

    @renewiegandt
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Commits on Jan 9, 2019

  1. documentation changes

    @JannikHamp
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  2. Merge pull request #45 from loosolab/peak_calling 

    added the shebang line
    @anastasiia
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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
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  5. get_motif_seq.R: added parameter tmp_path and cluster_id

    @renewiegandt
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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
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  8. updated check for trailing tabs in motiffiles

    @JannikHamp
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  9. removed echo from testing

    @JannikHamp
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  10. the structure is ready, this need to be adjusted to the data the foot… 

    …print_extraction parses
    @anastasiia
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  11. Added log file for part 2.2_motif_estimation

    @renewiegandt
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  12. more documentation, replce =, <-

    @JannikHamp
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  13. Parameter summary added

    @HendrikSchultheis
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  14. Added Shebang in response to #44

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

    updated script. Now the path of subscripts is automatically aquired. …
    @renewiegandt
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  16. Merge pull request #43 from loosolab/cluster 

    Cluster
    @renewiegandt
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  17. Merge branch 'dev' into estimation_motifs

    @renewiegandt
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  18. added missing shebangs to 2.2 scripts #44

    @renewiegandt
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  19. pipeline.nf: adjusting to new parameter required by 2.1 scripts

    @renewiegandt
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  20. fixing the bug with merging. The code will be edited soon to look nic… 

    …e and easy to understand
    @anastasiia
    anastasiia committed Jan 9, 2019
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  21. Merge branch 'peak_calling' of https://github.molgen.mpg.de/loosolab/… 

    …masterJLU2018 into peak_calling

merging peak calling
    @anastasiia
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  22. fixing the typo footprints and not footrpints

    @anastasiia
    anastasiia 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
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  5. pipeline.nf: removed code for debuging

    @renewiegandt
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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. the max_pos is the index, and so add always 1 after calculating it. O… 

    …therwise it could be 0 as index
    @anastasiia
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  9. fixed for correct contains_maxpos calculation

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

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

    @renewiegandt
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  12. Merge branch 'dev' into estimation_motifs

    @renewiegandt
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  13. adding a validation while printing to the output file. If there are p… 

    …roblems with start/end positions or max_pos, the footprint will not be written to the output file
    @anastasiia
    anastasiia committed Jan 10, 2019
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  14. Removed import os from get_best_motif.py

    @renewiegandt
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  15. Removed newline from get_motif_seq

    @renewiegandt
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  16. script for calculation of absolute max_pos values at start

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

    @JannikHamp
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  18. 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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  19. 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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  20. Merge branch 'estimation_motifs' of https://github.molgen.mpg.de/loos… 

    …olab/masterJLU2018 into estimation_motifs
    @renewiegandt
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  21. Merge branch 'dev' into tfbsscan-shebang

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

    Add shebang to tfbsscan
    @HendrikSchultheis
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  23. forgot $path to start the new Rscript. now fixed

    @JannikHamp
    JannikHamp committed Jan 10, 2019
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  24. deleting the print statements, adding some comments

    @anastasiia
    anastasiia committed Jan 10, 2019
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  25. 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
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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
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  7. changed name of output compareBed.stats in description

    @JannikHamp
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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
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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
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  3. pipeline.nf: Default of parameter max_size_fp is set to 200

    @renewiegandt
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  4. README.md: fixed typos

    @renewiegandt
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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
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  7. cast start and end column to integer64 to prevent scientific notation

    @HendrikSchultheis
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  8. fixed missing point

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

    @renewiegandt
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  10. making the list out of the dictionary in the merge function to ensure… 

    … the sorting before check for merging
    @anastasiia
    anastasiia committed Jan 12, 2019
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  11. deleting print statements

    @anastasiia
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  12. changing the name of max_bp_between to min_gap

    @anastasiia
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  13. 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
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  14. Update README.md 

    I think we needed the better explanation for the problem with MOODS
    @anastasiia
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  15. Merge pull request #63 from loosolab/cluster 

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

    @renewiegandt
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  17. fixed .bed.bed unconsitent output name

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

    …olab/masterJLU2018 into estimation_motifs
    @renewiegandt
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  19. yml: fixed version of python and numpy to prevent bug in 1.1

    @renewiegandt
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  20. remove personal path from nextflow.config

    @renewiegandt
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  21. renamed config files

    @renewiegandt
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  22. Update README and help message in pipeline

    @renewiegandt
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  23. pipeline.nf: added missing params.

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

    @renewiegandt
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  25. Updated configs to new parameteres

    @renewiegandt
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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

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

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

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    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

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    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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