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caravagnalab · Jan 7, 2025 · cc787a9 · cc787a9
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diff --git a/README.md b/README.md
@@ -41,7 +41,7 @@ different strategies will be applied.
 
 - Quality Control (`CNAqc`, `TINC`)
 - Variant Annotation (`VEP`, `maftools`)
-- Driver Annotation (`SOPRANO`, `dndsCV`)
+- Driver Annotation
 - Subclonal Deconvolution (`PyClone`, `MOBSTER`, `VIBER`)
 - Clone Tree Inference (`ctree`)
 - Signature Deconvolution (`SparseSignatures`, `SigProfiler`)
@@ -57,17 +57,13 @@ First, prepare a samplesheet with your input data that looks as follows:
 `samplesheet.csv`:
 
 ```csv
-dataset,patient,sample,normal_sample,vcf,vcf_tbi,cna_segments,cna_extra,cna_caller,cancer_type
-dataset1,patient1,S1,N1,patient1_S1.vcf.gz,patient1_S1.vcf.gz.tbi,/CNA/patient1/S1/segments.txt,/CNA/patient1/S1/purity_ploidy.txt,caller,PANCANCER
-dataset1,patient1,S2,N1,patient1_S1.vcf.gz,patient1_S1.vcf.gz.tbi,/CNA/patient1/S2/segments.txt,/CNA/patient1/S2/purity_ploidy.txt,caller,PANCANCER
+dataset,patient,tumour_sample,normal_sample,vcf,tbi,cna_segments,cna_extra,cna_caller,cancer_type
+dataset1,patient1,sample1,N1,patient1_sample1.vcf.gz,patient1_sample1.vcf.gz.tbi,/CNA/patient1/sample1/segments.txt,CNA/patient1/sample1/purity_ploidy.txt,caller,PANCANCER
+dataset1,patient1,sample2,N1,patient1_sample2.vcf.gz,patient1_sample2.vcf.gz.tbi,/CNA/patient1/sample2/segments.txt,CNA/patient1/sample2/purity_ploidy.txt,caller,PANCANCER
 ```
 
--->
-
 Now, you can run the pipeline using:
 
-<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
-
 ```bash
 nextflow run nf-core/tumourevo \
    -profile <docker/singularity/.../institute> \

diff --git a/docs/usage.md b/docs/usage.md
@@ -12,20 +12,16 @@ Through the analysis of variant and copy-number calls, it reconstructs the evolu
 
 ## Samplesheet input
 
-You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row as shown in the examples below.
+You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 10 columns, and a header row as shown in the examples below.
 
 ```bash
 --input '[path to samplesheet file]'
 ```
 
 ### Full samplesheet
 
-/_The pipeline will auto-detect whether a sample is single- or paired-end using the information provided in the samplesheet.
-The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 3 columns to
+The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 10 columns to
 match those defined in the table below.
-_/
-
-You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use the parameter `--input` to specify its location. It has to be a comma-separated file with at least 5 columns, and a header row as shown in the examples below.
 
 It is recommended to use the absolute path of the files, but a relative path should also work.
 
@@ -42,9 +38,9 @@ Output from different workflows, subworkflows and modules will be in a specific
 A minimal input sample sheet example for two samples from the same patient:
 
 ```csv title="samplesheet.csv"
-dataset,patient,sample,normal_sample,vcf,vcf_tbi,cna_segments,cna_extra,cna_caller,cancer_type
-dataset1,patient1,S1,N1,patient1_S1.vcf.gz,patient1_S1.vcf.gz.tbi,/CNA/patient1/S1/segments.txt,/CNA/patient1/S1/purity_ploidy.txt,caller,PANCANCER
-dataset1,patient1,S2,N1,patient1_S1.vcf.gz,patient1_S1.vcf.gz.tbi,/CNA/patient1/S2/segments.txt,/CNA/patient1/S2/purity_ploidy.txt,caller,PANCANCER
+dataset,patient,tumour_sample,normal_sample,vcf,tbi,cna_segments,cna_extra,cna_caller,cancer_type
+dataset1,patient1,sample1,N1,patient1_sample1.vcf.gz,patient1_sample1.vcf.gz.tbi,/CNA/patient1/sample1/segments.txt,CNA/patient1/sample1/purity_ploidy.txt,caller,PANCANCER
+dataset1,patient1,sample2,N1,patient1_sample2.vcf.gz,patient1_sample2.vcf.gz.tbi,/CNA/patient1/sample2/segments.txt,CNA/patient1/sample2/purity_ploidy.txt,caller,PANCANCER
 ```
 
 #### Overview: Samplesheet Columns
@@ -102,10 +98,10 @@ nextflow run nf-core/tumourevo \
 
 Minimal input file, two samples from the same patient:
 
-```bash
-dataset,patient,sample,normal_sample,vcf,vcf_tbi,cna_segments,cna_extra,cna_caller,cancer_type
-dataset1,patient1,S1,N1,patient1_S1.vcf.gz,patient1_S1.vcf.gz.tbi,/CNA/patient1/S1/segments.txt,/CNA/patient1/S1/purity_ploidy.txt,caller,PANCANCER
-dataset1,patient1,S2,N1,patient1_S1.vcf.gz,patient1_S1.vcf.gz.tbi,/CNA/patient1/S2/segments.txt,/CNA/patient1/S2/purity_ploidy.txt,caller,PANCANCER
+```csv
+dataset,patient,tumour_sample,normal_sample,vcf,tbi,cna_segments,cna_extra,cna_caller,cancer_type
+dataset1,patient1,sample1,N1,patient1_sample1.vcf.gz,patient1_sample1.vcf.gz.tbi,/CNA/patient1/sample1/segments.txt,CNA/patient1/sample1/purity_ploidy.txt,caller,PANCANCER
+dataset1,patient1,sample2,N1,patient1_sample2.vcf.gz,patient1_sample2.vcf.gz.tbi,/CNA/patient1/sample2/segments.txt,CNA/patient1/sample2/purity_ploidy.txt,caller,PANCANCER
 ```
 
 ##### 2. Single sample variant calling
@@ -114,10 +110,10 @@ If the variant calling performed independently on each sample, even if coming fr
 
 Input file for two patients without joint variant calling, bam files available:
 
-```bash
-dataset,patient,sample,normal_sample,vcf,vcf_tbi,cna_segments,cna_extra,cna_caller,cancer_type,tumour_bam,tumour_bai
-dataset1,patient1,S1,N1,patient1_S1.vcf.gz,patient1_S1.vcf.gz.tbi,/CNA/patient1/S1/segments.txt,/CNA/patient1/S1/purity_ploidy.txt,caller,PANCANCER,patient1/BAM/S1.bam,patient1/BAM/S1.bam.bai
-dataset1,patient1,S2,N1,patient1_S2.vcf.gz,patient1_S2.vcf.gz.tbi,/CNA/patient1/S2/segments.txt,/CNA/patient1/S2/purity_ploidy.txt,caller,PANCANCER,,patient1/BAM/S2.bam,patient1/BAM/S2.bam.bai
+```csv
+dataset,patient,tumour_sample,normal_sample,vcf,tbi,cna_segments,cna_extra,cna_caller,cancer_type,tumour_alignment,tumour_alignment_index
+dataset1,patient1,sample1,N1,patient1_sample1.vcf.gz,patient1_sample1.vcf.gz.tbi,/CNA/patient1/sample1/segments.txt,CNA/patient1/sample1/purity_ploidy.txt,caller,PANCANCER,patient1/BAM/sample1.bam,patient1/BAM/sample1.bam.bai
+dataset1,patient1,sample2,N1,patient1_sample2.vcf.gz,patient1_sample2.vcf.gz.tbi,/CNA/patient1/sample2/segments.txt,CNA/patient1/sample2/purity_ploidy.txt,caller,PANCANCER,patient1/BAM/sample2.bam,patient1/BAM/sample2.bam.bai
 ```
 
 If you can not include the bam files in the input csv, the pipeline will run anyway, treating each sample as independent.