Add read-based contig coverage instead of spades-based #186
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chasemc
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enhancement
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What else needs to be updated/implemented for this subworkflow? |
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Been awhile but I don't think reads are considered at all yet because it was extra complication switching the existing subworkflow to the metamap format. We'll have to decide on the best input format first. My vote would be to start with tsv: https://nf-co.re/mag/2.1.0/usage#samplesheet-input-file |
evanroyrees
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Jan 21, 2022
🐍 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
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Jan 24, 2022
* 🍏🐍📝🎨 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 * 🔥 Remove bowtie2/build from modules.json * 📝 Update param.input docstring for nextflow_schema.json * 🐛🔥 Remove unused open '(' in bowtie2 version retrieval * 🎨🐛 Fix bt2 db emit and samtools view input param (add -bS) * 📝 Add sample sheet information * 📝 Fix samplesheet table 🔥 Remove mentions of num_splits and other references in advanced to specifying multiple inputs * 🐛🔥📝 Fix typos update running modules section and next some of advanced params * 📝 Reformat resource allotment * 🔥 Remove incorrect usage of --input argument * 📝 Replace parameters.config with nf-params.json that will likely be used... * 📝 Replace attention with caution and bold some texts within caution * 📝🎨 Change using nf-core tools header to using nf-core * 📝 Add example sample_sheet.csv section header * 🐛 Fix python-formatting in Python API examples * 🎨📝 Reformat ambiguous information for note on coverage_tab input * 🐛📝 Fix nf-core/nextlow conda install section header * 🐛 python APIs headers not being visualized * 📝🐛 Fixing section headers * 🎨 Fix formatting for SLURM profile configuration section * 🔥 Remove already mentioned comment with link * 📝 Update data preparation with points to examples in sample sheet * 📝 Re-order examples for data preparation * 🎨🐛 fix resume code formatting in caution * 📝🎨 Move attention section for data preparation to sample sheet section
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Partially implemented subworkflow needs to be updated to nf-core 2 format
https://github.com/KwanLab/Autometa/blob/8934bf52ae7ab4b91018b0cfc9020f50280fd201/subworkflows/local/contig_coverage.nf
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