Add toolsheet-related implementations #443
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…ve remainder:true
… ch_report_input_files
…generation of report input channel
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Thanks @suzannejin - another big one. Will review thoroughly when I can, just give me some time :-) |
Unfortunately many parts of the pipeline had to be changed to properly use the toolsheets args, otherwise rare behaviours raise... However, if it makes the review process easier for you, I can split an subPR with the changes related to params.differential_method and params.functional_method, which are more independent to the rest. |
That's OK, I just need some dedicated time with it to understand and look for simplifications, as in the previous PRs. |
pinin4fjords
requested changes
Mar 21, 2025
mirpedrol
reviewed
Mar 21, 2025
| @@ -224,6 +224,16 @@ To override the above options, you may also supply your own features table as a | |||
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| By default, if you don't provide features, for non-array data the workflow will fall back to attempting to use the matrix itself as a source of feature annotations. For this to work you must make sure to set the `features_id_col`, `features_name_col` and `features_metadata_cols` parameters to the appropriate values, for example by setting them to 'gene_id' if that is the identifier column on the matrix. This will cause the gene ID to be used everywhere rather than more accessible gene symbols (as can be derived from the GTF), but the workflow should run. Please use this option for MaxQuant analysis, i.e. do not provide features. | |||
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| ## Toolsheet | |||
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| We provide a set of toolsheet files that define the tools that make sense to run for a given study type. These files are in the `assets` directory of the pipeline. | |||
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It would be good to add a link to the directory on github
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| We provide a set of toolsheet files that define the tools that make sense to run for a given study type. These files are in the `assets` directory of the pipeline. | ||
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| Each row defines a combination of differential analysis tool and functional analysis tool (optional), with the respective arguments. Note that the arguments defined in the toolsheet have highest priority, meaning that they will overwrite any other arguments defined in the command line or in the configuration files. |
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| Each row defines a combination of differential analysis tool and functional analysis tool (optional), with the respective arguments. Note that the arguments defined in the toolsheet have highest priority, meaning that they will overwrite any other arguments defined in the command line or in the configuration files. | |
| Each row defines a combination of differential analysis tool and functional analysis tool (optional), with the respective arguments. | |
| > [!WARNING] | |
| > Note that the arguments defined in the toolsheet have highest priority, meaning that they will overwrite any other arguments defined in the command line or in the configuration files. |
| @@ -90,9 +90,13 @@ params { | |||
| exploratory_log2_assays = 'raw,normalised' | |||
| exploratory_palette_name = 'Set1' | |||
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| // Tools options | |||
| analysis_name = null | |||
| toolsheet_custom = null | |||
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Could this be named only toolsheet? I think it is more intuitive. Or do you think it's confusing?
| } else if (params.study_type == 'maxquant') { | ||
| ch_toolsheet = Channel.fromList(samplesheetToList("${projectDir}/assets/toolsheet_maxquant.csv", "${projectDir}/assets/schema_tools.json")) | ||
| } else { | ||
| error("Please make sure to mention the correct study_type") |
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| error("Please make sure to mention the correct study_type") | |
| error("Please make sure to mention the correct study_type. The available options are: 'rnaseq', 'affy_array', 'geo_soft_file' or 'maxquant'") |
| def meta = [ | ||
| analysis_name: it[0].analysis_name, | ||
| diff_method : it[0].diff_method, | ||
| diff_args : getParams('differential', it[0].diff_method) + parseArgs(it[0].diff_args) + [differential_method: it[0].diff_method], |
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Could you explain what is getParams used for, and why do you give the string 'differential' or 'functional'?
It's also not clear to me why are you adding the [differential_method: it[0].diff_method] map to the arguments.
Thanks!
| // args_functional as a map to stay consistent. We also remove null values | ||
| // from files list. | ||
| def meta = (it[0].method_functional) ? it[0] : it[0] + [args_functional: [:]] | ||
| [it[0], it.tail().grep().flatten()] |
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could you add a comment describing this channel like you did with the ones before?
| def pattern_with_tools = params_pattern + "|${meta.method_differential}" + (meta.method_functional ? "|functional|${meta.method_functional}" : "") | ||
| // return params for report | ||
| params_with_tools.findAll{ k,v -> k.matches(~/(${pattern_with_tools}).*/) } + | ||
| [report_file_names, files.collect{ f -> f.name}].transpose().collectEntries() |
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please add a description of the channel
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Changes made to enable the usage of toolsheets:
gsea_runandgprofiler2_runflags intofunctional_method-> more consistent with the ch_tools behaviourdifferential_methodandfunctional_methodflagsNice to have, but left for next PRs (to not extend this one too much):
analysis_nameflagPR checklist
nf-core lint).nf-test test main.nf.test -profile test,docker).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).