The Nextflow pipeline accepts a CSV samplesheet with the following columns:
Columns
sample,bam,mfsd_bam,meth_bam,vcf,bed,maf,single_sample_maf,assay,pon,targets
| Column |
Type |
Required |
Description |
sample |
TEXT |
✓ |
Sample identifier |
bam |
PATH |
✓ |
WGS/Panel BAM file (all_unique for panels) |
mfsd_bam |
PATH |
|
Duplex BAM for mFSD (falls back to bam if empty) |
meth_bam |
PATH |
|
Bisulfite BAM for UXM |
vcf |
PATH |
|
VCF for mFSD |
bed |
PATH |
|
Pre-extracted .bed.gz |
maf |
PATH |
|
MAF for mFSD |
single_sample_maf |
BOOL |
|
Skip MAF filtering if true |
assay |
TEXT |
|
Assay code: XS1, XS2, WGS |
pon |
PATH |
|
Sample-specific PON (overrides assay) |
targets |
PATH |
|
Sample-specific targets (overrides assay) |
| Input Combination |
Workflow |
bam only |
Full run-all (extract → features) |
bam + vcf/maf |
run-all + mFSD |
bam + mfsd_bam + maf |
run-all with dual BAM support |
meth_bam only |
UXM methylation |
bed only |
FSC, FSR, FSD, WPS, OCF (no extract) |
Assay Resolution
When assay is set and --asset_dir is provided:
| Assay |
PON |
Targets |
Genes |
XS1 |
xs1.pon.parquet |
xs1.targets.bed |
128 |
XS2 |
xs2.pon.parquet |
xs2.targets.bed |
146 |
WGS |
wgs.pon.parquet |
None |
- |
Example
sample,bam,mfsd_bam,meth_bam,vcf,bed,maf,single_sample_maf,assay,pon,targets
# MSK-ACCESS V1 samples (auto-resolve PON/targets)
ACCESS_001,/data/sample1.bam,,,,,,,XS1,,
ACCESS_002,/data/sample2.bam,,,,,,/data/cohort.maf,false,XS2,,
# MSK-ACCESS V2 with duplex BAM for mFSD
ACCESS_V2,/data/sample.all_unique.bam,/data/sample.duplex.bam,,,,,maf.tsv,true,XS2,,
# WGS (no targets)
WGS_001,/data/wgs.bam,,,/data/wgs.vcf,,,,,WGS,,
# Custom PON/targets
CUSTOM,/data/custom.bam,,,,,,,,,/data/custom.pon.parquet,/data/custom.bed