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Start writing STAT solo #4

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Start writing STAT solo #4

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Commits on May 2, 2019

  1. Rename all nfcore/nf-core/kerimoff --> czbiohub

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    olgabot committed May 2, 2019
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  2. base off of nfcore, author is Olga

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    olgabot committed May 2, 2019
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  3. Add makefile for docker building

    @olgabot
    olgabot committed May 2, 2019
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  4. accept PRs to master from anywhere! mwah hahahaha"

    @olgabot
    olgabot committed May 2, 2019
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  5. Update docker image names

    @olgabot
    olgabot committed May 2, 2019
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  6. Merge pull request #1 from czbiohub/olgabot/rename-czbiohub 

    Olgabot/rename czbiohub
    @olgabot
    olgabot authored May 2, 2019
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  7. updating fastp

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    olgabot committed May 2, 2019
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  8. Update trimmer name, time and requirments

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    olgabot committed May 2, 2019
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  9. Fix parameter name for params.clip_r{1,2} --> params.five_prime_clip_… 

    …r{1,2}
    @olgabot
    olgabot committed May 2, 2019
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  10. Fix parameter name for params.clip_r{1,2} --> params.five_prime_clip_… 

    …r{1,2} AGAIN
    @olgabot
    olgabot committed May 2, 2019
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  11. Separate fastqc on trimmed reads

    @olgabot
    olgabot committed May 2, 2019
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  12. Fix naming of output trimming reports

    @olgabot
    olgabot committed May 2, 2019
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Commits on May 3, 2019

  1. fix test data'

    @olgabot
    olgabot committed May 3, 2019
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  2. Don't lint the pipeline for now

    @olgabot
    olgabot committed May 3, 2019
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  3. Merge pull request #3 from czbiohub/olgabot/fastp 

    Use fastp for trimming instead of trimgalore
    @olgabot
    olgabot authored May 3, 2019
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Commits on May 9, 2019

  1. Add notes about fastp and htseq

    @olgabot
    olgabot committed May 9, 2019
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  2. Remove subread (featureCounts) from requirements

    @olgabot
    olgabot committed May 9, 2019
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  3. Initial try of htseq-count

    @olgabot
    olgabot committed May 9, 2019
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  4. Add notes in changelog

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    olgabot committed May 9, 2019
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  5. update regex for htseq-count version

    @olgabot
    olgabot committed May 9, 2019
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  6. Add test example for makefile

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    olgabot committed May 9, 2019
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  7. update biotypes header to htseq-count

    @olgabot
    olgabot committed May 9, 2019
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  8. Rename to merge_htseq-count.py

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    olgabot committed May 9, 2019
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  9. specify memory for htseq-count

    @olgabot
    olgabot committed May 9, 2019
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  10. Use czbiohub/rnaseq container

    @olgabot
    olgabot committed May 9, 2019
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  11. Update merging of htseq-count gene-cell tables"

    @olgabot
    olgabot committed May 9, 2019
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  12. Missing pipe characters

    @olgabot
    olgabot committed May 9, 2019
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  13. Comment out sample correlation for now

    @olgabot
    olgabot committed May 9, 2019
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  14. Try updating the edger similarity

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    olgabot committed May 9, 2019
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Commits on May 10, 2019

  1. remove htseq-count merging python gscript

    @olgabot
    olgabot committed May 10, 2019
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  2. Remove sample correlation

    @olgabot
    olgabot committed May 10, 2019
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  3. Move merged htseqcounts into same folder

    @olgabot
    olgabot committed May 10, 2019
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Commits on May 21, 2019

  1. Change featurecounts-->htseq

    @olgabot
    olgabot committed May 21, 2019
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  2. Put biotypes back

    @olgabot
    olgabot committed May 21, 2019
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  3. Don't lint pipeline code

    @olgabot
    olgabot committed May 21, 2019
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  4. fix parsing of htseq-count output

    @olgabot
    olgabot committed May 21, 2019
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  5. remove copy-paste cruft

    @olgabot
    olgabot committed May 21, 2019
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  6. Merge pull request #10 from czbiohub/olgabot/htseq 

    [WIP] Add htseq-count
    @olgabot
    olgabot authored May 21, 2019
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  7. Add fastp version scraping

    @olgabot
    olgabot committed May 21, 2019
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  8. Make local test be testing hisat

    @olgabot
    olgabot committed May 21, 2019
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Commits on May 22, 2019

  1. Merge pull request #14 from czbiohub/olgabot/htseq 

    Add remaining htseq stuff
    @olgabot
    olgabot authored May 22, 2019
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  2. Use all test commands in Makefile

    @olgabot
    olgabot committed May 22, 2019
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  3. Add biohub config and transgenes

    @olgabot
    olgabot committed May 22, 2019
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  4. Add default work dir

    @olgabot
    olgabot committed May 22, 2019
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  5. Update test_biohub to use -profile czbiohub_aws

    @olgabot
    olgabot committed May 22, 2019
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  6. Fix biohub and aws configuration

    @olgabot
    olgabot committed May 22, 2019
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  7. Add resume to test biohub'

    @olgabot
    olgabot committed May 22, 2019
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  8. Fix transgene and aws conf

    @olgabot
    olgabot committed May 22, 2019
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  9. Start making references composable

    @olgabot
    olgabot committed May 22, 2019
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  10. Get multiple input genoes to work

    @olgabot
    olgabot committed May 22, 2019
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  11. whitespace

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    olgabot committed May 22, 2019
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  12. Add transgenes to czbiohub config

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    olgabot committed May 22, 2019
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  13. Update name for ERCCs location

    @olgabot
    olgabot committed May 22, 2019
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  14. use genome_names as variables

    @olgabot
    olgabot committed May 22, 2019
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  15. Change trimgalore --> fastp

    @olgabot
    olgabot committed May 22, 2019
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  16. Add ERCCs to test biohug

    @olgabot
    olgabot committed May 22, 2019
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  17. Fix typo

    @olgabot
    olgabot committed May 22, 2019
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  18. Show aws region and batch queue if aws specified

    @olgabot
    olgabot committed May 22, 2019
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  19. increase padding for summary

    @olgabot
    olgabot committed May 22, 2019
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  20. remove gtf printing

    @olgabot
    olgabot committed May 22, 2019
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  21. protect output with quotes

    @olgabot
    olgabot committed May 22, 2019
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Commits on May 23, 2019

  1. Remove sample correlation

    @olgabot
    olgabot committed May 23, 2019
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  2. add czbiohub logo to pipeline

    @olgabot
    olgabot committed May 23, 2019
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  3. Add aws batch info to summary

    @olgabot
    olgabot committed May 23, 2019
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  4. Fix merge conflict

    @olgabot
    olgabot committed May 23, 2019
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  5. Fix work dir specification

    @olgabot
    olgabot committed May 23, 2019
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  6. Add outdir for makefile

    @olgabot
    olgabot committed May 23, 2019
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  7. Fix merge conflict

    @olgabot
    olgabot committed May 23, 2019
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  8. remove comments

    @olgabot
    olgabot committed May 23, 2019
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  9. Add splicing, exon quant to testing

    @olgabot
    olgabot committed May 23, 2019
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  10. Test all aspects of pipelien

    @olgabot
    olgabot committed May 23, 2019
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  11. Also test hisat2 aligner

    @olgabot
    olgabot committed May 23, 2019
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  12. remove git rebase cruft

    @olgabot
    olgabot committed May 23, 2019
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  13. Don't test transcriptome for now

    @olgabot
    olgabot committed May 23, 2019
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  14. Add pigz to dockerfile

    @olgabot
    olgabot committed May 23, 2019
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  15. Sort genome names, change fastp name

    @olgabot
    olgabot committed May 23, 2019
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  16. Use different base directory for dexseq prepare annotation

    @olgabot
    olgabot committed May 23, 2019
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  17. Use home instead of for scripts

    @olgabot
    olgabot committed May 23, 2019
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  18. fastp --> trim_with_fastp

    @olgabot
    olgabot committed May 23, 2019
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  19. Move all utility scripts to be flat in bin/

    @olgabot
    olgabot committed May 23, 2019
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  20. use latest docker image

    @olgabot
    olgabot committed May 23, 2019
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Commits on May 24, 2019

  1. start writing STARsolo

    @olgabot
    olgabot committed May 24, 2019
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Commits on May 28, 2019

  1. Add storage options for star Genome generate container

    @olgabot
    olgabot committed May 28, 2019
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