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Add proteus module for maxquant data analysis #147
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Saving some progress, REMOVE pxnotebook_env.yml AND Dockerfilegit add…
WackerO 5356b0c
progress save for Px
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progress save
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Cleaning up some changes
WackerO 7757ba3
changed proteus configs
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Installed and integrated proteus
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Merge branch 'dev' of https://github.com/nf-core/differentialabundanc…
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prettier, removed an unnecessary file
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Added missing config
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linting
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Updated docs, fixed bugs with proteus integration, separated more cle…
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Merge branch 'dev' of https://github.com/nf-core/differentialabundance
WackerO 4b8d5bc
Changed list format of --features_log2_assays
WackerO c844121
Some fixes of log2_assays
WackerO 41e8cda
Removed process def from test_maxquant.config as it is not anymore ne…
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More cleanup, comment/docu changes
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Updated output doc
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Fixed NULL being printed in the report.html
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prettier
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Merge branch 'dev' of https://github.com/nf-core/differentialabundanc…
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made workflow more similar to previous version
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Merge branch 'dev' of https://github.com/nf-core/differentialabundanc…
WackerO 6b7a019
Pipeline finally runs again after changing proteus
WackerO 70ad1c9
Added proteus params table to report, renamed some params
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updated proteus module
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Merge branch 'dev' of https://github.com/nf-core/differentialabundanc…
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Merge branch 'dev' of https://github.com/nf-core/differentialabundanc…
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Merge branch 'dev' into add_proteus
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Working on review
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Merge branch 'add_proteus' of https://github.com/WackerO/differential…
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Finished the review changes, pipeline runs locally
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Restored shinyngs module
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module updates
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Cleanup, updated changelog, fixed output docs
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Original file line number | Diff line number | Diff line change |
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/* | ||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
Nextflow config file for running MaxQuant proteomics analysis | ||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
Defines settings specific to MaxQuant proteomics analysis | ||
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Use as follows: | ||
nextflow run nf-core/differentialabundance -profile maxquant,<docker/singularity> --outdir <OUTDIR> | ||
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---------------------------------------------------------------------------------------- | ||
*/ | ||
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params { | ||
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config_profile_name = 'MaxQuant profile' | ||
config_profile_description = 'Settings for MaxQuant analysis' | ||
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// Study | ||
study_type = 'maxquant' | ||
study_abundance_type = 'intensities' | ||
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// Features | ||
features_id_col = 'Majority protein IDs' | ||
features_name_col = 'Majority protein IDs' | ||
features_metadata_cols = 'Majority protein IDs' | ||
features_type = 'protein' | ||
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// Exploratory | ||
exploratory_assay_names = "raw,normalised,variance_stabilised" | ||
exploratory_final_assay = "variance_stabilised" | ||
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// Differential options | ||
differential_file_suffix = ".limma.results.tsv" | ||
differential_fc_column = "logFC" | ||
differential_pval_column = "P.Value" | ||
differential_qval_column = "adj.P.Val" | ||
differential_feature_id_column = "probe_id" | ||
differential_feature_name_column = "probe_id" | ||
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// Shiny does not work for this datatype | ||
shinyngs_build_app = false | ||
} |
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Original file line number | Diff line number | Diff line change |
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/* | ||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
Nextflow config file for running minimal tests | ||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
Defines input files and everything required to run a fast and simple | ||
pipeline test with MaxQuant Mass-spec data. | ||
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Use as follows: | ||
nextflow run nf-core/differentialabundance -profile test_maxquant,<docker/singularity> --outdir <OUTDIR> | ||
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---------------------------------------------------------------------------------------- | ||
*/ | ||
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includeConfig 'maxquant.config' | ||
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params { | ||
study_name = 'PXD043349' | ||
config_profile_name = 'MaxQuant test profile' | ||
config_profile_description = 'MaxQuant test dataset to check pipeline function' | ||
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// Limit resources so that this can run on GitHub Actions | ||
max_cpus = 2 | ||
max_memory = '6.GB' | ||
max_time = '6.h' | ||
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// Input data | ||
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/proteomics/maxquant/MaxQuant_samplesheet.tsv' | ||
matrix = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/proteomics/maxquant/MaxQuant_proteinGroups.txt' | ||
contrasts = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/proteomics/maxquant/MaxQuant_contrasts.csv' | ||
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// Features | ||
features_id_col = 'Majority protein IDs' | ||
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features_metadata_cols = 'Majority protein IDs' | ||
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// Observations | ||
observations_id_col = 'Experiment' | ||
observations_name_col = 'Name' | ||
proteus_measurecol_prefix = 'LFQ intensity ' | ||
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// Exploratory | ||
exploratory_main_variable = 'Celltype' | ||
exploratory_assay_names = 'raw,normalised' | ||
exploratory_final_assay = 'normalised' | ||
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// Differential | ||
differential_feature_id_column = 'probe_id' | ||
differential_feature_name_column = 'Majority protein IDs' | ||
differential_fc_column = 'logFC' | ||
differential_qval_column = 'adj.P.Val' | ||
} |
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This is repeated code from shinyngs, we should factor that out. I'll make a PR for it.
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@WackerO the function for this is now available in the latest shinyngs, you just have to update the container for the notebook.
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I still think we should use the factored-out conditional logging function here, so I've unresolved this.
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Ah of course, just had to update shinyngs for the rmarkdown report for that function to be found. I have for now added the [] removal in the report; maybe in a future release that part can be integrated into shiny as well