DSL2: `test_microbial` nf-test conversion

[TCLamnidis]

test_microbial nf-test conversion

[ilight1542]

Test config microbial.

Activated parts of pipeline:

• host removal
• sequence QC (falco)
• sequence preprocessing (fastp)
• excluding unmerged
• mapping (circularmapper)
• no damage rescaling
• deduplication (dedup)
• metagenomics (krakenuniq)
• host removal
• bedtools coverage
• genotyping (raw, freebayes)
• (default) damageprofiler
• (default) endorspy
• (default) preseq
• (default) qualimap

Outputs expected:

• falco: versions.yml; stats directory
• fastp: only stats directory, no preprocessing_savepreprocessedreads "${meta.sample_id}_${meta.library_id}_L${meta.lane}" '*.{log,html,json}'
• circularmapper: samtools sort and indexing outputs; stats directory: *.flagstat
• dedup: per libID/reference in data *.bai, *.csi, *.bam, stats directory: *.flagstat
• krakenuniq: single execution across samples (should be stable) '*.{txt,fastq.gz}'
• hostremoval: data directory, per reference, sampleid,library_id,lane_id (eg per lib+lane) - *.fq.gz
• bedtools: (BEDTOOLS_COVERAGE_DEPTH) - stats directory with per-sampleid, reference id file names
• freebayes: per reference cross sample *.vcf.gz (should it be across all samples, not ${meta.sample_id}_${meta.reference}? (and *.tbi)
• genotyping: raw bam output (final_bams)
• genotyping: bcftools indexing (bcftools_stats.txt)
• metagenomics: taxpasta (stats/krakenuniq_taxpasta_table.tsv)
• multiqc stuff
• preprocessing: falco processed, falco raw, fastp
• read filtering (filtered bams, per library, unmerged across samples)