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dvc.yaml
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# Autogenerated file with ./create-dvc-yaml.py. DO NOT EDIT
stages:
cluster_profiler_compare:
do:
cmd: ./docker-wrapper.sh ./src/integration/24-clusterprofiler.R --dataset-name
${key}
deps:
- ./src/integration/24-clusterprofiler.R
- ./src/shared/R-helpers/get_args.R
- ./src/shared/R-helpers/get_settings.R
- ${item.settings.inputs}
outs:
- ${item.settings.output_directory}
params:
- integration.cluster_profiler_compare.default_settings
- integration.cluster_profiler_compare.stages.${key}.settings
foreach: ${integration.cluster_profiler_compare.stages}
das:
do:
cmd: ./docker-wrapper.sh src/rnaseq/DAS_Analysis/DAS.sh --dataset-name ${key}
--input_dir ${item.settings.input_directory} --gtf ${item.settings.gtf} --out_dir
${item.settings.output_directory}
deps:
- ./src/rnaseq/DAS_Analysis/DAS.sh
- ./src/shared/R-helpers/get_args.R
- ./src/shared/R-helpers/get_settings.R
- ${item.settings.input_directory}
- ${item.settings.data_input}
- ${item.settings.gtf}
outs:
- ${item.settings.output_directory}
params:
- splicing_analysis_das.das.stages.${key}.settings
foreach: ${splicing_analysis_das.das.stages}
das_decompress_anno_file:
do:
cmd: zcat ${item.inputs} > ${item.output}
deps:
- ${item.inputs}
outs:
- ${item.output}:
cache: false
foreach:
human:
inputs: database/align-references/hsapiens/gencode.v37.annotation.gtf.gz
output: database/align-references/hsapiens/gencode.v37.annotation.gtf
mouse:
inputs: database/align-references/mmusculus/gencode.vM26.annotation.gtf.gz
output: database/align-references/mmusculus/gencode.vM26.annotation.gtf
das_ora:
do:
cmd: ./docker-wrapper.sh ./src/rnaseq/ORA/das_ora.R --dataset-name ${key}
deps:
- ./src/rnaseq/ORA/das_ora.R
- ./src/shared/R-helpers/get_args.R
- ./src/shared/R-helpers/get_settings.R
- ${item.settings.input}
outs:
- ${item.settings.output_directory}
params:
- splicing_analysis_das.das_ora.stages.${key}.settings
foreach: ${splicing_analysis_das.das_ora.stages}
das_prep:
do:
cmd: ./docker-wrapper.sh ./src/rnaseq/DAS_Analysis/das_prep.R --dataset-name
${key}
deps:
- ./src/shared/R-helpers/get_args.R
- ./src/shared/R-helpers/get_settings.R
- ./src/rnaseq/DAS_Analysis/das_prep.R
- ${item.settings.input_directory}
- ${item.settings.gtf}
- ${item.settings.nextflow}
- ${item.settings.annotation}
outs:
- ${item.settings.output_directory}
params:
- splicing_analysis_das.das_prep.stages.${key}.settings
foreach: ${splicing_analysis_das.das_prep.stages}
fastqscreen:
do:
cmd: ./docker-wrapper.sh fastq_screen --subset 0 --tag --outdir ${item.output}
--conf ${rnaseq.fastqscreen.default_settings.conf} ${item.inputs}
deps:
- ${item.inputs}
- ${rnaseq.fastqscreen.default_settings.conf}
outs:
- ${item.output}
foreach: ${rnaseq.fastqscreen.stages}
generate_genesets_pathwayscoring:
cmd: ./docker-wrapper.sh python ./src/integration/generate_genesets.py
deps:
- src/integration/generate_genesets.py
- database/genesets/raw_lists/
- database/uniprot/uniprot_HUMAN_9606_idmapping_selected.tab.gz
- database/biomaRt/ensembl_to_symbol_human.csv
- database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
- human_rat_mouse_protein_gene_link.csv.gz
outs:
- database/genesets/all_genesets.json.gz
map_de_genes:
do:
cmd: ./docker-wrapper.sh ./src/integration/22-map_de.py --stage ${key} --key
integration --method map_de_genes
deps:
- ./src/integration/22-map_de.py
- ${item.inputs.de}
- ${item.inputs.mapping}
- ${integration.map_de_genes.default_settings.species_mapping}
outs:
- ${item.output}
params:
- integration.map_de_genes.default_settings
- integration.map_de_genes.stages.${key}.settings
foreach: ${integration.map_de_genes.stages}
merge_all_pathways:
cmd: ./docker-wrapper.sh ./src/integration/merge_pathways.py
deps:
- src/integration/merge_pathways.py
- results/DTU/C9orf72-mouse/ORA
- results/DTU/FUS-mouse/ORA
- results/DTU/SOD1-mouse/ORA
- results/DTU/TDP43-mouse/ORA
- results/DTU/human/ORA
- results/DAS/C9orf72-mouse/ORA
- results/DAS/FUS-mouse/ORA
- results/DAS/SOD1-mouse/ORA
- results/DAS/TDP43-mouse/ORA
- results/DAS/human/ORA
- results/WGCNA/c9orf72_results
- results/WGCNA/fus_results
- results/WGCNA/human_results
- results/WGCNA/sod1_results
- results/WGCNA/tdp43_results
- results/WGCNA_rnaseq/c9orf72_results
- results/WGCNA_rnaseq/fus_results
- results/WGCNA_rnaseq/human_results
- results/WGCNA_rnaseq/sod1_results
- results/WGCNA_rnaseq/tdp43_results
- datasets/consortium/human-datasets/02_organized_data/rnaseq/gene-enrichment/gene_set_enrichment/
- datasets/consortium/SOD1-mouse/02_organized_data/rnaseq/gene-enrichment/gene_set_enrichment/
- datasets/consortium/FUS-mouse/02_organized_data/rnaseq/gene-enrichment/gene_set_enrichment/
- datasets/consortium/C9orf72-mouse/02_organized_data/rnaseq/gene-enrichment/gene_set_enrichment/
- datasets/consortium/TDP43-mouse/02_organized_data/rnaseq/gene-enrichment/gene_set_enrichment/
- datasets/consortium/human-datasets/02_organized_data/proteomics/gsea_enrichment/gsea_results/
- datasets/consortium/SOD1-mouse/02_organized_data/proteomics/gsea_enrichment/gsea_results/
- datasets/consortium/FUS-mouse/02_organized_data/proteomics/gsea_enrichment/gsea_results/
- datasets/consortium/C9orf72-mouse/02_organized_data/proteomics/gsea_enrichment/gsea_results/
- datasets/consortium/TDP43-mouse/02_organized_data/proteomics/gsea_enrichment/gsea_results/
- datasets/consortium/human-datasets/02_organized_data/rnaseq/genetonic/
- datasets/consortium/SOD1-mouse/02_organized_data/rnaseq/genetonic/
- datasets/consortium/FUS-mouse/02_organized_data/rnaseq/genetonic/
- datasets/consortium/C9orf72-mouse/02_organized_data/rnaseq/genetonic/
- datasets/consortium/TDP43-mouse/02_organized_data/rnaseq/genetonic/
outs:
- results/integration/pathways/all_pathways.csv
merge_de:
do:
cmd: ./docker-wrapper.sh ./src/integration/23-merge-de-lists.py --stage ${key}
--key integration --method cluster_profiler_merge
deps:
- ${item.inputs}
outs:
- ${item.output}:
cache: false
params:
- integration.cluster_profiler_merge.stages.${key}.settings
foreach: ${integration.cluster_profiler_merge.stages}
mofa_tp2sm:
do:
cmd: MX_DOCKERIMAGE="ghcr.io/imsb-uke/maxomod_pipeline-mofa" ./docker-wrapper.sh
Rscript src/shared/integrative/mofa_analysis.r --dataset-name ${key} --mofa-type
mofa_tp2sm
deps:
- src/shared/integrative/mofa_analysis.r
- ${item.omics.transcriptomics.annotation_file}
- ${item.omics.transcriptomics.expression_file}
- ${item.omics.proteomics.annotation_file}
- ${item.omics.proteomics.expression_file}
- ${item.omics.srna_mature.annotation_file}
- ${item.omics.srna_mature.keep_file}
- ${item.omics.srna_mature.expression_file}
- ${item.omics.metabolomics.annotation_file}
- ${item.omics.metabolomics.expression_file}
- ${item.omics.phosphoproteomics.annotation_file}
- ${item.omics.phosphoproteomics.expression_file}
outs:
- ${item.out_dir}
params:
- mofa_tp2sm.stages.${key}.organism
- mofa_tp2sm.stages.${key}.sex_selection
- mofa_tp2sm.stages.${key}.factor_combinations
- mofa_tp2sm.stages.${key}.model_training
- mofa_tp2sm.stages.${key}.topN_byVar
foreach: ${mofa_tp2sm.stages}
mofa_tp2sm_c9:
do:
cmd: MX_DOCKERIMAGE="ghcr.io/imsb-uke/maxomod_pipeline-mofa" ./docker-wrapper.sh
Rscript src/shared/integrative/mofa_analysis.r --dataset-name ${key} --mofa-type
mofa_tp2sm_c9
deps:
- src/shared/integrative/mofa_analysis.r
- ${item.omics.transcriptomics.annotation_file}
- ${item.omics.transcriptomics.expression_file}
- ${item.omics.proteomics.annotation_file}
- ${item.omics.proteomics.expression_file}
- ${item.omics.srna_mature.annotation_file}
- ${item.omics.srna_mature.keep_file}
- ${item.omics.srna_mature.expression_file}
- ${item.omics.metabolomics.annotation_file}
- ${item.omics.metabolomics.sample_mapping}
- ${item.omics.metabolomics.expression_file}
- ${item.omics.phosphoproteomics.annotation_file}
- ${item.omics.phosphoproteomics.sample_matching}
- ${item.omics.phosphoproteomics.expression_file}
outs:
- ${item.out_dir}
params:
- mofa_tp2sm_c9.stages.${key}.organism
- mofa_tp2sm_c9.stages.${key}.sex_selection
- mofa_tp2sm_c9.stages.${key}.factor_combinations
- mofa_tp2sm_c9.stages.${key}.model_training
- mofa_tp2sm_c9.stages.${key}.topN_byVar
foreach: ${mofa_tp2sm_c9.stages}
mofa_tp2sm_fus:
do:
cmd: MX_DOCKERIMAGE="ghcr.io/imsb-uke/maxomod_pipeline-mofa" ./docker-wrapper.sh
Rscript src/shared/integrative/mofa_analysis.r --dataset-name ${key} --mofa-type
mofa_tp2sm_fus
deps:
- src/shared/integrative/mofa_analysis.r
- ${item.omics.transcriptomics.annotation_file}
- ${item.omics.transcriptomics.expression_file}
- ${item.omics.proteomics.annotation_file}
- ${item.omics.proteomics.expression_file}
- ${item.omics.srna_mature.annotation_file}
- ${item.omics.srna_mature.keep_file}
- ${item.omics.srna_mature.expression_file}
- ${item.omics.metabolomics.annotation_file}
- ${item.omics.metabolomics.sample_mapping}
- ${item.omics.metabolomics.expression_file}
- ${item.omics.phosphoproteomics.annotation_file}
- ${item.omics.phosphoproteomics.expression_file}
outs:
- ${item.out_dir}
params:
- mofa_tp2sm_fus.stages.${key}.organism
- mofa_tp2sm_fus.stages.${key}.sex_selection
- mofa_tp2sm_fus.stages.${key}.factor_combinations
- mofa_tp2sm_fus.stages.${key}.model_training
- mofa_tp2sm_fus.stages.${key}.topN_byVar
foreach: ${mofa_tp2sm_fus.stages}
mofa_tps2:
do:
cmd: MX_DOCKERIMAGE="ghcr.io/imsb-uke/maxomod_pipeline-mofa" ./docker-wrapper.sh
Rscript src/shared/integrative/mofa_analysis.r --dataset-name ${key} --mofa-type
mofa_tps2
deps:
- src/shared/integrative/mofa_analysis.r
- ${item.omics.transcriptomics.annotation_file}
- ${item.omics.transcriptomics.expression_file}
- ${item.omics.proteomics.annotation_file}
- ${item.omics.proteomics.expression_file}
- ${item.omics.srna_mature.annotation_file}
- ${item.omics.srna_mature.keep_file}
- ${item.omics.srna_mature.expression_file}
- ${item.omics.srna_hairpin.annotation_file}
- ${item.omics.srna_hairpin.keep_file}
- ${item.omics.srna_hairpin.expression_file}
outs:
- ${item.out_dir}
params:
- mofa_tps2.stages.${key}.organism
- mofa_tps2.stages.${key}.sex_selection
- mofa_tps2.stages.${key}.factor_combinations
- mofa_tps2.stages.${key}.model_training
- mofa_tps2.stages.${key}.topN_byVar
foreach: ${mofa_tps2.stages}
mofa_tpsm_c9:
do:
cmd: MX_DOCKERIMAGE="ghcr.io/imsb-uke/maxomod_pipeline-mofa" ./docker-wrapper.sh
Rscript src/shared/integrative/mofa_analysis.r --dataset-name ${key} --mofa-type
mofa_tpsm_c9
deps:
- src/shared/integrative/mofa_analysis.r
- ${item.omics.transcriptomics.annotation_file}
- ${item.omics.transcriptomics.expression_file}
- ${item.omics.proteomics.annotation_file}
- ${item.omics.proteomics.expression_file}
- ${item.omics.srna_mature.annotation_file}
- ${item.omics.srna_mature.keep_file}
- ${item.omics.srna_mature.expression_file}
- ${item.omics.metabolomics.annotation_file}
- ${item.omics.metabolomics.sample_mapping}
- ${item.omics.metabolomics.expression_file}
outs:
- ${item.out_dir}
params:
- mofa_tpsm_c9.stages.${key}.organism
- mofa_tpsm_c9.stages.${key}.sex_selection
- mofa_tpsm_c9.stages.${key}.factor_combinations
- mofa_tpsm_c9.stages.${key}.model_training
- mofa_tpsm_c9.stages.${key}.topN_byVar
foreach: ${mofa_tpsm_c9.stages}
ora_dtu:
do:
cmd: ./docker-wrapper.sh ./src/rnaseq/ORA/dtu_ora.R --dataset-name ${key}
deps:
- ./src/rnaseq/ORA/dtu_ora.R
- ./src/shared/R-helpers/get_args.R
- ./src/shared/R-helpers/get_settings.R
- ${item.settings.inputdex}
- ${item.settings.inputdrim}
outs:
- ${item.settings.output_directory}
params:
- splicing_analysis.ora_dtu.stages.${key}.settings
foreach: ${splicing_analysis.ora_dtu.stages}
pathway_scores_proteomics:
do:
cmd: ./docker-wrapper.sh python3 ./src/shared/score_pathways.py --stage ${key}
--key integration --method pathway_scores_proteomics
deps:
- ./src/shared/score_pathways.py
- ${item.inputs.expression}
- ${item.inputs.genelists}
outs:
- ${item.output}.csv
- ${item.output}.ncount.csv
params:
- integration.pathway_scores_proteomics.default_settings
- integration.pathway_scores_proteomics.stages.${key}.settings
foreach: ${integration.pathway_scores_proteomics.stages}
pathway_scores_rnaseq:
do:
cmd: ./docker-wrapper.sh python3 ./src/shared/score_pathways.py --stage ${key}
--key integration --method pathway_scores_rnaseq
deps:
- ./src/shared/score_pathways.py
- ${item.inputs.expression}
- ${item.inputs.genelists}
outs:
- ${item.output}.csv
- ${item.output}.ncount.csv
params:
- integration.pathway_scores_rnaseq.default_settings
- integration.pathway_scores_rnaseq.stages.${key}.settings
foreach: ${integration.pathway_scores_rnaseq.stages}
phosphoproteomics_deg:
do:
cmd: ./docker-wrapper.sh ./src/phosphoproteomics/30-deg.R --dataset-name ${key}
deps:
- ./src/phosphoproteomics/30-deg.R
- ./src/shared/R-helpers/get_args.R
- ./src/shared/R-helpers/update_list.R
- ./src/shared/R-helpers/get_settings.R
- ./src/shared/R-helpers/cohort_to_factors.R
- ./src/shared/R-helpers/limma_analysis.R
- ${item.settings.cohort}
- ${item.settings.intensity_mat_for_limma}
outs:
- ${item.settings.output_directory}
params:
- proteomics.deg.default_settings
- proteomics.deg.stages.${key}.settings
foreach: ${phosphoproteomics.deg.stages}
phosphoproteomics_deg_boxplots:
do:
cmd: ./docker-wrapper.sh ./src/phosphoproteomics/47-boxplots_deg_results.py
--stage ${key}
deps:
- ./src/phosphoproteomics/47-boxplots_deg_results.py
- ${item.inputs.raw}
- ${item.inputs.metadata}
- ${item.inputs.degpath}
outs:
- ${item.output}
params:
- phosphoproteomics.deg_boxplots.default_settings
- phosphoproteomics.deg_boxplots.stages.${key}.settings
foreach: ${phosphoproteomics.deg_boxplots.stages}
phosphoproteomics_deg_count:
cmd: ./docker-wrapper.sh python ./src/phosphoproteomics/46-get_deg_counts.py
deps:
- ./src/phosphoproteomics/46-get_deg_counts.py
- ${phosphoproteomics.deg_count.sod1_female}
- ${phosphoproteomics.deg_count.tdp43_female}
- ${phosphoproteomics.deg_count.c9_female}
- ${phosphoproteomics.deg_count.fus_female}
- ${phosphoproteomics.deg_count.sod1_male}
- ${phosphoproteomics.deg_count.tdp43_male}
- ${phosphoproteomics.deg_count.c9_male}
- ${phosphoproteomics.deg_count.fus_male}
metrics:
- results/integration/phosphoproteomics/deg_counts.yaml
phosphoproteomics_deg_digestion:
do:
cmd: ./docker-wrapper.sh ./src/phosphoproteomics/40-deg_digestion.R --dataset-name
${key}
deps:
- ./src/phosphoproteomics/40-deg_digestion.R
- ./src/shared/R-helpers/get_args.R
- ./src/shared/R-helpers/update_list.R
- ./src/shared/R-helpers/get_settings.R
- ./src/shared/R-helpers/create_volcano_plot.R
- ${item.settings.de_results_rds}
outs:
- ${item.settings.output_directory}
params:
- phosphoproteomics.deg_digestion.default_settings
- phosphoproteomics.deg_digestion.stages.${key}.settings
foreach: ${phosphoproteomics.deg_digestion.stages}
phosphoproteomics_gsea_enrichment:
do:
cmd: ./docker-wrapper.sh ./src/phosphoproteomics/45-gsea_enrichment.R --dataset-name
${key}
deps:
- ./src/phosphoproteomics/45-gsea_enrichment.R
- ./src/shared/R-helpers/get_args.R
- ./src/shared/R-helpers/update_list.R
- ./src/shared/R-helpers/get_settings.R
- ./src/shared/R-helpers/gseGO_memoise.R
- ./src/shared/R-helpers/gseKEGG_memoise.R
- ./src/shared/R-helpers/memoise_decorator.R
- ${item.settings.uniprot_to_ensembl}
- ${item.settings.de_results_rds}
outs:
- ${item.settings.output_directory}
params:
- phosphoproteomics.gsea_enrichment.default_settings
- phosphoproteomics.gsea_enrichment.stages.${key}.settings
foreach: ${phosphoproteomics.gsea_enrichment.stages}
phosphoproteomics_organize_samples:
do:
cmd: ./docker-wrapper.sh ./src/phosphoproteomics/10-organize_samples.py --stage
${key}
deps:
- ./src/phosphoproteomics/10-organize_samples.py
- ${item.inputs.cohort}
- ${item.inputs.inputs}
- ${item.inputs.samplesheet}
outs:
- ${item.output}/cohort_filtered.csv
- ${item.output}/intensity_mat_filtered_imputed_log2transf_norm.csv
params:
- phosphoproteomics.organize_samples.default_settings
- phosphoproteomics.organize_samples.stages.${key}.settings
foreach: ${phosphoproteomics.organize_samples.stages}
phosphoproteomics_prefiltering_pca:
do:
cmd: ./docker-wrapper.sh ./src/phosphoproteomics/20-prefiltering_pca.R --dataset-name
${key}
deps:
- ./src/phosphoproteomics/20-prefiltering_pca.R
- ./src/shared/R-helpers/get_args.R
- ./src/shared/R-helpers/update_list.R
- ./src/shared/R-helpers/get_settings.R
- ./src/shared/R-helpers/get_top_n_variance.R
- ./src/shared/R-helpers/pc_scores_loadings_plot.R
- ./src/shared/R-helpers/pca_fit.R
- ${item.settings.cohort}
- ${item.settings.input_intensity}
outs:
- ${item.settings.output_directory}/pca
- ${item.settings.output_directory}/intensity_mat_filtered_imputed_log2transf_norm.rds
params:
- phosphoproteomics.prefiltering_pca.default_settings
- phosphoproteomics.prefiltering_pca.stages.${key}.settings
foreach: ${phosphoproteomics.prefiltering_pca.stages}
phosphoproteomics_string_ppi:
do:
cmd: ./docker-wrapper.sh ./src/phosphoproteomics/45-string_ppi.R --dataset-name
${key}
deps:
- ./src/phosphoproteomics/45-string_ppi.R
- ./src/shared/R-helpers/get_args.R
- ./src/shared/R-helpers/update_list.R
- ./src/shared/R-helpers/get_settings.R
- ${item.settings.uniprot_to_string}
- ${item.settings.de_result_thresholds_rds}
- ${item.settings.string_ppi_file}
outs:
- ${item.settings.output_directory}
params:
- phosphoproteomics.string_ppi.default_settings
- phosphoproteomics.string_ppi.stages.${key}.settings
foreach: ${phosphoproteomics.string_ppi.stages}
proteomics_additional_QC:
do:
cmd: ./docker-wrapper.sh ./src/proteomics/22-additional_QC.R --dataset-name
${key}
deps:
- ./src/proteomics/22-additional_QC.R
- ./src/shared/R-helpers/get_args.R
- ./src/shared/R-helpers/update_list.R
- ./src/shared/R-helpers/get_settings.R
- ${item.settings.cohort}
- ${item.settings.input_data}
outs:
- ${item.settings.output_directory}
params:
- proteomics.additional_QC.default_settings
- proteomics.additional_QC.stages.${key}.settings
foreach: ${proteomics.additional_QC.stages}
proteomics_deg:
do:
cmd: ./docker-wrapper.sh ./src/proteomics/30-deg.R --dataset-name ${key}
deps:
- ./src/proteomics/30-deg.R
- ./src/shared/R-helpers/get_args.R
- ./src/shared/R-helpers/update_list.R
- ./src/shared/R-helpers/get_settings.R
- ./src/shared/R-helpers/cohort_to_factors.R
- ./src/shared/R-helpers/limma_analysis.R
- ${item.settings.cohort}
- ${item.settings.intensity_mat_for_limma}
outs:
- ${item.settings.output_directory}
params:
- proteomics.deg.default_settings
- proteomics.deg.stages.${key}.settings
foreach: ${proteomics.deg.stages}
proteomics_deg_boxplots:
do:
cmd: ./docker-wrapper.sh ./src/proteomics/47-boxplots_deg_results.py --stage
${key}
deps:
- ./src/proteomics/47-boxplots_deg_results.py
- ${item.inputs.raw}
- ${item.inputs.metadata}
- ${item.inputs.degpath}
outs:
- ${item.output}
params:
- proteomics.deg_boxplots.default_settings
- proteomics.deg_boxplots.stages.${key}.settings
foreach: ${proteomics.deg_boxplots.stages}
proteomics_deg_count:
cmd: ./docker-wrapper.sh python ./src/proteomics/46-get_deg_counts.py
deps:
- ./src/proteomics/46-get_deg_counts.py
- ${proteomics.deg_count.sod1_female}
- ${proteomics.deg_count.tdp43_female}
- ${proteomics.deg_count.c9_female}
- ${proteomics.deg_count.human_female}
- ${proteomics.deg_count.fus_female}
- ${proteomics.deg_count.human_csf_female}
- ${proteomics.deg_count.sod1_male}
- ${proteomics.deg_count.tdp43_male}
- ${proteomics.deg_count.c9_male}
- ${proteomics.deg_count.human_male}
- ${proteomics.deg_count.fus_male}
- ${proteomics.deg_count.human_csf_male}
metrics:
- results/integration/proteomics/deg_counts.yaml
proteomics_deg_digestion:
do:
cmd: ./docker-wrapper.sh ./src/proteomics/40-deg_digestion.R --dataset-name
${key}
deps:
- ./src/proteomics/40-deg_digestion.R
- ./src/shared/R-helpers/get_args.R
- ./src/shared/R-helpers/update_list.R
- ./src/shared/R-helpers/get_settings.R
- ./src/shared/R-helpers/create_volcano_plot.R
- ${item.settings.de_results_rds}
outs:
- ${item.settings.output_directory}
params:
- proteomics.deg_digestion.default_settings
- proteomics.deg_digestion.stages.${key}.settings
foreach: ${proteomics.deg_digestion.stages}
proteomics_download_string_ppi:
cmd: ./src/proteomics/44-download-string-protein-protein-interactions.sh
deps:
- ./src/proteomics/44-download-string-protein-protein-interactions.sh
outs:
- database/stringdb/mouse.uniprot_2_string.2018.tsv.gz
- database/stringdb/human.uniprot_2_string.2018.tsv.gz
- database/stringdb/10090.protein.links.txt.gz
- database/stringdb/9606.protein.links.txt.gz
proteomics_ensemble_symbol_mappings_human:
cmd: ./src/proteomics/35-download-ensembl-to-symbol-human.R
deps:
- ./src/proteomics/35-download-ensembl-to-symbol-human.R
outs:
- database/biomaRt/ensembl_to_symbol_human.csv
- database/biomaRt/ensembl_to_symbol_human.rds
proteomics_ensemble_symbol_mappings_mouse:
cmd: ./src/proteomics/35-download-ensembl-to-symbol-mouse.R
deps:
- ./src/proteomics/35-download-ensembl-to-symbol-mouse.R
outs:
- database/biomaRt/ensembl_to_symbol_mouse.csv
- database/biomaRt/ensembl_to_symbol_mouse.rds
proteomics_gofigure:
do:
cmd: ./docker-wrapper.sh python3 src/shared/GoFigure/run_gofigure.py --key proteomics
--method gofigure --stage ${key}
deps:
- ${item.inputs}
- src/shared/GoFigure/gofigure.py
- src/shared/GoFigure/run_gofigure.py
- src/shared/GoFigure/data/
outs:
- ${item.outputs}
params:
- proteomics.gofigure.stages.${key}.settings.level
- proteomics.gofigure.stages.${key}.settings.commandline
foreach: ${proteomics.gofigure.stages}
proteomics_gsea_enrichment:
do:
cmd: ./docker-wrapper.sh ./src/proteomics/45-gsea_enrichment.R --dataset-name
${key}
deps:
- ./src/proteomics/45-gsea_enrichment.R
- ./src/shared/R-helpers/get_args.R
- ./src/shared/R-helpers/update_list.R
- ./src/shared/R-helpers/get_settings.R
- ./src/shared/R-helpers/gseGO_memoise.R
- ./src/shared/R-helpers/gseKEGG_memoise.R
- ./src/shared/R-helpers/memoise_decorator.R
- ${item.settings.protein_annotations_rds}
- ${item.settings.uniprot_to_ensembl}
- ${item.settings.de_results_rds}
outs:
- ${item.settings.output_directory}
params:
- proteomics.gsea_enrichment.default_settings
- proteomics.gsea_enrichment.stages.${key}.settings
foreach: ${proteomics.gsea_enrichment.stages}
proteomics_missing_values_analysis:
cmd: ./docker-wrapper.sh ./src/proteomics/21-missing-values-analysis.R
deps:
- ./src/proteomics/21-missing-values-analysis.R
- ./datasets/consortium/SOD1-mouse/02_organized_data/proteomics/organized/intensity.rds
- ./datasets/consortium/TDP43-mouse/02_organized_data/proteomics/organized/intensity.rds
- ./datasets/consortium/C9orf72-mouse/02_organized_data/proteomics/organized/intensity.rds
- ./datasets/consortium/FUS-mouse/02_organized_data/proteomics/organized/intensity.rds
- ./datasets/consortium/human-datasets/02_organized_data/proteomics/organized/intensity.rds
- ./datasets/consortium/SOD1-mouse/02_organized_data/proteomics/prefiltering-pca/intensity_mat_filtered.rds
- ./datasets/consortium/TDP43-mouse/02_organized_data/proteomics/prefiltering-pca/intensity_mat_filtered.rds
- ./datasets/consortium/C9orf72-mouse/02_organized_data/proteomics/prefiltering-pca/intensity_mat_filtered.rds
- ./datasets/consortium/FUS-mouse/02_organized_data/proteomics/prefiltering-pca/intensity_mat_filtered.rds
- ./datasets/consortium/human-datasets/02_organized_data/proteomics/prefiltering-pca/intensity_mat_filtered.rds
outs:
- ./results/proteomics-missing-values/
proteomics_nes_mapper:
do:
cmd: mkdir -p database/NES && zcat ${item} > database/NES/predicted_${key}.tmp
&& src/proteomics/NESmapper-1.0/NESmapper.pl -p src/proteomics/NESmapper-1.0/NES_profiles_trained.txt
database/NES/predicted_${key}.tmp > database/NES/predicted_${key}.txt && rm
database/NES/predicted_${key}.tmp
deps:
- ${item}
- src/proteomics/NESmapper-1.0/NES_profiles_trained.txt
- src/proteomics/NESmapper-1.0/NESmapper.pl
outs:
- database/NES/predicted_${key}.txt
foreach:
human: database/uniprot/human_proteome.fasta.gz
mouse: database/uniprot/mouse_proteome.fasta.gz
proteomics_organize_samples:
do:
cmd: ./docker-wrapper.sh ./src/proteomics/10-organize_samples.R --dataset-name
${key}
deps:
- ./src/proteomics/10-organize_samples.R
- ./src/shared/R-helpers/get_args.R
- ./src/shared/R-helpers/update_list.R
- ./src/shared/R-helpers/get_settings.R
- ${item.settings.cohort}
- ${item.settings.maxquant_input}
- ${item.settings.rename_samples}
outs:
- ${item.settings.output_directory}
params:
- proteomics.organize_samples.default_settings
- proteomics.organize_samples.stages.${key}.settings
foreach: ${proteomics.organize_samples.stages}
proteomics_prefiltering_pca:
do:
cmd: ./docker-wrapper.sh ./src/proteomics/20-prefiltering_pca.R --dataset-name
${key}
deps:
- ./src/proteomics/20-prefiltering_pca.R
- ./src/shared/R-helpers/get_args.R
- ./src/shared/R-helpers/update_list.R
- ./src/shared/R-helpers/get_settings.R
- ./src/shared/R-helpers/get_top_n_variance.R
- ./src/shared/R-helpers/pc_scores_loadings_plot.R
- ./src/shared/R-helpers/pca_fit.R
- ${item.settings.cohort}
- ${item.settings.input_directory}
outs:
- ${item.settings.output_directory}
params:
- proteomics.prefiltering_pca.default_settings
- proteomics.prefiltering_pca.stages.${key}.settings
foreach: ${proteomics.prefiltering_pca.stages}
proteomics_revigo:
do:
cmd: ./docker-wrapper.sh python ./src/shared/REVIGO/revigo_restful_advanced.py
--dataset_name ${key} --omics_type proteomics
deps:
- ./src/shared/REVIGO/revigo_restful_advanced.py
- ./datasets/consortium/${item.settings.biological_model}/02_organized_data/proteomics/gsea_enrichment
outs:
- ${item.settings.output_directory}
params:
- proteomics.revigo.stages.${key}.settings
foreach: ${proteomics.revigo.stages}
proteomics_string_ppi:
do:
cmd: ./docker-wrapper.sh ./src/proteomics/45-string_ppi.R --dataset-name ${key}
deps:
- ./src/proteomics/45-string_ppi.R
- ./src/shared/R-helpers/get_args.R
- ./src/shared/R-helpers/update_list.R
- ./src/shared/R-helpers/get_settings.R
- ${item.settings.uniprot_to_string}
- ${item.settings.de_result_thresholds_rds}
- ${item.settings.string_ppi_file}
outs:
- ${item.settings.output_directory}
params:
- proteomics.string_ppi.default_settings
- proteomics.string_ppi.stages.${key}.settings
foreach: ${proteomics.string_ppi.stages}
proteomics_uniprot_ensemble_mappings:
cmd: ./src/proteomics/44-download-uniprot-to-gene-mappings.sh
deps:
- ./src/proteomics/44-download-uniprot-to-gene-mappings.sh
outs:
- database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
- database/uniprot/uniprot_HUMAN_9606_idmapping_selected.tab.gz
rnaseq_deg:
do:
cmd: ./docker-wrapper.sh ./src/rnaseq/30-deg.R --dataset-name ${key}
deps:
- ./src/rnaseq/30-deg.R
- ./src/shared/R-helpers/get_args.R
- ./src/shared/R-helpers/update_list.R
- ./src/shared/R-helpers/get_settings.R
- ./src/shared/R-helpers/cohort_to_factors.R
- ./src/shared/R-helpers/deseq2_analysis.R
- ${item.settings.cohort}
- ${item.settings.prefiltpca_dir}
outs:
- ${item.settings.output_directory}
params:
- rnaseq.deg.default_settings
- rnaseq.deg.stages.${key}.settings
foreach: ${rnaseq.deg.stages}
rnaseq_deg_count:
cmd: ./docker-wrapper.sh python ./src/rnaseq/46-get_deg_counts.py
deps:
- ./src/rnaseq/46-get_deg_counts.py
- ${rnaseq.deg_count.sod1_female}
- ${rnaseq.deg_count.tdp43_female}
- ${rnaseq.deg_count.c9_female}
- ${rnaseq.deg_count.human_female}
- ${rnaseq.deg_count.fus_female}
- ${rnaseq.deg_count.sod1_male}
- ${rnaseq.deg_count.tdp43_male}
- ${rnaseq.deg_count.c9_male}
- ${rnaseq.deg_count.human_male}
- ${rnaseq.deg_count.fus_male}
metrics:
- results/integration/rnaseq/deg_counts.yaml
rnaseq_deg_digestion:
do:
cmd: ./docker-wrapper.sh ./src/rnaseq/40-deg-digestion.R --dataset-name ${key}
deps:
- ./src/rnaseq/40-deg-digestion.R
- ./src/shared/R-helpers/get_args.R
- ./src/shared/R-helpers/update_list.R
- ./src/shared/R-helpers/get_settings.R
- ./src/shared/R-helpers/remove_ensembl_version.R
- ./src/shared/R-helpers/create_volcano_plot.R
- ./src/shared/R-helpers/memoise_decorator.R
- ${item.settings.deg_dir}
- ${item.settings.prefiltpca_dir}
outs:
- ${item.settings.output_directory}
params:
- rnaseq.deg_digestion.default_settings
- rnaseq.deg_digestion.stages.${key}.settings
foreach: ${rnaseq.deg_digestion.stages}
rnaseq_download_refs:
cmd: ./src/rnaseq/01-download-alignment-refs.sh
outs:
- database/align-references/hsapiens/GRCh38.p13.genome.fa.gz
- database/align-references/hsapiens/GRCh38.primary_assembly.genome.fa.gz
- database/align-references/hsapiens/gencode.v37.transcripts.fa.gz
- database/align-references/hsapiens/gencode.v37.annotation.gtf.gz
- database/align-references/mmusculus/GRCm39.genome.fa.gz
- database/align-references/mmusculus/GRCm39.primary_assembly.genome.fa.gz
- database/align-references/mmusculus/gencode.vM26.transcripts.fa.gz
- database/align-references/mmusculus/gencode.vM26.annotation.gtf.gz
rnaseq_gene_enrichment:
do:
cmd: ./docker-wrapper.sh ./src/rnaseq/45-gsea-enrichment.R --dataset-name ${key}
deps:
- ./src/rnaseq/45-gsea-enrichment.R
- ./src/shared/R-helpers/get_args.R
- ./src/shared/R-helpers/update_list.R
- ./src/shared/R-helpers/get_settings.R
- ./src/shared/R-helpers/remove_ensembl_version.R
- ./src/shared/R-helpers/gseGO_memoise.R
- ./src/shared/R-helpers/memoise_decorator.R
- ${item.settings.deg_dir}
outs:
- ${item.settings.output_directory}
params:
- rnaseq.gene_enrichment.default_settings
- rnaseq.gene_enrichment.stages.${key}.settings
foreach: ${rnaseq.gene_enrichment.stages}
rnaseq_gene_gene_correlation:
do:
cmd: ./docker-wrapper.sh ./src/rnaseq/50-gene-gene-correlation.R --dataset-name
${key}
deps:
- ./src/rnaseq/50-gene-gene-correlation.R
- ./src/shared/R-helpers/get_args.R
- ./src/shared/R-helpers/update_list.R
- ./src/shared/R-helpers/get_settings.R
- ./src/shared/R-helpers/remove_ensembl_version.R
- ./src/shared/R-helpers/gseGO_memoise.R
- ./src/shared/R-helpers/memoise_decorator.R
- ${item.settings.cohort}
- ${item.settings.deg_dir}
- ${item.settings.prefiltpca_dir}
outs:
- ${item.settings.output_directory}
params:
- rnaseq.gene_gene_correlation.default_settings
- rnaseq.gene_gene_correlation.stages.${key}.settings
foreach: ${rnaseq.gene_gene_correlation.stages}
rnaseq_genetonic:
do:
cmd: ./docker-wrapper.sh ./src/rnaseq/51-genetonic.R --dataset-name ${key}
deps:
- ./src/rnaseq/51-genetonic.R
- ${item.settings.inputs_female}
- ${item.settings.inputs_male}
- ${item.settings.annotation}
outs:
- ${item.settings.output_directory}
params:
- rnaseq.genetonic.default_settings
- rnaseq.genetonic.stages.${key}.settings
foreach: ${rnaseq.genetonic.stages}
rnaseq_gofigure:
do:
cmd: ./docker-wrapper.sh python3 src/shared/GoFigure/run_gofigure.py --key rnaseq
--method gofigure --stage ${key}
deps:
- ${item.inputs}
- src/shared/GoFigure/gofigure.py
- src/shared/GoFigure/run_gofigure.py
- src/shared/GoFigure/data/
outs:
- ${item.outputs}
params:
- rnaseq.gofigure.stages.${key}.settings.level
- rnaseq.gofigure.stages.${key}.settings.commandline
foreach: ${rnaseq.gofigure.stages}
rnaseq_merge_raw:
do:
cmd: ./src/rnaseq/merge_inputs.py --stage ${key}
deps:
- ./src/rnaseq/merge_inputs.py
- ${item.inputs.new}
- ${item.inputs.old}
outs:
- ${item.output}
foreach: ${rnaseq.rnaseq_merge.stages}
rnaseq_nextflow:
do:
cmd: ./src/rnaseq/10-nextflow.py --dataset-name ${key}
deps:
- ./src/rnaseq/10-nextflow.py
- ${item.settings.input_directory}
- ${item.settings.cohort}
- ${item.settings.fasta}
- ${item.settings.gtf}
outs:
- ${item.settings.output_directory}/samplesheet.csv
- ${item.settings.output_directory}/nextflow_ids_to_samples.csv
- ${item.settings.output_directory}/results/
params:
- rnaseq.nextflow.default_settings
- rnaseq.nextflow.stages.${key}.settings
foreach: ${rnaseq.nextflow.stages}
rnaseq_prefiltering_pca:
do:
cmd: ./docker-wrapper.sh ./src/rnaseq/20-prefiltering-pca.R --dataset-name ${key}
deps:
- ./src/rnaseq/20-prefiltering-pca.R
- ./src/shared/R-helpers/cohort_to_factors.R
- ./src/shared/R-helpers/get_args.R
- ./src/shared/R-helpers/update_list.R
- ./src/shared/R-helpers/get_settings.R
- ./src/shared/R-helpers/get_top_n_variance.R
- ./src/shared/R-helpers/pc_scores_loadings_plot.R
- ./src/shared/R-helpers/pca_fit.R
- ${item.settings.cohort}
- ${item.settings.nfid_to_sample_id}
- ${item.settings.counts}
outs:
- ${item.settings.output_directory}
params:
- rnaseq.prefiltering_pca.default_settings
- rnaseq.prefiltering_pca.stages.${key}.settings
foreach: ${rnaseq.prefiltering_pca.stages}
rnaseq_proteomics_intersection:
do:
cmd: ./docker-wrapper.sh ./src/integration/21-rnaseq-proteomics-intersection.R
--dataset-name ${key}
deps:
- ./src/integration/21-rnaseq-proteomics-intersection.R
- ./src/shared/R-helpers/get_args.R
- ./src/shared/R-helpers/update_list.R
- ./src/shared/R-helpers/get_settings.R
- ./src/shared/R-helpers/remove_ensembl_version.R
- ${item.settings.proteomics_de_results}
- ${item.settings.protein_group_to_proteins}
- ${item.settings.rnaseq_de_results}
- ${item.settings.uniprot_to_ensembl}
outs:
- ${item.settings.output_directory}
params:
- integration.rnaseq_proteomics_intersection.default_settings
- integration.rnaseq_proteomics_intersection.stages.${key}.settings
foreach: ${integration.rnaseq_proteomics_intersection.stages}
rnaseq_revigo:
do:
cmd: ./docker-wrapper.sh python ./src/shared/REVIGO/revigo_restful_advanced.py
--dataset_name ${key} --omics_type rnaseq
deps:
- ./src/shared/REVIGO/revigo_restful_advanced.py
- ./datasets/consortium/${item.settings.biological_model}/02_organized_data/rnaseq/gene-enrichment
outs:
- ${item.settings.output_directory}
params:
- rnaseq.revigo.stages.${key}.settings
foreach: ${rnaseq.revigo.stages}
rnaseq_srna_intersection:
do:
cmd: ./docker-wrapper.sh ./src/integration/20-rnaseq-srna-intersection.R --dataset-name
${key}
deps:
- ./src/integration/20-rnaseq-srna-intersection.R
- ./src/shared/R-helpers/get_args.R
- ./src/shared/R-helpers/update_list.R
- ./src/shared/R-helpers/get_settings.R
- ./src/shared/R-helpers/remove_ensembl_version.R
- ${item.settings.rnaseq_prefiltpca_dir}/ENSG_to_symbol.rds
- ${item.settings.rnaseq_de_digested_dir}/de_tables/de_result_thresholds.rds
- ${item.settings.srna_deg_digestion_dir}/de_results_with_targets.rds
outs:
- ${item.settings.output_directory}
params:
- integration.rnaseq_srna_intersection.default_settings
- integration.rnaseq_srna_intersection.stages.${key}.settings
foreach: ${integration.rnaseq_srna_intersection.stages}
splicing_analysis:
do:
cmd: ./docker-wrapper.sh ./src/rnaseq/DTU_Analysis/DTU.R --dataset-name ${key}
deps:
- ./src/rnaseq/DTU_Analysis/DTU.R
- ./src/shared/R-helpers/get_args.R
- ./src/shared/R-helpers/get_settings.R
- ./src/rnaseq/DTU_Analysis/DEXSeq_DTU_analysis.R
- ./src/rnaseq/DTU_Analysis/DRIMSeq_DTU_analysis.R
- ./src/rnaseq/DTU_Analysis/stageR_DTU_significanceTesting.R
- ${item.settings.cohort}
- ${item.settings.input_directory}
- ${item.settings.gtf}
- ${item.settings.nfs_to_sample_id}
outs:
- ${item.settings.output_directory}
params:
- splicing_analysis.dtu.stages.${key}.settings
foreach: ${splicing_analysis.dtu.stages}
sra_fastq_dump:
cmd: mkdir -p datasets/consortium/00_download/fastq && MX_DOCKERIMAGE="ncbi/sra-tools"
./docker-wrapper.sh sh ./src/shared/sra_fastqdump.sh
deps:
- ./src/shared/sra_fastqdump.sh
- datasets/consortium/00_download/SRR_Acc_List.txt
- datasets/consortium/00_download/prefetch
frozen: true
outs:
- datasets/consortium/00_download/fastq:
cache: false
sra_organize:
cmd: ./docker-wrapper.sh python3 ./src/shared/sra_organize.py
frozen: true