Workflow User Configuration

Changes in the source directory config file will be passed down to any workflow run that is subsequently installed. Changes in a run directory will only apply to the concerned run after you use cylc reload

See also

Configuring the workflow

Configuration Options

The main configuration file can be found in the rose-suite.conf file at the root of the workflow directory.

Rose Configuration rose-suite.conf

User configuration for bioreactor-workflow.

Config [template variables]
Config cfg__validate_conda_envs= False

Should the workflow validate the conda environments for packages’ presence and versions before running.

default:

False

type:

bool

Config cfg__input_strategy= 'internal'

internal | local.

  • internal: will look for .raw files in $CYLC_WORKFLOW_RUN_DIR/raws.

  • local: will look for .raw files in cfg__local_runs_dir/$CYLC_WORKFLOW_RUN_NAME.

default:

‘internal’

type:

str

Config cfg__local_runs_dir= ''

Used if cfg__input_strategy is set to local. If there is a subdirectory in the one defined here that shares the same name as the workflow run, the workflow will look for .raw files inside.

optional:

yes

default:

None

type:

str (path)

Config cfg__trim_values= [0, 0]

Tuple for the number of scans to trim at the start and at the end of the flowgram. If set to [0, 0], no trimming will be done.

default:

[0, 0]

type:

list<int>

Config cfg__tic_threshold= 0.70
Fraction of max(TIC). Only scans with an TIC above it will be kept by binneR

as part of the injection window.

default:

0.70

type:

float

Config cfg__scans_window= ''

Will override cfg__tic_threshold if set. Interval of scans to be kept by binneR. Must be a string with the format ‘start-end’ in scan numbers (eg. ‘10-20’). If cfg__trim_values is set, this interval refers to scan numbers AFTER trimming.

optional:

yes

default:

None

type:

str

Config cfg__ppm_tol= 8

Tolerance (ppm) for metabolite identification.

default:

8

type:

int|float

Config cfg__dmz_tol= 0.001

Minimum threshold for m/z deviation tolerance in Dalton (dmz).

default:

0.001

type:

int|float

Config cfg__toggle_influxdb= False

Should the workflow send data to an InfluxDB instance for visualization. If set to True, the following configuration options must be set.

See also

Visualizing results with InfluxDB

default:

False

type:

bool

Config cfg__influxdb_url= 'http://localhost:8086'

URL of the running InfluxDB instance.

optional:

yes

default:

None

type:

str (URL)

Config cfg__influxdb_org= 'my-organization'

Organization to write to in the InfluxDB instance. Must exist already.

optional:

yes

default:

None

type:

str

Config cfg__influxdb_auth_token= ''

Authorization token for the InfluxDB instance. Must have complete write access to the organization, in order to create buckets and write data.

optional:

yes

default:

None

type:

str

Config cfg__influxdb_reuse_bucket= False

Should the workflow reuse the InfluxDB bucket if it already exists. By default, the workflow will create a new bucket with the same name as the run. If there is already one, an error will be raised. If set to True, it will skip creation.

This can have unexpected consequences if data points are overwritten by re-processing the same .raw files. The main use case is getting around the 2-buckets limitation of the free tier of InfluxDB Cloud, by reusing them for subsequent experiments.

optional:

yes

default:

False

type:

bool

Input Tables

The input tables are stored in the config/ directory at the root of the workflow directory.

compounds_db.csv

Exemple

Isobaric ID

Metabolites IDs

Precursor Name

Precursor Formula

Precursor m/z

Precursor Adduct

Precursor Charge

Retention Time

Ref Isobaric ID

Coeff A

Coeff B

acetate

bigg_001

Acetate

C2H4O2

59.01385

[M-H]

-1

0.3

13c-acetate

0.461711288

0.806159876

13c-acetate

13C-Acetate

C2H4O2

61.02056

[M2C13-H]

-1

0.3

13c-acetate

1

0

propionate

bigg_002

Propionate

C3H6O2

73.0295

[M-H]

-1

0.3

13c-glucose

gly

bigg_003

Gly

C2H5NO2

74.02475

[M-H]

-1

0.3

13c-glucose

The table is validated against the following schema:

compounds_db.resource.json
  1{
  2  "name": "compounds_db",
  3  "type": "table",
  4  "path": "../config/compounds_db.csv",
  5  "scheme": "file",
  6  "format": "csv",
  7  "mediatype": "text/csv",
  8  "encoding": "utf-8",
  9  "dialect": {
 10    "csv": {
 11      "delimiter": ";",
 12      "header": true
 13    }
 14  },
 15  "schema": {
 16    "fields": [
 17      {
 18        "name": "Isobaric ID",
 19        "type": "string",
 20        "example": "hexose",
 21        "description": "Unique identifier for compound(s) that can't be distinguished by mass."
 22      },
 23      {
 24        "name": "Metabolites IDs",
 25        "type": "string",
 26        "example": "glc__D fru fru_B",
 27        "description": "List of identifiers in the metabolic model for the compound(s)."
 28      },
 29      {
 30        "name": "Precursor Name",
 31        "type": "string",
 32        "example": "Glucose",
 33        "description": "Human readable name of the compound(s)."
 34      },
 35      {
 36        "name": "Precursor Formula",
 37        "type": "string",
 38        "example": "C6H12O6",
 39        "description": "Chemical formula of the compound(s)."
 40      },
 41      {
 42        "name": "Precursor m/z",
 43        "type": "number",
 44        "example": 180.0634,
 45        "description": "Mass-to-charge ratio of the compound(s). Should be unique.",
 46        "constraints": {
 47          "required": true,
 48          "unique": true,
 49          "minimum": 0
 50        }
 51      },
 52      {
 53        "name": "Precursor Adduct",
 54        "type": "string",
 55        "example": "[M-H]",
 56        "description": "Adduct of the compound(s)."
 57      },
 58      {
 59        "name": "Precursor Charge",
 60        "type": "integer",
 61        "example": -1,
 62        "description": "Charge of the compound(s).",
 63        "constraints": {
 64          "required": true
 65        }
 66      },
 67      {
 68        "name": "Retention Time",
 69        "type": "number",
 70        "example": 0.5,
 71        "description": "Retention time of the compound(s) in minutes.",
 72        "constraints": {
 73          "minimum": 0
 74        }
 75      },
 76      {
 77        "name": "Ref Isobaric ID",
 78        "type": "string",
 79        "example": "13c-glucose",
 80        "description": "compound that should be used for relative quantification. Must be in the Isobaric ID column."
 81      },
 82      {
 83        "name": "Coeff A",
 84        "type": "number",
 85        "example": 0.26,
 86        "description": "Coefficient A for the calibration curve."
 87      },
 88      {
 89        "name": "Coeff B",
 90        "type": "number",
 91        "example": 10.45,
 92        "description": "Coefficient B for the calibration curve."
 93      }
 94    ],
 95    "missingValues": [
 96      ""
 97    ],
 98    "primaryKey": "Isobaric ID",
 99    "foreignKeys": [
100      {
101        "fields": "Ref Isobaric ID",
102        "reference": {
103          "resource": "",
104          "fields": "Isobaric ID"
105        }
106      }
107    ]
108  }
109}