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Feature/streamline inputs #34

Merged
merged 86 commits into from
Jan 8, 2020
Merged

Feature/streamline inputs #34

merged 86 commits into from
Jan 8, 2020

Commits on Dec 10, 2019

  1. use small genomes to generate examples and stramline input definitions

    @rsuchecki
    rsuchecki committed Dec 10, 2019
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  2. corrected urls

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    rsuchecki committed Dec 10, 2019
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Commits on Dec 11, 2019

  1. relaxed allowed target name regex

    @rsuchecki
    rsuchecki committed Dec 11, 2019
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  2. stingency settings not ensembl specific, moved to main config

    @rsuchecki
    rsuchecki committed Dec 11, 2019
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  3. refactoring gtf/gff3 fileds def

    @rsuchecki
    rsuchecki committed Dec 11, 2019
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  4. major re-work of input staging and multitude of related changes

    @rsuchecki
    rsuchecki committed Dec 11, 2019
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  5. updated repr pep filtering

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    rsuchecki committed Dec 11, 2019
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Commits on Dec 12, 2019

  1. relaxed req to include supercontigs not just chromosomes

    @rsuchecki
    rsuchecki committed Dec 12, 2019
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  2. added sequencesToPlace spec to test config

    @rsuchecki
    rsuchecki committed Dec 12, 2019
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  3. restored core functionality after re-structure

    @rsuchecki
    rsuchecki committed Dec 12, 2019
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  4. cleanup, comments

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    rsuchecki committed Dec 12, 2019
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  5. added samtools container def

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    rsuchecki committed Dec 12, 2019
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  6. optional faidx process if idx no provided

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    rsuchecki committed Dec 12, 2019
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  7. added data set from non Esembl source

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    rsuchecki committed Dec 12, 2019
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  8. generalised gff3-based pep conversion to Ensembl style, also allows p… 

    …ass-through of already existing records
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  9. allowing user-specified chromosome id pattern for block and feature J… 

    …SON generation
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    rsuchecki committed Dec 12, 2019
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Commits on Dec 13, 2019

  1. updated and documented test data sets

    @rsuchecki
    rsuchecki committed Dec 13, 2019
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  2. travis stub

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    rsuchecki committed Dec 13, 2019
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  3. opted for smaller samtools container

    @rsuchecki
    rsuchecki committed Dec 13, 2019
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  4. hack to handle gz (not bgz) files fro chr lengths

    @rsuchecki
    rsuchecki committed Dec 13, 2019
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  5. minor

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    rsuchecki committed Dec 13, 2019
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  6. Update README.md

    @rsuchecki
    rsuchecki authored Dec 13, 2019
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  7. Update .travis.yaml

    @rsuchecki
    rsuchecki authored Dec 13, 2019
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  8. Update .travis.yaml

    @rsuchecki
    rsuchecki authored Dec 13, 2019
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  9. Update .travis.yaml

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    rsuchecki authored Dec 13, 2019
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  10. Update .travis.yaml

    @rsuchecki
    rsuchecki authored Dec 13, 2019
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Commits on Dec 17, 2019

  1. test profile with local data

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    rsuchecki committed Dec 17, 2019
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  2. travis data download and untar

    @rsuchecki
    rsuchecki committed Dec 17, 2019
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  3. Merge branch 'feature/streamline-inputs' into feature/streamline-inputs

    @rsuchecki
    rsuchecki authored Dec 17, 2019
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  4. travis fixes

    @rsuchecki
    rsuchecki committed Dec 17, 2019
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  5. merge conflict res

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    rsuchecki committed Dec 17, 2019
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Commits on Dec 18, 2019

  1. ubu version for travis

    @rsuchecki
    rsuchecki committed Dec 18, 2019
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  2. updated dep

    @rsuchecki
    rsuchecki committed Dec 18, 2019
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  3. for GH actions

    @rsuchecki
    rsuchecki committed Dec 18, 2019
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  4. docker user change for GH actions

    @rsuchecki
    rsuchecki committed Dec 18, 2019
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  5. docker groovy test for GHA

    @rsuchecki
    rsuchecki committed Dec 18, 2019
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  6. docker user

    @rsuchecki
    rsuchecki committed Dec 18, 2019
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  7. docker grp exists

    @rsuchecki
    rsuchecki committed Dec 18, 2019
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Commits on Dec 19, 2019

  1. added go for singularity

    @rsuchecki
    rsuchecki committed Dec 19, 2019
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  2. added groovy image with ps

    @rsuchecki
    rsuchecki committed Dec 19, 2019
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  3. reconf

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    rsuchecki committed Dec 19, 2019
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Commits on Jan 3, 2020

  1. test profile updates 

    - fix for groovy @grab failing with singularity (read only file-system)
- fix errorStrategy config
    @rsuchecki
    rsuchecki committed Jan 3, 2020
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  2. added Singularity install to GH actions

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    rsuchecki committed Jan 3, 2020
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  3. Singularity dependencies @ GH actions

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    rsuchecki committed Jan 3, 2020
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  4. working around https://github.com/sylabs/singularity/issues/3634

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    rsuchecki committed Jan 3, 2020
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  5. test singularity pull form docker

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    rsuchecki committed Jan 3, 2020
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  6. explicit use of gawk - may matter on alpine

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  7. workaround for 

    nextflow-io/nextflow#1210
sylabs/singularity#3634
    @rsuchecki
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  8. leaner fastx container

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    rsuchecki committed Jan 3, 2020
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  9. fastx and reconf

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    rsuchecki committed Jan 3, 2020
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  10. fix path to script, renamed tasks

    @rsuchecki
    rsuchecki committed Jan 3, 2020
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Commits on Jan 5, 2020

  1. test wspace path

    @rsuchecki
    rsuchecki committed Jan 5, 2020
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  2. added missing script, fixed GH actions cmd

    @rsuchecki
    rsuchecki committed Jan 5, 2020
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  3. ansi-lo on and try docker again

    @rsuchecki
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  4. docker workflow test

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    rsuchecki committed Jan 5, 2020
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  5. fix typo

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    rsuchecki committed Jan 5, 2020
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  6. fix typo

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    rsuchecki committed Jan 5, 2020
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Commits on Jan 6, 2020

  1. fix for permission denied GH actions (?)

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    rsuchecki committed Jan 6, 2020
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  2. fix for groovy grapes in docker

    @rsuchecki
    rsuchecki committed Jan 6, 2020
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  3. test

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  4. test

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  5. test

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  6. test

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  7. another docker test

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  8. GH A job.needs experiemnt

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  9. GH A tidy

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  10. GH A fix indent

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  11. GH A fix job

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    rsuchecki committed Jan 6, 2020
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  12. added GH actions CI badge

    @rsuchecki
    rsuchecki committed Jan 6, 2020
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  13. re-implemented: duplicate emissions if multiple annotations per refer… 

    …ence assembly
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    rsuchecki committed Jan 6, 2020
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  14. updated datastes in line with feature dev

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    rsuchecki committed Jan 6, 2020
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  15. another badge ver

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    rsuchecki committed Jan 6, 2020
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  16. fix

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    rsuchecki committed Jan 6, 2020
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Commits on Jan 7, 2020

  1. added EP datasets

    @rsuchecki
    rsuchecki committed Jan 7, 2020
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  2. ensure non-empty process out

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    rsuchecki committed Jan 7, 2020
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  3. generalised for different gff3 interpretations

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  4. Delete .travis.yaml

    @rsuchecki
    rsuchecki authored Jan 7, 2020
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  5. Update README.md

    @rsuchecki
    rsuchecki authored Jan 7, 2020
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  6. Update README.md

    @rsuchecki
    rsuchecki authored Jan 7, 2020
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Commits on Jan 8, 2020

  1. At & Bd ref fasta not needed

    @rsuchecki
    rsuchecki committed Jan 8, 2020
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  2. speeding things up: gawk in jq container and up resources

    @rsuchecki
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  3. do not report markers placed outside pseudochromosomes (e.g. on scaff… 

    …olds)
    @rsuchecki
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  4. id pattern match extended to seq placement

    @rsuchecki
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  5. Merge branch 'feature/streamline-inputs' of github.com:plantinformati… 

    …cs/pretzel-input-generator into feature/streamline-inputs
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  6. redundant-ish

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  7. added TOC

    @rsuchecki
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