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Restores mapping to nf-core; Keeps gatk *Spark #84

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Restores mapping to nf-core; Keeps gatk *Spark #84

wants to merge 70 commits into from

Commits on Oct 21, 2019

  1. Adds GenomeChronicler; Changes "withLabel:VEP" -> "withName:VEP"

    @cgpu
    cgpu committed Oct 21, 2019
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  2. Creates minimal bam channel with only file

    @cgpu
    cgpu committed Oct 21, 2019
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  3. C-out for testing

    @cgpu
    cgpu committed Oct 21, 2019
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  4. Added url; baseDir doee not work when on aws instance

    @cgpu
    cgpu committed Oct 21, 2019
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  5. Adds back nf-core functions; WIP testing

    @cgpu
    cgpu committed Oct 21, 2019
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  6. Adds genomechronicler; Comments out all following processes; WIP

    Ubuntu committed Oct 21, 2019
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  7. Changes outpit dir; WIP

    Ubuntu committed Oct 21, 2019
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Commits on Oct 22, 2019

  1. Fixes reports for GenomeChronicler; WIP (vep html not implemented)

    @cgpu
    cgpu committed Oct 22, 2019
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  2. WIP; report update

    @cgpu
    cgpu committed Oct 22, 2019
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Commits on Oct 25, 2019

  1. Absorbs path-release 2.5.1-Årjep-Ålkatjjekna 🎉

    @cgpu
    cgpu committed Oct 25, 2019
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  2. Merge branch 'nf-core-master'

    @cgpu
    cgpu committed Oct 25, 2019
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  3. Restores channel name from nfcore

    @cgpu
    cgpu committed Oct 25, 2019
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  4. Changes MultiQC loc; enables display

    @cgpu
    cgpu committed Oct 25, 2019
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  5. Updated docker build used

    @cgpu
    cgpu committed Oct 25, 2019
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  6. Added --resultsDir to reflect .pl changes

    @cgpu
    cgpu committed Oct 25, 2019
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  7. Adds --resultsDir flag requirement

    EC2 Default User committed Oct 25, 2019
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Commits on Oct 26, 2019

  1. Update to reflect PGP-UK/GenomeChronicler@65df2a9

    @cgpu
    cgpu committed Oct 26, 2019
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Commits on Oct 30, 2019

  1. Removed resources limitation from samtools sort

    @cgpu
    cgpu committed Oct 30, 2019
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  2. Decreased --MAX_RECORDS_IN_RAM

    @cgpu
    cgpu committed Oct 30, 2019
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Commits on Oct 31, 2019

  1. Restoring to default 500000

    @cgpu
    cgpu committed Oct 31, 2019
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Commits on Nov 1, 2019

  1. Removes java options, MAX_RECORDS_IN_RAM and TMP_DIR

    @cgpu
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  2. Revert "Removes java options, MAX_RECORDS_IN_RAM and TMP_DIR" 

    This reverts commit eeb3078.
    @cgpu
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  3. Added labels memory and cpus max to MarkDuplicates

    @cgpu
    cgpu committed Nov 1, 2019
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  4. Updated MAX_RECORDS_IN_RAM to extremely low value (500)

    @cgpu
    cgpu committed Nov 1, 2019
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Commits on Nov 13, 2019

  1. Merge pull request #2 from nf-core/master 

    Update README.md
    @cgpu
    cgpu committed Nov 13, 2019
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Commits on Nov 20, 2019

  1. Updates container version

    @cgpu
    cgpu committed Nov 20, 2019
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  2. Reverts to previous container tag

    @cgpu
    cgpu committed Nov 20, 2019
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Commits on Nov 24, 2019

  1. Adds spark version of MarkDuplicates and BaseRecalibrator

    @cgpu
    cgpu committed Nov 24, 2019
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  2. Merge branch 'master' of https://github.com/cgpu/sarek

    @cgpu
    cgpu committed Nov 24, 2019
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  3. Adds cpus and container declaration for Spark versions of gatk tools

    @cgpu
    cgpu committed Nov 24, 2019
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  4. Minor typo

    @cgpu
    cgpu committed Nov 24, 2019
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  5. Modifies MarkDuplicates command

    @cgpu
    cgpu committed Nov 24, 2019
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Commits on Nov 25, 2019

  1. Adds updated lowercase params to Spark tools

    @cgpu
    cgpu committed Nov 25, 2019
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  2. Adds verbosity ERROR

    @cgpu
    cgpu committed Nov 25, 2019
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  3. Adding error verbosity

    @cgpu
    cgpu committed Nov 25, 2019
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  4. Adding error verbosity

    @cgpu
    cgpu committed Nov 25, 2019
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  5. Adds redirection of log message to file (now it prints to sterr)

    @cgpu
    cgpu committed Nov 25, 2019
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  6. Changes temp_dir from container's tmp to s3 remote workdir; Changes .… 

    …bai-> bam.bai
    @cgpu
    cgpu committed Nov 25, 2019
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  7. Restricts resources alloced to BaseRecal

    @cgpu
    cgpu committed Nov 25, 2019
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  8. Adds explicit declaration of maxForks for processes with --intervals

    @cgpu
    cgpu committed Nov 25, 2019
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  9. Adds ApplyBQSRSpark

    @cgpu
    cgpu committed Nov 25, 2019
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  10. Defines maxForks for --intervals processes

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  11. Defines maxForks for --intervals processes

    @cgpu
    cgpu committed Nov 25, 2019
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  12. Adds custom genome GRCh38_PGP_UK

    @cgpu
    cgpu committed Nov 25, 2019
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  13. Adds default genome to match GenomeChronicler resources

    @cgpu
    cgpu committed Nov 25, 2019
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Commits on Nov 26, 2019

  1. Removes residue bwaIndex from GRCh38

    @cgpu
    cgpu committed Nov 26, 2019
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  2. Removes GenomeChronicler .dict, .fa.fai

    @cgpu
    cgpu committed Nov 26, 2019
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  3. Testing 2FA

    @cgpu
    cgpu committed Nov 26, 2019
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  4. Update nextflow.config

    @cgpu
    cgpu committed Nov 26, 2019
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Commits on Nov 27, 2019

  1. Adds explicit memory definition for processes

    @cgpu
    cgpu committed Nov 27, 2019
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  2. Merge branch 'master' of cgpu/sarek

    @cgpu
    cgpu committed Nov 27, 2019
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  3. Adds more resources to BaseRecalibratorSpark processes

    @cgpu
    cgpu committed Nov 27, 2019
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  4. Adds less resources to BaseRecalibratorSpark processes

    @cgpu
    cgpu committed Nov 27, 2019
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  5. Adds ultra many resources; To revert back after test

    @cgpu
    cgpu committed Nov 27, 2019
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  6. Restricts resources; Needed for using instances with Mem.GB/vCPU rati… 

    …o equal to 4
    @cgpu
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Commits on Nov 28, 2019

  1. Update resources for PGP-UK

    @cgpu
    cgpu committed Nov 28, 2019
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Commits on Dec 4, 2019

  1. Addresses #3 ; Known issue with bwa | smatools pipe

    @cgpu
    cgpu committed Dec 4, 2019
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  2. Updates resource alloc to *Spark versions; Adds retry for MultiQC

    @cgpu
    cgpu committed Dec 4, 2019
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  3. Adds new image built with PGP-UK/GenomeChronicler@5513c6f

    @cgpu
    cgpu committed Dec 4, 2019
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  4. Adds verbosity INFO for debugging

    @cgpu
    cgpu committed Dec 4, 2019
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  5. Freezes broadinstitute/gatk to 4.1.4.0

    @cgpu
    cgpu committed Dec 4, 2019
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Commits on Dec 7, 2019

  1. Change GATK Spark tools verbosity to debug

    @cgpu
    cgpu committed Dec 7, 2019
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  2. Restricts resource alloc of MarkDuplicatesSpark

    @cgpu
    cgpu committed Dec 7, 2019
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Commits on Dec 8, 2019

  1. Removes explicit resource alloc from bamqc (qualimap)

    @cgpu
    cgpu committed Dec 8, 2019
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  2. Removes metrics file; Refer to this: https://gatkforums.broadinstitut… 

    …e.org/gatk/discussion/23441/markduplicatespark-is-slower-than-normal-markduplicates
    @cgpu
    cgpu committed Dec 8, 2019
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  3. Downgrades gatk from 4.1.4.0 to 4.1.3.0

    @cgpu
    cgpu committed Dec 8, 2019
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  4. Returns mapping to nfcore version 2.5.1

    @cgpu
    cgpu committed Dec 8, 2019
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Commits on Dec 20, 2019

  1. Reformats bwa mem | samtools sort command; WIP suboptimal resource … 

    …usage
    @cgpu
    cgpu committed Dec 20, 2019
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Commits on Dec 23, 2019

  1. Addresses PGP-UK#5 ;WIP

    @cgpu
    cgpu committed Dec 23, 2019
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  2. Restores mapping to nf-core; Keeps gatk *Spark

    @cgpu
    cgpu committed Dec 23, 2019
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