Patterns¶
A pattern is a token replaced by the true value at program runtime. These patterns are used to describe where files will be placed.
Patterns are used to construct file names and header values in the specification for all file formats. See BAM for an example.
Available patterns¶
Global¶
These patterns are available in all contexts:
asic_id¶
[A-F0-9]+| Examples |
|---|
433146BC99436123 |
123455434 |
An internal identifier for the ASIC on the flow cell or Flongle adapter
flow_cell_id¶
[A-Z0-9_-]+| Examples |
|---|
FXX12345 |
PXX12345 |
AAA123 |
Unique identifier printed onto the flow cell, potentially entered by the user.
machine_id¶
[A-Za-z0-9-_]+| Examples |
|---|
my-sequencer |
GXB12345 |
PCA100090 |
An identifier for the machine MinKNOW is running on. For Oxford Nanopore devices like GridIONs or PromethIONs, this is the serial number printed on the device. For customer-supplied computers, this is the hostname.
device_id¶
[A-Za-z0-9-_]+| Examples |
|---|
X1 |
MN12345 |
1A |
P2S-12345-A |
Identifier for the flow cell position which ran the experiment.
version_string¶
[0-9]+\.[0-9]+\.[0-9]+(\.[0-9]+)?(~.+)?| Examples |
|---|
1.2.3 |
1.2.3~rc1 |
Version information for the software component that is writing the file.
sample_id¶
[a-zA-Z0-9_\.-]+| Examples |
|---|
My_Sample |
my-sample-1 |
A user-supplied identifier for the library running in the protocol
protocol_group_id¶
[a-zA-Z0-9_\.-]+| Examples |
|---|
My_Group |
my-group-1 |
A user-supplied identifier for a group of protocols
daq_start_time¶
[0-9]{8}_[0-9]{4}| Examples |
|---|
20240103_1424 |
The time acquisition started, formatted as :%Y%m%d_%H%M.
run_id¶
[0-9a-f]{40}| Examples |
|---|
de9f2c7fd25e1b3afad3e85a0bd17d9b100db4b3 |
The full run id for the running acquisition.
short_run_id¶
[0-9a-f]{8}| Examples |
|---|
de9f2c7f |
The first 8 characters of the full run_id.
protocol_run_id¶
[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}| Examples |
|---|
acde070d-8c4c-4f0d-9d8a-162843c10333 |
The full protocol run id for the running protocol.
short_protocol_run_id¶
[0-9a-f]{8}| Examples |
|---|
acde070d |
The first 8 characters of the protocol_run_id.
protocol_purpose¶
[a-zA-Z0-9_]+| Examples |
|---|
sequencing_run |
The purpose of the running protocol.
Read¶
These patterns are available when processing a read:
batch_number¶
[0-9]+| Examples |
|---|
0 |
1 |
4000 |
The index of the file or folder being generated, allowing a set of sequential files or folders to be output, eg: '0', '1', '2'...
type¶
[a-zA-Z0-9_]+| Examples |
|---|
positive_control |
The type of the data the read's associated barcode is related to (one of: test_sample, positive_control, negative_control, no_template_control, positive_control_1, positive_control_2)
alias¶
[a-zA-Z0-9_\.-]+| Examples |
|---|
My_Sample_Alias |
my-sample-alias-1 |
The user-supplied alias for the read's associated barcode
basecall_model_version_id¶
[a-z0-9_@\.]+| Examples |
|---|
rna004_130bps_fast@v5.1.0 |
A unique identifier for the basecall model used in the protocol.
basecall_status_skip_or_empty¶
skip|| Examples |
|---|
skip |
|
skip if the read has skipped basecalling, ```` otherwise
basecall_status¶
pass|fail|skip| Examples |
|---|
pass |
fail |
skip |
pass, fail or skip depending on the basecall status of the read
read_start_time¶
\d{4}-\d{2}-\d{2}T\d{2}:\d{2}:\d{2}(?:\.\d+)?(Z|[\+-]\d{2}:\d{2})?| Examples |
|---|
2025-01-13T10:45:28.681306+00:00 |
2016-01-19T15:21:32.59+02:00 |
The read start time as an RFC 3339 string
pore_type¶
[a-zA-Z0-9_\.]+| Examples |
|---|
r9.4.1 |
r10.4.1 |
not_set |
The type of the pore in use for this read
channel_name¶
[0-9]+| Examples |
|---|
1 |
512 |
3000 |
The 1 indexed number for the channel on which the read was sequenced.
read_id¶
[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}| Examples |
|---|
acde070d-8c4c-4f0d-9d8a-162843c10333 |
A unique UUID for the sequenced read (unique even if the read was split in the basecaller)
parent_read_id¶
[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}| Examples |
|---|
acde070d-8c4c-4f0d-9d8a-162843c10333 |
A unique UUID for the read sent into the basecaller, potentially duplicated if split in basecaller