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Merge pull request #75 from cmap/test_param_separation
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Adding param separation
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@jdavis3141
jdavis3141 authored Oct 17, 2024
2 parents 49ca560 + 5505ba8 commit af61ab1
Showing 1 changed file with 32 additions and 17 deletions.
49 changes: 32 additions & 17 deletions scripts/make_config_file.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -2,36 +2,51 @@ import hudson.model.*
import jenkins.model.*
import groovy.json.JsonSlurper

String sectionHeaderStyleGreen = ' color: white; background: green; font-family: Roboto, sans-serif !important; padding: 5px; text-align: center; '
String sectionHeaderStyleRed = ' color: white; background: red; font-family: Roboto, sans-serif !important; padding: 5px; text-align: center; '
String separatorStyleCss = ' border: 0; border-bottom: 1px dashed #ccc; background: #999; '

pipeline {
agent any
// Define parameters that can be edited via the Jenkins UI
parameters {
separator(
name: "Group_1",
sectionHeader: "User Inputs",
separatorStyle: separatorStyleCss,
sectionHeaderStyle: sectionHeaderStyleGreen
)
booleanParam(name: 'TRIGGER_BUILD', defaultValue: true, description: 'Check this to trigger the build. If unchecked, the build will not be triggered and only the config.json will be generated.')
booleanParam(name: 'CREATE_CELLDB_METADATA', defaultValue: true, description: 'Check this to trigger the create_celldb_metadata job.')
booleanParam(name: 'CREATE_SAMPLE_META', defaultValue: false, description: 'Check this to trigger the create_sample_meta job.')
booleanParam(name: 'CREATE_CELLDB_METADATA', defaultValue: true, description: 'Create cell metadata, use when cell info is registered in cellDB.')
booleanParam(name: 'CREATE_SAMPLE_META', defaultValue: false, description: 'Get metadata from COMET, use only if screen is registered.')
string(name: 'SCREEN', defaultValue: '', description: 'Screen name from COMET, necessary if using COMET for sample metadata.')
booleanParam(name: 'COLLATE_FASTQ_READS', defaultValue: true, description: 'Check this to trigger the collate_fastq_reads job.')
booleanParam(name: 'FILTER_COUNTS', defaultValue: true, description: 'Check this to trigger the filter_counts job.')
booleanParam(name: 'FILTER_COUNTS_QC', defaultValue: true, description: 'Check this to trigger the filteredCounts_QC job.')
booleanParam(name: 'CBNORMALIZE', defaultValue: true, description: 'Check this to trigger the CBnormalize job.')
booleanParam(name: 'COMPUTE_LFC', defaultValue: true, description: 'Check this to trigger the compute_l2fc job.')
booleanParam(name: 'COLLAPSE', defaultValue: true, description: 'Check this to trigger the collapse job.')
booleanParam(name: 'REMOVE_DATA', defaultValue: false, description: 'Select if there is experimental data that needs to be removed before normalization. TODO: expand on this.')
booleanParam(name: 'PULL_POOL_ID', defaultValue: false, description: 'Flag indicating whether to pull pool IDs from CellDB - only applicable to cell sets (i.e. EXT.PR500.CS01.1.A, EXT.PR500.CS01.1.B, etc).')
booleanParam(name: 'CBNORMALIZE', defaultValue: true, description: 'Run normalization.')
booleanParam(name: 'COMPUTE_LFC', defaultValue: true, description: 'Compute the fold changes.')
booleanParam(name: 'COLLAPSE', defaultValue: true, description: 'Collapse replicates.')
booleanParam(name: 'REMOVE_DATA', defaultValue: false, description: 'Select if there is experimental data that needs to be removed prior to normalization.')
booleanParam(name: 'CONVERT_SUSHI', defaultValue: false, description: 'Convert output column headers to format for MTS pipeline and upload to s3.')
booleanParam(name: 'RUN_EPS_QC', defaultValue: false, description: 'Run EPS QC')
string(name: 'BUILD_DIR', defaultValue: '/cmap/obelix/pod/prismSeq/', description: 'Output path to deposit build. Format should be /directory/PROJECT_CODE/BUILD_NAME')
string(name: 'BUILD_NAME', defaultValue: '', description: 'Build name')
string(name: 'SCREEN', defaultValue: '', description: 'Screen name from COMET, necessary if using COMET for sample metadata.')
string(name: 'SEQ_TYPE', defaultValue: 'DRAGEN', description: 'Choose DRAGEN, MiSeq, HiSeq, or NovaSeq. MiSeq and HiSeq/NovaSeq return files named differently. This setting sets the INDEX_1, INDEX_2, and BARCODE_SUFFIX parameters in fastq2readcount. Select DRAGEN if fastq files are from the DRAGEN pipeline from GP. Choosing NovaSeq reverses index 2.')
string(name: 'CTL_TYPES', defaultValue: 'negcon', description: 'Type to mark as control in compute_LFC')
string(name: 'DAYS', defaultValue: '', description: 'If running the sushi_to_mts module, provide any days/timepoints (separated by commas) that should be dropped from output data. No quotes needed (ie, 2,8).')
booleanParam(name: 'RUN_EPS_QC', defaultValue: false, description: 'Generates an EPS specific QC report.')
string(name: 'BUILD_DIR', defaultValue: '/cmap/obelix/pod/prismSeq/', description: 'Output path to deposit build files. Format should be /directory/PROJECT_CODE/BUILD_NAME')
string(name: 'BUILD_NAME', defaultValue: '', description: 'Build name, files will start with this prefix.')
string(name: 'SEQ_TYPE', defaultValue: 'DRAGEN', description: 'Choose DRAGEN, MiSeq, HiSeq, or NovaSeq. MiSeq and HiSeq/NovaSeq return files named differently. This setting sets the INDEX_1, INDEX_2, and BARCODE_SUFFIX parameters in fastq2readcount. Select DRAGEN if fastq files are from the DRAGEN pipeline from GP. Choosing NovaSeq reverses index 2.')
string(name: 'SIG_COLS', defaultValue: 'cell_set,treatment,dose,dose_unit,day', description: 'Columns that encode all experimental conditions')
string(name: 'CTL_TYPES', defaultValue: 'negcon', description: 'Perturbation type to mark as negative control when computing fold changes.')
string(name: 'CONTROL_COLS', defaultValue: 'cell_set,day', description: 'Set of columns that define individual controls; should be a subset of SIG_COLS')
separator(
name: "Group_1",
sectionHeader: "Do Not Edit",
separatorStyle: separatorStyleCss,
sectionHeaderStyle: sectionHeaderStyleRed
)
string(name: 'GIT_BRANCH', defaultValue: 'main', description: 'Pipeline branch to use')
booleanParam(name: 'USE_LATEST', defaultValue: true, description: 'Check this to use the most up to date version from the specified branch. If not checked, will use the specified commit.')
string(name: 'COMMIT_ID', defaultValue: '', description: 'Specific commit ID to use (leave empty if using the latest commit in the branch or if already specified in the config file.)')
string(name: 'CELL_SET_META', defaultValue: 'cell_set_meta.csv', description: 'Cell set metadata')
string(name: 'ID_COLS', defaultValue: 'cell_set,treatment,dose,dose_unit,day,bio_rep,tech_rep', description: 'Columns to concat to create unique ID for each sample-replicate')
string(name: 'CONTROL_COLS', defaultValue: 'cell_set,day', description: 'Set of columns that define individual controls')
string(name: 'SIG_COLS', defaultValue: 'cell_set,treatment,dose,dose_unit,day', description: 'Signature columns')
string(name: 'ID_COLS', defaultValue: 'pcr_plate,pcr_well', description: 'Columns to concat to create unique ID for each sample-replicate')
string(name: 'SEQUENCING_INDEX_COLS', defaultValue: 'index_1,index_2,flowcell_names', description: 'Sequencing index columns')
string(name: 'CONTROL_BARCODE_META', defaultValue: 'CB_meta.csv', description: 'Metadata for control barcodes.')
string(name: 'COUNT_COL_NAME', defaultValue: 'normalized_n', description: 'Field used to calculate L2FC')
Expand Down Expand Up @@ -102,7 +117,7 @@ pipeline {
'SEQ_TYPE', 'API_URL', 'BUILD_DIR', 'INDEX_1', 'INDEX_2', 'BARCODE_SUFFIX', 'REVERSE_INDEX2',
'SAMPLE_META', 'CONTROL_BARCODE_META', 'CTL_TYPES', 'ID_COLS', 'SIG_COLS',
'CONTROL_COLS', 'COUNT_THRESHOLD', 'COUNT_COL_NAME', 'BUILD_NAME', 'CONVERT_SUSHI',
'PULL_POOL_ID', 'RUN_EPS_QC', 'PSEUDOCOUNT', 'REMOVE_DATA', 'DAYS', 'SEQUENCING_INDEX_COLS',
'CREATE_CELLDB_METADATA', 'RUN_EPS_QC', 'PSEUDOCOUNT', 'REMOVE_DATA', 'DAYS', 'SEQUENCING_INDEX_COLS',
'RAW_COUNTS', 'CELL_SET_META', 'CELL_LINE_META', 'FILTERED_COUNTS', 'LFC', 'COUNTS', 'ANNOTATED_COUNTS',
'COLLAPSED_VALUES', 'NORMALIZED_COUNTS', 'API_URL', 'FILTER_COUNTS_QC', 'ASSAY_POOL_META', 'SCREEN'
]
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