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🍏🎨 add/update coverage handling #223

Merged
merged 25 commits into from
Jan 24, 2022
Merged

🍏🎨 add/update coverage handling #223

merged 25 commits into from
Jan 24, 2022

Commits on Jan 21, 2022

  1. 🍏🐍📝🎨 add/update nxf inputs/outputs 

    🐍 Add typehints to bedtools.py
📝🍏🔥 Remove instances of num_splits
📝🍏🎨 Change --input to accept samplesheets instead of metagenomes
🍏🎨 Update check_samplesheet.py for Autometa-nxf samplesheet validation/formatting
🍏🔥 Remove partially-implemented align_reads.nf subworkflow
🍏🎨 Add align_reads.nf process
🍏🎨 Add when directive to CONTIG_COVERAGE processes
🍏🎨 Add when directive to SPADES_KMER_COVERAGE process
🍏🎨 Change coverages emit to coverage
🍏🎨📝 Update configs to match updated processes
🍏 Add three channels to INPUT_CHECK (reads, coverage, metagenome)
🍏🎨 Add & mix three different coverage channels in AUTOMETA to coverage_ch
🍏🎨 fixes #186
🍏🎨 Add functionality to accept pre-computed coverage tables
🍏🎨 meta.id is now retrieved from provided sample column in input samplesheet
    @evanroyrees
    evanroyrees committed Jan 21, 2022
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  2. 🔥 Remove bowtie2/build from modules.json

    @evanroyrees
    evanroyrees committed Jan 21, 2022
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  3. 📝 Update param.input docstring for nextflow_schema.json

    @evanroyrees
    evanroyrees committed Jan 21, 2022
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Commits on Jan 22, 2022

  1. 🐛🔥 Remove unused open '(' in bowtie2 version retrieval

    @evanroyrees
    evanroyrees committed Jan 22, 2022
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Commits on Jan 23, 2022

  1. 🎨🐛 Fix bt2 db emit and samtools view input param (add -bS)

    @evanroyrees
    evanroyrees committed Jan 23, 2022
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Commits on Jan 24, 2022

  1. 📝 Add sample sheet information

    @evanroyrees
    evanroyrees committed Jan 24, 2022
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  2. 📝 Fix samplesheet table 

    🔥 Remove mentions of num_splits and other references in advanced to specifying multiple inputs
    @evanroyrees
    evanroyrees committed Jan 24, 2022
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  3. 🐛🔥📝 Fix typos update running modules section and next some of advance… 

    …d params
    @evanroyrees
    evanroyrees committed Jan 24, 2022
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  4. 📝 Reformat resource allotment

    @evanroyrees
    evanroyrees committed Jan 24, 2022
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  5. 🔥 Remove incorrect usage of --input argument

    @evanroyrees
    evanroyrees committed Jan 24, 2022
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  6. 📝 Replace parameters.config with nf-params.json that will likely be u… 

    …sed...
    @evanroyrees
    evanroyrees committed Jan 24, 2022
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  7. 📝 Replace attention with caution and bold some texts within caution

    @evanroyrees
    evanroyrees committed Jan 24, 2022
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  8. 📝🎨 Change using nf-core tools header to using nf-core

    @evanroyrees
    evanroyrees committed Jan 24, 2022
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  9. 📝 Add example sample_sheet.csv section header

    @evanroyrees
    evanroyrees committed Jan 24, 2022
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  10. 🐛 Fix python-formatting in Python API examples

    @evanroyrees
    evanroyrees committed Jan 24, 2022
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  11. 🎨📝 Reformat ambiguous information for note on coverage_tab input

    @evanroyrees
    evanroyrees committed Jan 24, 2022
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  12. 🐛📝 Fix nf-core/nextlow conda install section header

    @evanroyrees
    evanroyrees committed Jan 24, 2022
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  13. 🐛 python APIs headers not being visualized

    @evanroyrees
    evanroyrees committed Jan 24, 2022
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  14. 📝🐛 Fixing section headers

    @evanroyrees
    evanroyrees committed Jan 24, 2022
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  15. 🎨 Fix formatting for SLURM profile configuration section

    @evanroyrees
    evanroyrees committed Jan 24, 2022
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  16. 🔥 Remove already mentioned comment with link

    @evanroyrees
    evanroyrees committed Jan 24, 2022
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  17. 📝 Update data preparation with points to examples in sample sheet

    @evanroyrees
    evanroyrees committed Jan 24, 2022
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  18. 📝 Re-order examples for data preparation

    @evanroyrees
    evanroyrees committed Jan 24, 2022
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  19. 🎨🐛 fix resume code formatting in caution

    @evanroyrees
    evanroyrees committed Jan 24, 2022
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  20. 📝🎨 Move attention section for data preparation to sample sheet section

    @evanroyrees
    evanroyrees committed Jan 24, 2022
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