🍏🎨 add/update coverage handling

[evanroyrees]

🐍 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]

Test run using below samplesheet is in progress (deep-thought). Waiting to make sure CONTIG_COVERAGE workflow is functional.

samplesheet name: test_three_coverage_channels.csv

sample,assembly,fastq_1,fastq_2,coverage_tab,cov_from_contig_headers
78.125Mbp_from_spades,/home/evan/autometa_test_data/autometa_test_data/simulated_communities/78.125Mbp/metagenome.fna.gz,,/home/evan/autometa_test_data/autometa_test_data/simulated_communities/78.125Mbp/reverse_reads.fastq.gz,,1
78.125Mbp_coverage_tab,/home/evan/autometa_test_data/autometa_test_data/simulated_communities/78.125Mbp/metagenome.fna.gz,,,/home/evan/benchmarking/simulated/raw/78.125Mbp_coverage.tsv,0
78.125Mbp_from_alignments,/home/evan/autometa_test_data/autometa_test_data/simulated_communities/78.125Mbp/metagenome.fna.gz,/home/evan/autometa_test_data/autometa_test_data/simulated_communities/78.125Mbp/forward_reads.fastq.gz,/home/evan/autometa_test_data/autometa_test_data/simulated_communities/78.125Mbp/reverse_reads.fastq.gz,,0

{
    "input": "/home/evan/Autometa/test_three_coverage_channels.csv",
    "autometa_image_tag": "dev"
}

Results for 78.125Mbp_from_spades and 78.125Mbp_coverage_tab inputs were successful 👍