multi-run.csv.example

# Multi-run table — EXAMPLE, not a template.
#
# Nothing copies this file. Read it, then write your own table with only the rows and columns
# your comparison actually needs.
#
# To use one:
#     1. write your table, anywhere in your project directory
#     2. in parameters.config, set   multiRun     = true
#                                    multiRunFile = 'your-table.csv'
#
# The table is read before any compute is spent: an unusable one stops the run outright, and a
# usable one is printed in full - the runs, where each one's results go, and what differs - in
# step 0's report.
#
# ---------------------------------------------------------------------------------------
# THE RULES, ALL FOUR OF THEM
#
# 1. One column must be RunID. It names the run and becomes a directory, so keep it to
#    letters, digits, dot, dash and underscore. Results go to storageDir/<RunID>/.
#
# 2. Every other column is a parameter name spelt exactly as parameters.config spells it,
#    with NO `params.` prefix. Nested ones are dotted: trim_galore.quality, bcftools.maxDepth.
#    ANY parameter may be varied, including the ones the pipeline normally computes for
#    itself. A name that is not a parameter is refused rather than ignored.
#
# 3. A BLANK CELL MEANS "take it from parameters.config", so a table is only as long as the
#    difference between the runs. There is therefore no way to set a parameter to an empty
#    string here.
#
# 4. A value containing a comma must be quoted - "-a AD,DP,SP,INFO/AD". The default
#    readPattern, *_R{1,2}.fq.gz, is exactly such a value.
#
# Blank lines and lines starting with # are ignored, so you can keep a run in the file with a
# # in front of it instead of deleting it.
#
# ---------------------------------------------------------------------------------------
# WHAT HAPPENS TO THE VALUES YOU SET
#
# Setting an INPUT to a computed value moves the computed value with it: poolSize re-derives
# filterFalsePositives.sensitivity, trim_galore.quality re-derives trim_galore.options,
# bcftools.maxDepth re-derives bcftools.mpileupOptions, threads re-derives the whole cores
# ladder. You do not have to keep those in step by hand.
#
# Setting a COMPUTED value directly is used exactly as written, and then nothing is derived
# from its inputs any more - pin bcftools.mpileupOptions and bcftools.maxDepth stops meaning
# anything for that run. Step 0 names any column that does this.
#
# ---------------------------------------------------------------------------------------
# FOUR EXAMPLES. Pick the shape you need; do not use all of them at once.

# --- one: the same reads against two reference genomes ---------------------------------
# The commonest reason to want this. Everything else comes from parameters.config.
#
# RunID,referenceFile,gffFile
# lab_strain,lab_strain.fasta.gz,lab_strain.gff.gz
# field_isolate,field_isolate.fasta.gz,field_isolate.gff.gz

# --- two: one reference, three trimming stringencies ------------------------------------
# Note the blank cell on the first row: it takes the configured quality, so the baseline is
# whatever parameters.config already says rather than a number repeated here.
#
# RunID,trim_galore.quality
# trim_default,
# trim_20,20
# trim_30,30

# --- three: a filtering sweep ------------------------------------------------------------
# These diverge late - nothing before variant calling differs between them.
#
# RunID,vcffilter.minDP,vcffilter.minQUAL,filterFalsePositives.sampleThreshold
# lenient,10,20,0.1
# standard,20,30,0.2
# strict,40,50,0.3

# --- four: varying pool size, and pinning something outright -----------------------------
# pool_50 and pool_200 let sensitivity be re-derived from poolSize. pinned_depth does the
# opposite: it writes the mpileup options itself, so bcftools.maxDepth no longer feeds them.
# Step 0 will point that column out.
#
# RunID,poolSize,bcftools.mpileupOptions
# pool_50,50,
# pool_200,200,
# pinned_depth,,"-B -C 50 -q 30 -Q 30 -d 8000 -a AD,DP,SP,INFO/AD -Ou"

# ---------------------------------------------------------------------------------------
# A REAL, USABLE TABLE. Two references, and the second trimmed harder. Delete or replace it.
RunID,referenceFile,gffFile,trim_galore.quality
reference_a,reference_a.fasta.gz,reference_a.gff.gz,
reference_b,reference_b.fasta.gz,reference_b.gff.gz,30