Add documentation

README.md

@@ -23,12 +23,31 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
      <img title="tomte workflow" src="docs/images/tomte_pipeline_metromap.png">
 </p>
 
-1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
-3. Trim reads ([`FASTP`](https://github.com/OpenGene/fastp))
-4. Align reads to the genome ([`STAR`](https://github.com/alexdobin/STAR))
-5. Alignment QC ([`Picard CollectRnaSeqMetrics`](https://broadinstitute.github.io/picard/))
-6. Transcript quantification ([`Salmon`](https://salmon.readthedocs.io/en/latest/))
+1. Trim reads ([`FASTP`](https://github.com/OpenGene/fastp))
+2. Transcript quantification ([`Salmon`](https://salmon.readthedocs.io/en/latest/))
+3. Align reads to the genome ([`STAR`](https://github.com/alexdobin/STAR))
+4. Output junction tracks
+5. Output bigwig ([`UCSC wigToBigWig`](https://genome.ucsc.edu/goldenPath/help/bigWig.html))
+6. Choice to subsample overrepresented regions ([`Samtools`](https://github.com/samtools/samtools/))
+7. Choice to downsample number of reads ([`Samtools`](https://github.com/samtools/samtools/))
+8. Detection of aberrant expression ([`DROP`](https://github.com/gagneurlab/drop/))
+9. Detection of aberrant splicing ([`DROP`](https://github.com/gagneurlab/drop/))
+10. Filter aberrant expression and aberrant splicing results
+11. Guided transcript assembly ([`StringTie`](https://ccb.jhu.edu/software/stringtie/))
+12. Filtering results of guided transcript assembly ([`GffCompare`](https://github.com/gpertea/gffcompare))
+13. To Call SNVs either path a or b can be followed. Path A will run by default
+    a. Call SNVs
+14. ([`BCFtools Mpileups`](https://samtools.github.io/bcftools/bcftools.html#mpileup))
+15. b. Call SNVs
+    1. Split cigar reads ([`SplitN Cigar Reads`](https://gatk.broadinstitute.org/hc/en-us/articles/360036858811-SplitNCigarReads))
+    2. Haplotype caller ([`Haplotype Caller`](https://gatk.broadinstitute.org/hc/en-us/articles/360037225632-HaplotypeCaller))
+    3. Variant filtration ([`Variant Filtration`](https://gatk.broadinstitute.org/hc/en-us/articles/360037434691-VariantFiltration))
+    4. BCFtools statistics ([`BCFtools stats`](https://samtools.github.io/bcftools/bcftools.html#stats))
+16. Allele Specific Read Counter ([`ASEReadCounter`](https://gatk.broadinstitute.org/hc/en-us/articles/360037428291-ASEReadCounter))
+17. Asses allelic inbalance ([`BootstrapAnn`](https://github.com/J35P312/BootstrapAnn#bootstrapann))
+18. Annotation ([`VEP`](https://github.com/Ensembl/ensembl-vep))
+19. Alignment QC ([`Picard CollectRnaSeqMetrics`](https://broadinstitute.github.io/picard/))
+20. Present QCs ([`MultiQC`](http://multiqc.info/))
 
 ## Usage
 
@@ -74,11 +93,11 @@ For more details about the output files and reports, please refer to the [output
 
 ## Credits
 
-tomte was originally written by Clinical Genomics Stockholm.
+genomic-medicine-sweden/tomte was written by Clinical Genomics Stockholm, Sweden, with major contributions from [Lucía Peña-Pérez](https://github.com/Lucpen), [Anders Jemt](https://github.com/jemten), and [Jesper Eisfeldt](https://github.com/J35P312).
 
-We thank the following people for their extensive assistance in the development of this pipeline:
+Additional contributors were [Ramprasad Neethiraj](https://github.com/ramprasadn), [Esmee ten Berk de Boer](https://github.com/Esmeetbdb), [Vadym Ivanchuk](https://github.com/ivadym), and [Mei Wu](https://github.com/projectoriented).
 
-<!-- TODO nf-core: If applicable, make list of people who have also contributed -->
+We thank the nf-core community for their extensive assistance in the development of this pipeline.
 
 ## Contributions and Support
 
@@ -88,10 +107,7 @@ For further information or help, don't hesitate to get in touch by opening an [i
 
 ## Citations
 
-<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
-<!-- If you use  nf-core/tomte for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
-
-<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
+If you use nf-core/raredisease for your analysis, please cite it using the following doi: [10.5281/zenodo.7995798](https://doi.org/10.5281/zenodo.7995798)
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 

bin/drop_filter_results.py

@@ -76,6 +76,9 @@ def filter_outrider_results(
     df_family_annotated_aberrant_expression_top_hits = annotate_with_hgnc(
         df_family_aberrant_expression_top_hits, out_drop_gene_name
     )
+    df_family_annotated_aberrant_expression_top_hits.to_csv(
+        "OUTRIDER_provided_samples_top_hits.tsv", sep="\t", index=False, header=True
+    )
     filter_by_gene_panel(df_family_annotated_aberrant_expression_top_hits, gene_panel, "OUTRIDER")
 
 

conf/modules.config

@@ -318,7 +318,7 @@ process {
 
 process {
     withName: '.*ANALYSE_TRANSCRIPTS:DROP_SAMPLE_ANNOT' {
-        ext.when = {params.run_drop_ae|params.run_drop_as}
+        ext.when = {params.run_drop_ae_switch|params.run_drop_as_switch}
         publishDir = [
             path: { "${params.outdir}/analyse_transcripts/drop" },
             mode: params.publish_dir_mode,
@@ -327,7 +327,7 @@ process {
     }
 
     withName: '.*ANALYSE_TRANSCRIPTS:DROP_CONFIG_RUN_AE' {
-        ext.when = {params.run_drop_ae}
+        ext.when = {params.run_drop_ae_switch}
         publishDir = [
             path: { "${params.outdir}/analyse_transcripts/drop/AE" },
             mode: params.publish_dir_mode,
@@ -336,7 +336,7 @@ process {
     }
 
     withName: '.*ANALYSE_TRANSCRIPTS:DROP_CONFIG_RUN_AS' {
-        ext.when = {params.run_drop_as}
+        ext.when = {params.run_drop_as_switch}
         publishDir = [
             path: { "${params.outdir}/analyse_transcripts/drop/AS" },
             mode: params.publish_dir_mode,
@@ -345,7 +345,7 @@ process {
     }
 
     withName: '.*ANALYSE_TRANSCRIPTS:DROP_FILTER_RESULTS' {
-        ext.when = {params.run_drop_ae | params.run_drop_as}
+        ext.when = {params.run_drop_ae_switch|params.run_drop_as_switch}
         publishDir = [
             path: { "${params.outdir}/analyse_transcripts/drop" },
             mode: params.publish_dir_mode,

docs/README.md

@@ -6,7 +6,5 @@ The tomte documentation is split into the following pages:
   - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags.
 - [Output](output.md)
   - An overview of the different results produced by the pipeline and how to interpret them.
-- [Parameters](parameters.md)
-  - An overview of the different pipeline parameters.
 
 You can find a lot more documentation about installing, configuring and running nf-core and nf-core based pipelines on the website: [https://nf-co.re](https://nf-co.re)