Plotting Module (CLI)

Default behavior

run-megqc-plotting --inputdata /path/dataset

If no mode flags are provided, MEGqc defaults to --qa-subject.

QA modes

# Subject-level QA
run-megqc-plotting --inputdata /path/dataset --qa-subject

# Dataset-level QA group
run-megqc-plotting --inputdata /path/dataset --qa-group

# Cross-dataset QA
run-megqc-plotting --inputdata /path/ds1 /path/ds2 --qa-multisample

# All QA modes valid for inputs
run-megqc-plotting --inputdata /path/ds1 /path/ds2 --qa-all

QC modes

# Dataset-level QC group
run-megqc-plotting --inputdata /path/dataset --qc-group

# Specific attempt
run-megqc-plotting --inputdata /path/dataset --qc-group --attempt 2

# Explicit input TSV
run-megqc-plotting --inputdata /path/dataset --qc-group --input_tsv /path/to/Global_Quality_Index_attempt_2.tsv

# Cross-dataset QC
run-megqc-plotting --inputdata /path/ds1 /path/ds2 --qc-multisample

# All QC modes
run-megqc-plotting --inputdata /path/ds1 /path/ds2 --qc-all

All modes

run-megqc-plotting --inputdata /path/ds1 /path/ds2 --all

Profile-aware plotting

run-megqc-plotting \
  --inputdata /path/dataset \
  --qa-group \
  --analysis_mode reuse \
  --analysis_id qa_pass_01

Performance controls

run-megqc-plotting --inputdata /path/dataset --qa-group --njobs 4

Run run-megqc-plotting --help for the full flag set.