qbic-pipelines · WackerO · Mar 5, 2024 · Aug 21, 2023 · Feb 5, 2024 · Feb 5, 2024
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
diff --git a/.editorconfig b/.editorconfig
diff --git a/.gitattributes b/.gitattributes
diff --git a/.github/.dockstore.yml b/.github/.dockstore.yml
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
diff --git a/.github/workflows/push_github_container_reg.yml b/.github/workflows/push_github_container_reg.yml
diff --git a/.gitignore b/.gitignore
diff --git a/.gitpod.yml b/.gitpod.yml
diff --git a/.nf-core.yml b/.nf-core.yml
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
diff --git a/.prettierignore b/.prettierignore
diff --git a/.prettierrc.yml b/.prettierrc.yml
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- [#225](https://github.com/qbic-pipelines/rnadeseq/pull/225) Added param for pathway analysis datasources
 - [#215](https://github.com/qbic-pipelines/rnadeseq/pull/215) Added gene_name to boxplot titles and filenames; increased threshold before overlapping PCA labels are hidden
 - [#213](https://github.com/qbic-pipelines/rnadeseq/pull/213) Added smrnaseq input support
 - [#212](https://github.com/qbic-pipelines/rnadeseq/pull/212) Added computational methods if no --software_versions
@@ -17,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
+- [#225](https://github.com/qbic-pipelines/rnadeseq/pull/225) Shortened names of some output files
 - [#219](https://github.com/qbic-pipelines/rnadeseq/pull/219) Release 2.2 to master
 - [#220](https://github.com/qbic-pipelines/rnadeseq/pull/220) Commit suggestions from PR review for release 2.2
 - [#218](https://github.com/qbic-pipelines/rnadeseq/pull/218) Preparing release 2.2 with version bumps
@@ -34,6 +36,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+- [#225](https://github.com/qbic-pipelines/rnadeseq/pull/225) Fixed too many devices error from tryCatch around normalized heatmaps
 - [#212](https://github.com/qbic-pipelines/rnadeseq/pull/212) Fixed movability of interactive gostplots
 - [#208](https://github.com/qbic-pipelines/rnadeseq/pull/208) Fixed relevel bug, the function should now finally work!
 - [#207](https://github.com/qbic-pipelines/rnadeseq/pull/207) Fixed check of samples in counts vs metadata

diff --git a/CITATIONS.md b/CITATIONS.md
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
diff --git a/Dockerfile b/Dockerfile
diff --git a/LICENSE b/LICENSE
diff --git a/README.md b/README.md
diff --git a/assets/RNAseq_report.Rmd b/assets/RNAseq_report.Rmd
diff --git a/assets/adaptivecard.json b/assets/adaptivecard.json
diff --git a/assets/email_template.html b/assets/email_template.html
diff --git a/assets/email_template.txt b/assets/email_template.txt
diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
diff --git a/assets/nf-core-rnadeseq_logo_light.png b/assets/nf-core-rnadeseq_logo_light.png
diff --git a/assets/references.bibtex b/assets/references.bibtex
diff --git a/assets/schema_input.json b/assets/schema_input.json
diff --git a/assets/sendmail_template.txt b/assets/sendmail_template.txt
diff --git a/assets/slackreport.json b/assets/slackreport.json
diff --git a/bin/Execute_report.R b/bin/Execute_report.R
@@ -34,6 +34,7 @@ option_list = list(
     make_option("--set_background", action="store_true", default=TRUE, help="Whether to use a background list for pathway analysis; if true, will only consider expressed genes (i.e. mean counts > 0) for PA."),
     make_option("--custom_background", type="character", default=NULL, help="Path to a custom background list TXT for pathway analysis; if provided, will only consider genes in that list for PA."),
     make_option(c("-w", "--min_DEG_pathway"), type="integer", default=NULL, help="min. number of genes DE in a pathway for this pathway to be considered enriched.", metavar="integer"),
+    make_option("--datasources", type="character", default=NULL, help="Which datasources to use for pathway analysis.", metavar="character"),
 
     make_option(c("-s", "--proj_summary"), type="character", default=NULL, help="Project summary file", metavar="character"),
     make_option(c("--path_quote"), type="character", default=NULL, help="Path to the quote PDF", metavar="character"),
@@ -82,6 +83,7 @@ rmarkdown::render(opt$report, output_file = opt$output, knit_root_dir = wd, outp
                                 custom_background = opt$custom_background,
                                 keytype = opt$keytype,
                                 min_DEG_pathway = opt$min_DEG_pathway,
+                                datasources = opt$datasources,
 
                                 path_proj_summary = opt$proj_summary,
                                 path_quote = opt$path_quote,

diff --git a/conf/base.config b/conf/base.config
diff --git a/conf/igenomes.config b/conf/igenomes.config
diff --git a/conf/modules.config b/conf/modules.config
diff --git a/conf/test.config b/conf/test.config
diff --git a/conf/test_batcheffect.config b/conf/test_batcheffect.config
diff --git a/conf/test_contrast_list.config b/conf/test_contrast_list.config
diff --git a/conf/test_contrast_matrix.config b/conf/test_contrast_matrix.config
diff --git a/conf/test_custom_gmt.config b/conf/test_custom_gmt.config
@@ -30,4 +30,5 @@ params {
     run_pathway_analysis = true
     genome = 'GRCm38'
     custom_gmt = 'https://raw.githubusercontent.com/qbic-pipelines/rnadeseq/dev/testdata/gprofiler_full_mmusculus.ENSG.gmt'
+    datasources = 'KEGG,REAC'
 }
diff --git a/conf/test_full.config b/conf/test_full.config
diff --git a/conf/test_no_multiqc.config b/conf/test_no_multiqc.config
diff --git a/conf/test_relevel.config b/conf/test_relevel.config
diff --git a/conf/test_smrnaseq.config b/conf/test_smrnaseq.config
diff --git a/conf/test_star_rsem.config b/conf/test_star_rsem.config
diff --git a/conf/test_star_salmon.config b/conf/test_star_salmon.config
diff --git a/conf/test_use_vst.config b/conf/test_use_vst.config
diff --git a/docs/README.md b/docs/README.md
diff --git a/docs/images/nf-core-rnadeseq_logo_dark.png b/docs/images/nf-core-rnadeseq_logo_dark.png
diff --git a/docs/images/nf-core-rnadeseq_logo_light.png b/docs/images/nf-core-rnadeseq_logo_light.png
diff --git a/docs/output.md b/docs/output.md
@@ -52,7 +52,7 @@ If pathway analysis was run, this directory contains the zipped pathway analysis
 
 - `*_gost_pathway_venn_diagram.pdf/png`
   - Venn diagrams showing the numbers of enriched pathways when using a background gene list vs when not using a bg list.
-- `*_KEGG_pathway_enrichment_plot.pdf/png`
+- `*_pathway_enrichment_plot.pdf/png`
   - Barplots showing the proportion of differentially expressed genes in the pathway.
 - `KEGG_pathways/`
   - Contains the KEGG pathways graphs with the log fold change of the differentially expressed genes.

diff --git a/docs/usage.md b/docs/usage.md
diff --git a/environment.yml b/environment.yml
diff --git a/lib/nfcore_external_java_deps.jar b/lib/nfcore_external_java_deps.jar
diff --git a/main.nf b/main.nf
diff --git a/modules.json b/modules.json
diff --git a/modules/local/report.nf b/modules/local/report.nf
@@ -37,6 +37,7 @@ process REPORT {
     def custom_gmt_opt = custom_gmt.name != 'NO_FILE3' ? "--custom_gmt $custom_gmt" : ''
     def set_background_opt = params.set_background ? "--set_background TRUE" : "--set_background FALSE"
     def custom_background_opt = custom_background.name != 'NO_FILE7' ? "--custom_background $custom_background" : ''
+    def datasources_opt = params.datasources ? "--datasources $params.datasources" : ''
 
     def quote_opt = params.quote != 'NO_FILE5' ? "--path_quote $params.quote" : ''
     def software_versions_opt = params.software_versions != 'NO_FILE6' ? "--software_versions $params.software_versions" : ''
@@ -76,6 +77,7 @@ process REPORT {
         --species_library $params.species_library \
         --keytype $params.keytype \
         --min_DEG_pathway $params.min_DEG_pathway \
+        $datasources_opt \
         $quote_opt \
         $software_versions_opt \
         --proj_summary $proj_summary \

diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
diff --git a/nextflow.config b/nextflow.config
@@ -39,6 +39,7 @@ params {
     custom_gmt = 'NO_FILE3'
     set_background = true
     custom_background = 'NO_FILE7'
+    datasources = null
 
     // Additional args for the report
     project_summary = null

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -125,7 +125,7 @@
                 },
                 "custom_gmt": {
                     "type": "string",
-                    "description": "Path to custom GMT file for gost query, this allows e.g. to query older versions of databases for pathway analysis, not necessary if --skip_pathway_analysis = true."
+                    "description": "Path to custom GMT file for gost query, this allows e.g. to query older versions of databases for pathway analysis, not necessary if --skip_pathway_analysis = true. If --datasources is set, the GMT file will be filtered for these datasources."
                 },
                 "set_background": {
                     "type": "boolean",
@@ -140,6 +140,10 @@
                     "type": "integer",
                     "default": 1,
                     "description": "Integer indicating how many genes in a pathway must be differentially expressed to be considered as enriched, and report these pathways in tables and the final report. The default value is 1."
+                },
+                "datasources": {
+                    "type": "string",
+                    "description": "Which datasources to use for pathway analysis, comma-separated string like 'KEGG,REAC'. See param 'sources' on https://rdrr.io/cran/gprofiler2/man/gost.html for a list of available sources. If not set, will use all sources. If set while a --custom_gmt is provided, will filter the GMT for these datasources (will not filter for the GO subtypes like GO:BP, just for GO)."
                 }
             }
         },

diff --git a/pyproject.toml b/pyproject.toml
diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
diff --git a/testdata/MultiQC.zip b/testdata/MultiQC.zip
diff --git a/testdata/QDESQ/QDESQ_Sample_preparations.tsv b/testdata/QDESQ/QDESQ_Sample_preparations.tsv
diff --git a/testdata/QDESQ/QDESQ_design.txt b/testdata/QDESQ/QDESQ_design.txt
diff --git a/testdata/QDESQ/star_rsem/QDESQ081AU.genes.results b/testdata/QDESQ/star_rsem/QDESQ081AU.genes.results
diff --git a/testdata/QDESQ/star_rsem/QDESQ082A4.genes.results b/testdata/QDESQ/star_rsem/QDESQ082A4.genes.results
diff --git a/testdata/QDESQ/star_rsem/QDESQ083AC.genes.results b/testdata/QDESQ/star_rsem/QDESQ083AC.genes.results
diff --git a/testdata/QDESQ/star_rsem/QDESQ084AK.genes.results b/testdata/QDESQ/star_rsem/QDESQ084AK.genes.results
diff --git a/testdata/QDESQ/star_rsem/QDESQ085AS.genes.results b/testdata/QDESQ/star_rsem/QDESQ085AS.genes.results
diff --git a/testdata/QDESQ/star_rsem/QDESQ086A2.genes.results b/testdata/QDESQ/star_rsem/QDESQ086A2.genes.results
diff --git a/testdata/QDESQ/star_rsem/QDESQ087AA.genes.results b/testdata/QDESQ/star_rsem/QDESQ087AA.genes.results
diff --git a/testdata/QDESQ/star_rsem/QDESQ088AI.genes.results b/testdata/QDESQ/star_rsem/QDESQ088AI.genes.results
diff --git a/testdata/QDESQ/star_salmon/QDESQ081AU/quant.sf b/testdata/QDESQ/star_salmon/QDESQ081AU/quant.sf
diff --git a/testdata/QDESQ/star_salmon/QDESQ082A4/quant.sf b/testdata/QDESQ/star_salmon/QDESQ082A4/quant.sf
diff --git a/testdata/QDESQ/star_salmon/QDESQ083AC/quant.sf b/testdata/QDESQ/star_salmon/QDESQ083AC/quant.sf
diff --git a/testdata/QDESQ/star_salmon/QDESQ084AK/quant.sf b/testdata/QDESQ/star_salmon/QDESQ084AK/quant.sf
diff --git a/testdata/QDESQ/star_salmon/QDESQ085AS/quant.sf b/testdata/QDESQ/star_salmon/QDESQ085AS/quant.sf
diff --git a/testdata/QDESQ/star_salmon/QDESQ086A2/quant.sf b/testdata/QDESQ/star_salmon/QDESQ086A2/quant.sf
diff --git a/testdata/QDESQ/star_salmon/QDESQ087AA/quant.sf b/testdata/QDESQ/star_salmon/QDESQ087AA/quant.sf
diff --git a/testdata/QDESQ/star_salmon/QDESQ088AI/quant.sf b/testdata/QDESQ/star_salmon/QDESQ088AI/quant.sf
diff --git a/testdata/Sample_preparations.tsv b/testdata/Sample_preparations.tsv
diff --git a/testdata/contrast_list.tsv b/testdata/contrast_list.tsv
diff --git a/testdata/contrast_matrix.tsv b/testdata/contrast_matrix.tsv
diff --git a/testdata/design.txt b/testdata/design.txt
diff --git a/testdata/design_batcheffect.txt b/testdata/design_batcheffect.txt
diff --git a/testdata/gprofiler_full_mmusculus.ENSG.gmt b/testdata/gprofiler_full_mmusculus.ENSG.gmt
diff --git a/testdata/merged_gene_counts.txt b/testdata/merged_gene_counts.txt
diff --git a/testdata/offer_example.pdf b/testdata/offer_example.pdf
diff --git a/testdata/relevel.tsv b/testdata/relevel.tsv
diff --git a/testdata/report_options.yml b/testdata/report_options.yml
diff --git a/testdata/requested_genes.txt b/testdata/requested_genes.txt
diff --git a/testdata/smrnaseq/counts/QABCD00001_mature.sorted.idxstats b/testdata/smrnaseq/counts/QABCD00001_mature.sorted.idxstats
diff --git a/testdata/smrnaseq/counts/QABCD00001_mature_hairpin.sorted.idxstats b/testdata/smrnaseq/counts/QABCD00001_mature_hairpin.sorted.idxstats
diff --git a/testdata/smrnaseq/counts/QABCD00002_mature.sorted.idxstats b/testdata/smrnaseq/counts/QABCD00002_mature.sorted.idxstats
diff --git a/testdata/smrnaseq/counts/QABCD00002_mature_hairpin.sorted.idxstats b/testdata/smrnaseq/counts/QABCD00002_mature_hairpin.sorted.idxstats
diff --git a/testdata/smrnaseq/counts/QABCD00003_mature.sorted.idxstats b/testdata/smrnaseq/counts/QABCD00003_mature.sorted.idxstats
diff --git a/testdata/smrnaseq/counts/QABCD00003_mature_hairpin.sorted.idxstats b/testdata/smrnaseq/counts/QABCD00003_mature_hairpin.sorted.idxstats
diff --git a/testdata/smrnaseq/counts/QABCD00004_mature.sorted.idxstats b/testdata/smrnaseq/counts/QABCD00004_mature.sorted.idxstats
diff --git a/testdata/smrnaseq/counts/QABCD00004_mature_hairpin.sorted.idxstats b/testdata/smrnaseq/counts/QABCD00004_mature_hairpin.sorted.idxstats
diff --git a/testdata/smrnaseq/counts/QABCD00005_mature.sorted.idxstats b/testdata/smrnaseq/counts/QABCD00005_mature.sorted.idxstats
diff --git a/testdata/smrnaseq/counts/QABCD00005_mature_hairpin.sorted.idxstats b/testdata/smrnaseq/counts/QABCD00005_mature_hairpin.sorted.idxstats
diff --git a/testdata/smrnaseq/counts/QABCD00006_mature.sorted.idxstats b/testdata/smrnaseq/counts/QABCD00006_mature.sorted.idxstats
diff --git a/testdata/smrnaseq/counts/QABCD00006_mature_hairpin.sorted.idxstats b/testdata/smrnaseq/counts/QABCD00006_mature_hairpin.sorted.idxstats
diff --git a/testdata/smrnaseq/counts/QABCD00007_mature.sorted.idxstats b/testdata/smrnaseq/counts/QABCD00007_mature.sorted.idxstats
diff --git a/testdata/smrnaseq/counts/QABCD00007_mature_hairpin.sorted.idxstats b/testdata/smrnaseq/counts/QABCD00007_mature_hairpin.sorted.idxstats
diff --git a/testdata/smrnaseq/counts/QABCD00008_mature.sorted.idxstats b/testdata/smrnaseq/counts/QABCD00008_mature.sorted.idxstats
diff --git a/testdata/smrnaseq/counts/QABCD00008_mature_hairpin.sorted.idxstats b/testdata/smrnaseq/counts/QABCD00008_mature_hairpin.sorted.idxstats
diff --git a/testdata/smrnaseq/design.txt b/testdata/smrnaseq/design.txt
diff --git a/testdata/smrnaseq/requested_genes.txt b/testdata/smrnaseq/requested_genes.txt
diff --git a/testdata/smrnaseq/samplesheet.tsv b/testdata/smrnaseq/samplesheet.tsv
diff --git a/testdata/software_versions.csv b/testdata/software_versions.csv
diff --git a/testdata/software_versions_rsem.yml b/testdata/software_versions_rsem.yml
diff --git a/testdata/software_versions_salmon.yml b/testdata/software_versions_salmon.yml
diff --git a/testdata/software_versions_smrnaseq.yml b/testdata/software_versions_smrnaseq.yml
diff --git a/testdata/summary.tsv b/testdata/summary.tsv
diff --git a/tests/test.yml b/tests/test.yml
diff --git a/tests/test_batcheffect.yml b/tests/test_batcheffect.yml
diff --git a/tests/test_contrast_list.yml b/tests/test_contrast_list.yml
diff --git a/tests/test_contrast_matrix.yml b/tests/test_contrast_matrix.yml
diff --git a/tests/test_custom_gmt.yml b/tests/test_custom_gmt.yml
diff --git a/tests/test_full.yml b/tests/test_full.yml
diff --git a/tests/test_no_multiqc.yml b/tests/test_no_multiqc.yml
diff --git a/tests/test_relevel.yml b/tests/test_relevel.yml
diff --git a/tests/test_smrnaseq.yml b/tests/test_smrnaseq.yml
diff --git a/tests/test_star_rsem.yml b/tests/test_star_rsem.yml
diff --git a/tests/test_star_salmon.yml b/tests/test_star_salmon.yml
diff --git a/tests/test_use_vst.yml b/tests/test_use_vst.yml
diff --git a/tower.yml b/tower.yml
diff --git a/workflows/rnadeseq.nf b/workflows/rnadeseq.nf