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Dev to my branch #37

Merged
merged 44 commits into from
Jan 4, 2019
Merged

Dev to my branch #37

merged 44 commits into from
Jan 4, 2019

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. refactoring; renamed reduce_bed to reduce_sequence

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

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

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

    @HendrikSchultheis
    HendrikSchultheis committed Dec 19, 2018
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  8. 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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  9. check whether jellyfish is installed

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

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

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

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

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

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

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

    @renewiegandt
    renewiegandt committed Dec 19, 2018
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  17. 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 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. 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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  9. Merge pull request #31 from loosolab/anastasiia-patch-1 

    missing points in readme
    @renewiegandt
    renewiegandt committed Jan 3, 2019
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