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| Config keyword | Description |
|---|---|
organism_defaults |
Name of a file in SeA-SnaP/defaults/ where default values for an organism are defined |
organism: |
(overwrite organism_defaults) |
|---name |
name of the organism, e.g. "human" |
|---genus |
name of the genus, e.g. "Homo Sapiens" |
|---taxon |
taxon number, e.g. 9606 |
|---files: |
|
...|---genome |
path to a genome file (.fa); required |
...|---transcriptome |
path to a transcriptome file; if empty "" it will be automatically generated |
...|---gtf |
path to a gtf file with genome annotation; required |
...|---bed |
path to a bed file; only required for infer_experiment |
...|---seqc_gtf |
path to a gtf file; only required for qc |
|---star_index |
path to a folder with indices for STAR; auto-generated if empty |
|---salmon_index |
path to a folder with indices for Salmon; auto-generated if empty |
|---R: |
|
...|---annotations |
annotation string for R's AnnotationDbi, e.g. "org.Hs.eg.db" |
pipeline_param: |
(general pipeline settings) |
|---out_path_pattern |
path pattern for output files. Wildcards can be used inside braces {...}.Available wildcards: {step}, {extension} and---mapping: {sample}, {mate}, {batch}, {flowcell}, {lane}, {library}---DE: {contrast}, {mapping}default mapping: mapping/{step}/{sample}.{mate}/out/{step}.{sample}.{mate}.{extension}default DE: DE/{contrast}/{step}/out/{step}.{contrast}.{extension} |
|---log_path_pattern |
path pattern for log files. Wildcards can be used inside braces {...}.Available wildcards: {step}, {extension} and---mapping: {sample}, {mate}, {batch}, {flowcell}, {lane}, {library}---DE: {contrast}, {mapping}default mapping: mapping/{step}/{sample}.{mate}/report/{step}.{sample}.{mate}.{extension}default DE: DE/{contrast}/{step}/report/{step}.{contrast}.{extension} |
|---in_path_pattern |
path pattern for input files. Wildcards can be used inside braces {...}.Available wildcards mapping: {sample}, {mate}, {batch}, {flowcell}, {lane}, {library}Available wildcards DE: same as out_path_pattern for mappingdefault mapping: ../input/{sample}/{sample}.{mate}default DE: mapping/{step}/{sample}.{mate}/out/{step}.{sample}.{mate}.{extension} |
|---report_snippets |
directory containing Rmd snippets; default: SeA-SnaP/report/ |
|---input_choice: |
(set choices for the choose_input() path handler method) |
...|---mapping |
For DE: list of rules to use as an input for DESeq2; first entry used if no wildcard {mapping} was set in the out_path_patternOptions: "import_gene_counts" for input from STARs gene counts, import_featurecounts for input from FeatureCounts and "import_sf" for input from Salmon sf files |
| Config keyword | Description |
|---|---|
pipeline_param: |
(general pipeline settings) |
|---mapping_results |
list of options which algorithm to use. Options: "salmon-transcript_counts" for Salmon. "star-gene_counts" for STAR. |
|---QC_results |
list of options which QC steps to perform. Options: "fastqc", "dupradar", "infer_experiment" |
rule_options: |
(set parameters for rules) |
|---star: |
|
...|---cmd_opt |
a string with additional command line options for STAR |
...|---trim |
trim fastq files? Options: "yes" or "no" |
|---star_index: |
|
...|---cmd_opt |
a string with additional command line options for STAR index generation; e.g. set "--sjdbOverhang <read len -1>" |
|---salmon: |
|
...|---cmd_opt |
a string with additional command line options for Salmon |
...|---trim |
trim fastq files? Options: "yes" or "no" |
|---salmon_index: |
|
...|---cmd_opt |
a string with additional command line options for Salmon index generation |
| Config keyword | Description |
|---|---|
experiment: |
(settings about the experiment) |
|---covariate_file: |
|
...|---star |
covariate file to use for input from STAR; default: covariate_file.txt |
...|---salmon |
covariate file to use for input from Salmon; default: covariate_file.txt |
|---design_formula |
design formula to be used by DESeq2; default: "~ group" |
|---columns: |
(define level order for specific columns; default: empty) |
| ...|--- <column name> | list with level names of the column in the wished order (first level will be the reference by default) |
filters: |
(set filters for input data) |
|---low_counts |
exclude genes with counts lower than ; default: 0 |
|---min_counts |
include only features with at least min_counts counts in at least min_count_n samples default: not set |
|---min_count_n |
(see above) |
|---experiment_blacklist |
exclude certain entries of the covariate file from analysis given as a dictionary of the form: {: [, ...]} e.g. exclude samples: {"group": ["sample1", "sample1"]} default: {} |
|---experiment_whitelist |
only allow certain entries of the covariate file for analysis given as a dictionary of the form: {: [, ...]} |
contrasts: |
(define which contrasts to produce and how) |
|---contrast_list: |
List of contrast definitions (see following); default: empty |
| ...|---(list entry) | |
......|---title |
name of contrast, e.g. "nonclassical vs classical" |
......|---ratio |
|
.........|---column |
column in covariate file, e.g. "condition" |
.........|---numerator |
numerator of the contrast (a level of column), e.g. "nonclassical" |
.........|---denominator |
denominator of the contrast (a level of column), e.g. "classical" |
......|---coef |
alt. to ratio; the coefficient of DESeq2 results, e.g. "condition_classical_vs_nonclassical" |
......|---vector |
alt. to ratio; a list with entries corresponding to columns in the design matrix, defining the linear combination, e.g. [1,1,0,-1,0] |
......|---goseq |
whether to run GO and KEGG enrichment analysis with goseq; "true" or "false" |
......|---cluster_profiler |
|
.........|---run |
whether to run cluster_profiler; "true" or "false" |
.........|---MSigDb: |
test for MSigDb annotation: |
............|---categories: |
list of MSigDb categories to test; e.g. ["H","C1","C2"]; if categories is not set, tests all categories |
............|---type |
whether to run gene set enrichment analysis or overrepresentation analysis; options: "gsea" or "ora"; default: "gsea" |
.........|---GO: |
test for GO annotation: |
............|---ontologies: |
list of GO ontologies to test; e.g. ["MF","BP","CC"]; if ontologies is not set, tests all three |
............|---type |
whether to run gene set enrichment analysis or overrepresentation analysis; options: "gsea" or "ora"; default: "gsea" |
............|---pval: |
p-value cutoff to use; default 0.05 |
............|---qval: |
q-value cutoff to use, only for ORA; default 0.2 |
.........|---KEGG: |
test for KEGG pathway annotation: |
............|---type |
whether to run gene set enrichment analysis or overrepresentation analysis; options: "gsea" or "ora"; default: "gsea" |
............|---kegg_organism_code |
kegg code for the organism; e.g. "mmu" for mouse or "hsa" for human |
............|---pval: |
p-value cutoff to use; default 0.05 |
............|---qval: |
q-value cutoff to use, only for ORA; default 0.2 |
.........|---KEGG_modules: |
test for KEGG module annotation: |
............|---type |
whether to run gene set enrichment analysis or overrepresentation analysis; options: "gsea" or "ora"; default: "gsea" |
............|---kegg_organism_code |
kegg code for the organism; e.g. "mmu" for mouse or "hsa" for human |
............|---pval: |
p-value cutoff to use; default 0.05 |
............|---qval: |
q-value cutoff to use, only for ORA; default 0.2 |
......|---... |
any key from defaults (overwrite them for this contrast) |
|---defaults: |
|
...|---max_p_adj |
FDR cutoff 'alpha' for DESeq2's results function; default: 0.1 |
...|---ranking_by |
rank results by (column in results table): log2FoldChange for log2 fold change (the effect size estimate), pvalue for the p-value, padj for the multiple testing corrected p-value |
...|---ranking_order |
R expression for ordering (with ranking_by) with 'x' as input, e.g. "-abs(x)" |
...|---results_parameters: |
|
......|---lfcThreshold |
test for log fold change higher than ; default: 0 |
......|---altHypothesis |
alternative hypothesis of the test Options: greater, less, greaterAbs, lessAbs (see results)default: greaterAbs |
......|---independentFiltering |
perform independent filtering; "yes" or "no" |
...|---lfcShrink_parameters: |
|
......|---type |
algorithm to use for log fold change shrinkage; Options: none, apeglm, ashr, normaldefault: "none" |
...|---ORA: |
|
......|---fdr_threshold |
FDR threshold to determine which results to use for over-representation analysis; default: 0.1 |
report: |
(define which snippets to include in the report) |
|---report_snippets |
List of report snippets (Rmd files) in the report/ directory. Snippets will be appended in the order defined in this list (see section Adding Rmd Snippets) |
|---defaults: |
|
...|---... |
default lists of report snippets (Rmd files) added to the report in blocks; a dict with block name as key and snippet list as value |
|---snippet_parameters: |
parameters used in report snippets: |
...|---Normalisation_QC: |
parameters used in Normalisation_QC sub-folder: |
......|---n_most_varying |
analyse the n most varying genes |
......|---annotation_columns |
columns of the covariate table used to annotate PCA and clustering |
...|---contrast: |
parameters used in contrast sub-folder: |
......|---filter_results: |
parameters to filter DESeq2 results table: |
.........|---qval |
threshold on qvalue, display rows with q-value < qval only; default 0.1 |
......|---filter_goseq: |
parameters to filter goseq results table: |
.........|---qval |
threshold on qvalue, display rows with q-value < qval only; default 0.1 |
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