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Develop #160

Merged
merged 76 commits into from
May 7, 2021
Merged

Develop #160

merged 76 commits into from
May 7, 2021

Commits on Jan 18, 2021

  1. Add argumentparser

    @boulund
    boulund committed Jan 18, 2021
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  2. Add try-except to genus_one parsing

    @boulund
    boulund committed Jan 18, 2021
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  3. Move main logic into function, add __name__ == "__main__"

    @boulund
    boulund committed Jan 18, 2021
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  4. Put stain_db in separate function

    @boulund
    boulund committed Jan 18, 2021
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  5. Added try-except to second genus

    @emilio-r
    emilio-r committed Jan 18, 2021
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  6. Added new flags to sendsketch_to... call

    @emilio-r
    emilio-r committed Jan 18, 2021
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  7. Fixed typo

    @emilio-r
    emilio-r authored Jan 18, 2021
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  8. Removed linebreak from stain

    @emilio-r
    emilio-r authored Jan 18, 2021
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  9. Changed variable name to avoid possible overwrite.

    @emilio-r
    emilio-r authored Jan 18, 2021
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  10. Added two more genera

    @emilio-r
    emilio-r authored Jan 18, 2021
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  11. Fixed indentation on new genera

    @emilio-r
    emilio-r committed Jan 18, 2021
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Commits on Feb 1, 2021

  1. ValueError changed to IndexError

    @emilio-r
    emilio-r authored Feb 1, 2021
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  2. Merge pull request #141 from ctmrbio/cleanup-sendsketch-to-prokka 

    Cleanup sendsketch to prokka
    @emilio-r
    emilio-r authored Feb 1, 2021
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  3. Merge branch 'master' into develop

    @abhi18av
    abhi18av committed Feb 1, 2021
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Commits on Feb 2, 2021

  1. Rename ctmrnas.config to ctmr_nas.config

    @boulund
    boulund committed Feb 2, 2021
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  2. Update CHANGELOG

    @boulund
    boulund committed Feb 2, 2021
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  3. Add first draft of CTMR Gandalf profile

    @boulund
    boulund committed Feb 2, 2021
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  4. Merge branch 'rename-ctmrnas' into add-gandalf-profile

    @boulund
    boulund committed Feb 2, 2021
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  5. Made shovill.log standard output

    @emilio-r
    emilio-r authored Feb 2, 2021
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  6. Add ctmr_gandalf.config to changelog

    @boulund
    boulund committed Feb 2, 2021
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  7. Merge pull request #153 from ctmrbio/rename-ctmrnas 

    Rename ctmrnas profile and add new section to changelog
    @boulund
    boulund authored Feb 2, 2021
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  8. Add ctmr_gandalf profile to available options

    @boulund
    boulund committed Feb 2, 2021
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  9. Merge pull request #156 from ctmrbio/add-gandalf-profile 

    Add ctmr_gandalf profile
    @boulund
    boulund authored Feb 2, 2021
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  10. Merge pull request #157 from ctmrbio/add-gandalf-profile 

    Add ctmr_gandalf profile to available options
    @boulund
    boulund authored Feb 2, 2021
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  11. Update changelog

    @boulund
    boulund committed Feb 2, 2021
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  12. Always publish shovill.log 

    Make shovill.log part of the default output files from shovill
    @boulund
    boulund authored Feb 2, 2021
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  13. Move rename_fasta.py to shovill process

    @boulund
    boulund committed Feb 2, 2021
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  14. Reduce the search scope for MultiQC

    @boulund
    boulund committed Feb 2, 2021
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  15. Update changelog

    @boulund
    boulund committed Feb 2, 2021
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  16. Merge pull request #158 from ctmrbio/145-limit-mqc-search 

    Reduce the search scope for MultiQC
    @abhi18av
    abhi18av authored Feb 2, 2021
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Commits on Feb 3, 2021

  1. Added python to shovill and changed to conda.

    @emilio-r
    emilio-r authored Feb 3, 2021
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Commits on Feb 19, 2021

  1. Workaround for sketch skipping

    @emilio-r
    emilio-r authored Feb 19, 2021
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  2. Merge pull request #159 from ctmrbio/Retry-workaround 

    Workaround for sketch skipping
    @abhi18av
    abhi18av authored Feb 19, 2021
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Commits on Feb 21, 2021

  1. Rename the prokka_gram #148

    @abhi18av
    abhi18av committed Feb 21, 2021
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  2. Update script to generate mock data

    @abhi18av
    abhi18av committed Feb 21, 2021
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  3. Fix stub typo

    @abhi18av
    abhi18av committed Feb 21, 2021
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  4. Enable docker in the profiles

    @abhi18av
    abhi18av committed Feb 21, 2021
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Commits on Apr 5, 2021

  1. Add docs for prokka_signal_peptides

    @abhi18av
    abhi18av committed Apr 5, 2021
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Commits on Apr 15, 2021

  1. First draft of taxonomic classification with kraken2

    @boulund
    boulund committed Apr 15, 2021
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Commits on Apr 16, 2021

  1. Rewrite sendsketch_to_prokka to classify_kreport

    @boulund
    boulund committed Apr 16, 2021
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  2. Rewrite affected modules to handle new classification format

    @boulund
    boulund committed Apr 16, 2021
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  3. Fix broken syntax

    @boulund
    boulund committed Apr 16, 2021
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  4. Update docs

    @boulund
    boulund committed Apr 16, 2021
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  5. Fix typo

    @boulund
    boulund committed Apr 16, 2021
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  6. Tweak ctmr_gandalf profile

    @boulund
    boulund committed Apr 16, 2021
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  7. add Campylobacter to gramstain db

    @boulund
    boulund committed Apr 16, 2021
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  8. Replace space with tab

    @boulund
    boulund committed Apr 16, 2021
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  9. Change kraken2_min_proportion to 1.00

    @boulund
    boulund committed Apr 16, 2021
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  10. Use Mixed spp. for mixed genera samples

    @boulund
    boulund committed Apr 16, 2021
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  11. Give warning if no kraken2_db specified

    @boulund
    boulund committed Apr 16, 2021
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  12. Move kraken2_db warning message

    @boulund
    boulund committed Apr 16, 2021
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  13. Replace sendsketch with kraken2 

    Replace sendsketch with kraken2
    @boulund
    boulund authored Apr 16, 2021
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Commits on Apr 19, 2021

  1. updated flowchart to new format

    @emilio-r
    emilio-r committed Apr 19, 2021
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  2. updated path to flowchart

    @emilio-r
    emilio-r committed Apr 19, 2021
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  3. Remade flowchart

    @emilio-r
    emilio-r committed Apr 19, 2021
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Commits on May 4, 2021

  1. Fixed typo

    @emilio-r
    emilio-r authored May 4, 2021
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  2. updated flowchart for 3.1

    @emilio-r
    emilio-r committed May 4, 2021
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  3. Cleanup docker image and re-organize params

    @abhi18av
    abhi18av committed May 4, 2021
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  4. Fix docker profile

    @abhi18av
    abhi18av committed May 4, 2021
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Commits on May 5, 2021

  1. Specified python version for MultiQC

    @emilio-r
    emilio-r authored May 5, 2021
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  2. fix typo in param names

    @abhi18av
    abhi18av authored May 5, 2021
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  3. Add script to download and setup kraken db

    @abhi18av
    abhi18av authored May 5, 2021
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Commits on May 6, 2021

  1. Fixed typo in flowchart

    @emilio-r
    emilio-r committed May 6, 2021
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  2. Update the NF versions

    @abhi18av
    abhi18av committed May 6, 2021
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  3. Mention Kraken DB installation process

    @abhi18av
    abhi18av committed May 6, 2021
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  4. Merge pull request #165 from ctmrbio/abhinav/update-docker-profile 

    Update docker file to accomodate kraken
    @boulund
    boulund authored May 6, 2021
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  5. Update CHANGELOG.md

    @boulund
    boulund authored May 6, 2021
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Commits on May 7, 2021

  1. Add version to nextflow manifest, use workflow.manifest.version in ma… 

    …in script
    @boulund
    boulund committed May 7, 2021
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  2. Bump version in docs

    @boulund
    boulund committed May 7, 2021
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  3. Add optional args to --help output

    @boulund
    boulund committed May 7, 2021
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  4. Do not print profiles_that_require_project in run settings summary

    @boulund
    boulund committed May 7, 2021
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  5. Fix flowchart in docs/intro

    @boulund
    boulund committed May 7, 2021
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  6. Fix typo in file extension

    @boulund
    boulund committed May 7, 2021
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  7. Update docs, rename kraken2 db download script

    @boulund
    boulund committed May 7, 2021
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  8. Typo in flowchart filename, again

    @boulund
    boulund committed May 7, 2021
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  9. Improve user experience if --reads is not provided

    @boulund
    boulund committed May 7, 2021
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