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example_config.yaml
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example_config.yaml
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---
# This file is in YAML format.
# The YAML specification can be found at https://yaml.org/spec/
# A gentle introduciton to YAML can be found at:
# https://www.cloudbees.com/blog/yaml-tutorial-everything-you-need-get-started
# The chromatography type is determined is from the LCMS output file names.
# Aliases map alternative identifiers in the file name to the canonical name.
chromatography_types:
- name: HILIC
aliases:
- HILICZ
- Ag683775
- name: C18
aliases: []
# A Metatlas "workflow" contains:
# 1) A unique name consisting solely of letters, numbers, and dashes
# 2) A RT alignment step
# 3) Zero or more analysis steps
#
# Each RT alignment or analysis step contains an atlas definition.
# The atlas definition contains three fields:
# 1) name - name of the atlas as stored in the database
# 2) unique_id - unique_id field associated with the atlas in the database
# 3) do_alignment - if True, then the atlas should be copied and RT shifted to
# be in alignment with the experimental data.
#
# Each RT alignment or analysis step contains a set of parameters.
# These parameters are substituted into the RT-Alignment.ipynb
# or Targeted.ipynb notebook. Please see the notebook files for
# documentation of the parameters and their values:
# https://github.com/biorack/metatlas/blob/main/notebooks/reference/RT-Alignment.ipynb
# https://github.com/biorack/metatlas/blob/main/notebooks/reference/Targeted.ipynb
workflows:
- name: JGI-HILIC
rt_alignment:
atlas:
name: HILICz150_ANT20190824_TPL_QCv3_Unlab_POS
unique_id: e7fba1813272439498405436a28b90b2
parameters:
groups_controlled_vocab: ["QC", "InjBl", "ISTD"]
include_groups:
always: ["QC"]
exclude_groups:
always: ["NEG"]
use_poly_model: True
msms_refs: /global/cfs/cdirs/metatlas/projects/spectral_libraries/msms_refs_v3.tab
google_folder: 0B-ZDcHbPi-aqZzE5V3hOZFc0dms
analyses:
- name: QC-POS
atlas:
name: HILICz150_ANT20190824_TPL_QCv3_Unlab_POS
unique_id: e7fba1813272439498405436a28b90b2
parameters:
polarity: positive
groups_controlled_vocab: ["QC", "InjBl", "ISTD"]
include_groups:
always: ["QC"]
exclude_groups:
always: ["NEG"]
generate_qc_outputs: True
- name: ISTDsEtc-POS
atlas:
name: HILICz150_ANT20190824_TPL_IS_LabUnlab2_POS
unique_id: c6db576b879043768125c4e03e6a8f6e
do_alignment: True
parameters:
copy_atlas: True
draft: True
polarity: positive
groups_controlled_vocab: ["QC", "InjBl", "ISTD"]
exclude_groups:
always: ["QC", "NEG", "FPS"]
exclude_lcmsruns:
always: ["QC"]
gui: ["InjBl", "Blank", "blank"]
chromatograms: ["InjBl", "Blank", "blank"]
data_sheets: ["InjBl", "Blank", "blank"]
generate_qc_outputs: True
generate_analysis_outputs: True
- name: EMA-POS
atlas:
name: HILICz150_ANT20190824_TPL_EMA_Unlab_POS
unique_id: 89694aa326cd46958d38d8e9066de16c
do_alignment: True
parameters:
copy_atlas: True
draft: True
polarity: positive
groups_controlled_vocab: ["QC", "InjBl", "ISTD"]
exclude_groups:
always: ["QC", "NEG", "FPS"]
exclude_lcmsruns:
always: ["QC"]
gui: ["InjBl", "Blank", "blank"]
chromatograms: ["InjBl", "Blank", "blank"]
data_sheets: ["InjBl", "Blank", "blank"]
require_all_evaluated: True
filter_removed: True
num_points: 5
peak_height: 4e5
generate_analysis_outputs: True
- name: QC-NEG
atlas:
name: HILICz150_ANT20190824_TPL_QCv3_Unlab_NEG
unique_id: 5b77242ad9c04e76a745e51e9d6a3c4b
parameters:
polarity: negative
groups_controlled_vocab: ["QC", "InjBl", "ISTD"]
include_groups:
always: ["QC"]
exclude_groups:
always: ["POS"]
generate_qc_outputs: True
- name: ISTDsEtc-NEG
atlas:
name: HILICz150_ANT20190824_TPL_IS_LabUnlab2_NEG
unique_id: e299c951fc8b48ea82524a6c9615f418
do_alignment: True
parameters:
copy_atlas: True
draft: True
polarity: negative
groups_controlled_vocab: ["QC", "InjBl", "ISTD"]
exclude_groups:
always: ["QC", "POS", "FPS"]
exclude_lcmsruns:
always: ["QC"]
gui: ["InjBl", "Blank", "blank"]
chromatograms: ["InjBl", "Blank", "blank"]
data_sheets: ["InjBl", "Blank", "blank"]
generate_qc_outputs: True
generate_analysis_outputs: True
- name: EMA-NEG
atlas:
name: HILICz150_ANT20190824_TPL_EMA_Unlab_NEG
unique_id: a5f7bc81caa94853bbd6ee4b44e09187
do_alignment: True
parameters:
copy_atlas: True
draft: True
polarity: negative
groups_controlled_vocab: ["QC", "InjBl", "ISTD"]
exclude_groups:
always: ["QC", "POS", "FPS"]
exclude_lcmsruns:
always: ["QC"]
gui: ["InjBl", "Blank", "blank"]
chromatograms: ["InjBl", "Blank", "blank"]
data_sheets: ["InjBl", "Blank", "blank"]
require_all_evaluated: True
filter_removed: True
num_points: 5
peak_height: 4e5
generate_analysis_outputs: True
- name: JGI-C18
rt_alignment:
atlas:
name: C18_20220215_TPL_IS_Unlab_POS
unique_id: 322ed4c5fabe49349bcbc2857fbcd0dc
parameters:
groups_controlled_vocab: ["QC", "InjBl", "ISTD"]
include_groups:
always: ["QC"]
exclude_groups:
always: ["NEG"]
use_poly_model: True
msms_refs: /global/cfs/cdirs/metatlas/projects/spectral_libraries/msms_refs_v3.tab
google_folder: 0B-ZDcHbPi-aqZzE5V3hOZFc0dms
analyses:
- name: QC-POS
atlas:
name: C18_20220215_TPL_IS_Unlab_POS
unique_id: 322ed4c5fabe49349bcbc2857fbcd0dc
parameters:
polarity: positive
groups_controlled_vocab: ["QC", "InjBl", "ISTD"]
include_groups:
always: ["QC"]
exclude_groups:
always: ["NEG"]
generate_qc_outputs: True
- name: ISTDsEtc-POS
atlas:
name: C18_20220215_TPL_IS_Unlab_POS
unique_id: 322ed4c5fabe49349bcbc2857fbcd0dc
do_alignment: True
rt_offset: 0.2
parameters:
copy_atlas: True
draft: True
polarity: positive
groups_controlled_vocab: ["QC", "InjBl", "ISTD"]
exclude_groups:
always: ["QC", "NEG", "FPS"]
exclude_lcmsruns:
always: ["QC"]
gui: ["InjBl", "Blank", "blank"]
chromatograms: ["InjBl", "Blank", "blank"]
data_sheets: ["InjBl", "Blank", "blank"]
generate_qc_outputs: True
generate_analysis_outputs: True
- name: EMA-POS
atlas:
name: C18_20220531_TPL_EMA_Unlab_POS
unique_id: 669b750765634159a7f16645e6cf7758
do_alignment: True
rt_offset: 0.2
parameters:
copy_atlas: True
draft: True
polarity: positive
groups_controlled_vocab: ["QC", "InjBl", "ISTD"]
exclude_groups:
always: ["QC", "NEG", "FPS"]
exclude_lcmsruns:
always: ["QC"]
gui: ["InjBl", "Blank", "blank"]
chromatograms: ["InjBl", "Blank", "blank"]
data_sheets: ["InjBl", "Blank", "blank"]
require_all_evaluated: True
filter_removed: True
num_points: 3
peak_height: 1e6
msms_score: 0.6
generate_analysis_outputs: True
- name: QC-NEG
atlas:
name: C18_20220215_TPL_IS_Unlab_NEG
unique_id: db58154082824230be4f7fee93e4ebd9
parameters:
polarity: negative
groups_controlled_vocab: ["QC", "InjBl", "ISTD"]
include_groups:
always: ["QC"]
exclude_groups:
always: ["POS"]
generate_qc_outputs: True
- name: ISTDsEtc-NEG
atlas:
name: C18_20220215_TPL_IS_Unlab_NEG
unique_id: db58154082824230be4f7fee93e4ebd9
do_alignment: True
rt_offset: 0.2
parameters:
copy_atlas: True
draft: True
polarity: negative
groups_controlled_vocab: ["QC", "InjBl", "ISTD"]
exclude_groups:
always: ["QC", "POS", "FPS"]
exclude_lcmsruns:
always: ["QC"]
gui: ["InjBl", "Blank", "blank"]
chromatograms: ["InjBl", "Blank", "blank"]
data_sheets: ["InjBl", "Blank", "blank"]
generate_qc_outputs: True
generate_analysis_outputs: True
- name: EMA-NEG
atlas:
name: C18_20220531_TPL_EMA_Unlab_NEG
unique_id: 19b4c10e304246cbbbe5fd3574770e5d
do_alignment: True
rt_offset: 0.2
parameters:
copy_atlas: True
draft: True
polarity: negative
groups_controlled_vocab: ["QC", "InjBl", "ISTD"]
exclude_groups:
always: ["QC", "POS", "FPS"]
exclude_lcmsruns:
always: ["QC"]
gui: ["InjBl", "Blank", "blank"]
chromatograms: ["InjBl", "Blank", "blank"]
data_sheets: ["InjBl", "Blank", "blank"]
require_all_evaluated: True
filter_removed: True
num_points: 3
peak_height: 1e6
msms_score: 0.6
generate_analysis_outputs: True
- name: Hybrid
rt_alignment:
atlas:
name: HILICz150_ANT20190824_TPL_QCv3_Unlab_POS
unique_id: e7fba1813272439498405436a28b90b2
parameters:
use_poly_model: True
msms_refs: /global/cfs/cdirs/metatlas/projects/spectral_libraries/msms_refs_v3.tab
google_folder: 0B-ZDcHbPi-aqZzE5V3hOZFc0dms
analyses:
- name: EMA-POS
atlas:
name: HILICz150_ANT20190824_TPL_EMA_Unlab_POS
unique_id: 89694aa326cd46958d38d8e9066de16c
do_alignment: True
parameters:
copy_atlas: True
polarity: positive
filter_removed: True
generate_qc_outputs: True
generate_analysis_outputs: True
- name: EMA-NEG
atlas:
name: HILICz150_ANT20190824_TPL_EMA_Unlab_NEG
unique_id: a5f7bc81caa94853bbd6ee4b44e09187
do_alignment: True
parameters:
copy_atlas: True
polarity: negative
filter_removed: True
generate_qc_outputs: True
generate_analysis_outputs: True