Automatic restart & General csv file updates

conf/modules.config

@@ -988,7 +988,7 @@ process{
     // VCF QC
     withName: 'BCFTOOLS_STATS'{
         ext.when         = { !(params.skip_tools && params.skip_tools.contains('bcftools')) }
-        ext.prefix       = { "${vcf.minus(".vcf.gz")}" }
+        ext.prefix       = { "${vcf.baseName.minus(".vcf")}" }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/reports/bcftools" },
@@ -998,7 +998,7 @@ process{
 
     withName: 'VCFTOOLS_.*'{
         ext.when         = { !(params.skip_tools && params.skip_tools.contains('vcftools')) }
-        ext.prefix       = { "${variant_file.minus(".vcf.gz")}" }
+        ext.prefix       = { "${variant_file.baseName.minus(".vcf")}" }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/reports/vcftools" },
@@ -1021,7 +1021,7 @@ process{
 // ANNOTATE
 
     withName: 'ENSEMBLVEP' {
-        ext.prefix       = { "${vcf.minus(".vcf.gz")}_VEP.ann.vcf" }
+        ext.prefix       = { "${vcf.baseName.minus(".vcf")}_VEP.ann.vcf" }
         ext.args          = [
             '--everything --filter_common --per_gene --total_length --offline',
             (params.vep_dbnsfp && params.dbnsfp)                                  ? '--plugin dbNSFP,dbNSFP.gz,rs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AF' : '',
@@ -1039,11 +1039,11 @@ process{
 
     withName: ".*:ANNOTATION_MERGE:ENSEMBLVEP" {
         // Output file will have format *_snpEff_VEP.ann.vcf
-        ext.prefix       = { "${vcf.minus(".vcf")}_VEP.ann.vcf" }
+        ext.prefix       = { "${vcf.baseName}_VEP.ann.vcf" }
     }
 
     withName: 'SNPEFF' {
-        ext.prefix       = { "${vcf.minus(".vcf.gz")}_snpEff.ann.vcf" }
+        ext.prefix       = { "${vcf.baseName.minus(".vcf")}_snpEff.ann.vcf" }
         ext.args          = '-nodownload -canon -v'
         if (!params.snpeff_cache) container = { params.snpeff_genome ? "nfcore/snpeff:5.0.${params.snpeff_genome}" : "nfcore/snpeff:5.0.${params.genome}" }
         publishDir       = [
@@ -1063,7 +1063,7 @@ process{
     }
 
     withName: 'NFCORE_SAREK:SAREK:ANNOTATE:ANNOTATION_SNPEFF:TABIX_BGZIPTABIX' {
-        ext.prefix       = { "${input.minus(".vcf")}_snpEff.ann.vcf" }
+        ext.prefix       = { "${input.baseName}_snpEff.ann.vcf" }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/annotation/${meta.id}/${meta.variantcaller}" },
@@ -1073,11 +1073,11 @@ process{
     }
 
     withName: 'NFCORE_SAREK:SAREK:ANNOTATE:ANNOTATION_ENSEMBLVEP:TABIX_BGZIPTABIX' {
-        ext.prefix       = { "${input.minus(".vcf")}_VEP.ann.vcf" }
+        ext.prefix       = { "${input.baseName}_VEP.ann.vcf" }
     }
 
     withName: 'NFCORE_SAREK:SAREK:ANNOTATE:ANNOTATION_MERGE:TABIX_BGZIPTABIX' {
-        ext.prefix       = { "${input.minus(".vcf")}_snpEff_VEP.ann.vcf" }
+        ext.prefix       = { "${input.baseName}_snpEff_VEP.ann.vcf" }
     }
 
     // MULTIQC

docs/usage.md

@@ -64,13 +64,13 @@ Multiple `CSV` files can be specified if the path is enclosed in quotes.
 | `cram`    | Full path to CRAM file                                                                                                                                                                                                                                                                                          |
 | `crai`    | Full path to CRAM index file                                                                                                                                                                                                                                                                                    |
 | `table`   | Full path to recalibration table file                                                                                                                                                                                                                                                                           |
-| `mpileup` | Full path to pileup file                                                                                                                                                                                                                                                                                        |
+| `vcf`     | Full path to vcf file                                                                                                                                                                                                                                                                                           |
 
 An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
 
 #### Start with mapping (`--step mapping` [default])
 
-This step can be started either from `fastq` files or (u)`bam`s. The `CSV` must contain at least the columns `patient`, `sample`, `lane`, and either `fastq_1/fastq_2` or `bam`.
+This step can be started either from `fastq` files or `(u)bam`s. The `CSV` must contain at least the columns `patient`, `sample`, `lane`, and either `fastq_1/fastq_2` or `bam`.
 
 ##### Examples
 
@@ -144,6 +144,26 @@ patient,sample,cram,crai
 patient1,test_sample,test_mapped.cram,test_mapped.cram.crai
 ```
 
+The `Sarek`-generated `CSV` file is stored under `results/csv/mapped.csv` if in a previous run `--save_bam_mapped` was set and will automatically be used as an input when specifying the parameter `--step prepare_recalibration`. Otherwise this file will need to be manually generated.
+
+##### Full samplesheet
+
+In this example, all possible columns are used including the `gender` and `status` information per patient:
+
+```console
+patient,gender,status,sample,bam,bai
+patient1,XX,0,test_sample,test_mapped.bam,test_mapped.bam.bai
+patient1,XX,1,tumor_sample,test2_mapped.bam,test2_mapped.bam.bai
+patient1,XX,1,relapse_sample,test3_mapped.bam,test3_mapped.bam.bai
+```
+
+```console
+patient,gender,status,sample,cram,crai
+patient1,XX,0,normal_sample,test_mapped.cram,test_mapped.cram.crai
+patient1,XX,1,tumor_sample,test2_mapped.cram,test2_mapped.cram.crai
+patient1,XX,1,relapse_sample,test3_mapped.cram,test3_mapped.cram.crai
+```
+
 ##### Prepare Recalibration
 
 For starting directly from preparing recalibration, the `CSV` file must contain at least the columns `patient`, `sample`, `bam`, `bai` or `patient`, `sample`, `cram`, `crai`.
@@ -152,37 +172,37 @@ Example:
 
 ```console
 patient,sample,bam,bai
-patient1,test_sample,test_mapped.bam,test_mapped.bam.bai
+patient1,test_sample,test_md.bam,test_md.bam.bai
 ```
 
 ```console
 patient,sample,cram,crai
-patient1,test_sample,test_mapped.cram,test_mapped.cram.crai
+patient1,test_sample,test_md.cram,test_md.cram.crai
 ```
 
-The `Sarek`-generated `CSV` file is stored under `results/Preprocessing/CSV/duplicates_marked_no_table.csv` and will automatically be used as an input when specifying the parameter `--step prepare_recalibration`.
+The `Sarek`-generated `CSV` file is stored under `results/csv/markduplicates_no_table.csv` and will automatically be used as an input when specifying the parameter `--step prepare_recalibration`.
 
 ##### Full samplesheet
 
 In this example, all possible columns are used including the `gender` and `status` information per patient:
 
 ```console
 patient,gender,status,sample,bam,bai
-patient1,XX,0,test_sample,test_mapped.bam,test_mapped.bam.bai
-patient1,XX,1,tumor_sample,test2_mapped.bam,test2_mapped.bam.bai
-patient1,XX,1,relapse_sample,test3_mapped.bam,test3_mapped.bam.bai
+patient1,XX,0,test_sample,test_md.bam,test_md.bam.bai
+patient1,XX,1,tumor_sample,test2_md.bam,test2_md.bam.bai
+patient1,XX,1,relapse_sample,test3_md.bam,test3_md.bam.bai
 ```
 
 ```console
 patient,gender,status,sample,cram,crai
-patient1,XX,0,normal_sample,test_mapped.cram,test_mapped.cram.crai
-patient1,XX,1,tumor_sample,test2_mapped.cram,test2_mapped.cram.crai
-patient1,XX,1,relapse_sample,test3_mapped.cram,test3_mapped.cram.crai
+patient1,XX,0,normal_sample,test_md.cram,test_md.cram.crai
+patient1,XX,1,tumor_sample,test2_md.cram,test2_md.cram.crai
+patient1,XX,1,relapse_sample,test3_md.cram,test3_md.cram.crai
 ```
 
-#### Start with base quality recalibration (`--step recalibrate`)
+#### Start with base quality score recalibration (`--step recalibrate`)
 
-For starting from base quality recalibration the `CSV` file must contain at least the columns `patient`, `sample`, `bam`, `bai`, `table` or `patient`, `sample`, `cram`, `crai`, `table` containing the paths to _non-recalibrated CRAM/BAM_ files and the associated recalibration table.
+For starting from base quality score recalibration the `CSV` file must contain at least the columns `patient`, `sample`, `bam`, `bai`, `table` or `patient`, `sample`, `cram`, `crai`, `table` containing the paths to _non-recalibrated CRAM/BAM_ files and the associated recalibration table.
 
 Example:
 
@@ -196,7 +216,7 @@ patient,sample,cram,crai,table
 patient1,test_sample,test_mapped.cram,test_mapped.cram.crai,test.table
 ```
 
-The `Sarek`-generated `CSV` file is stored under `results/Preprocessing/CSV/duplicates_marked.csv` and will automatically be used as an input when specifying the parameter `--step recalibrate`.
+The `Sarek`-generated `CSV` file is stored under `results/csv/markduplicates.csv` and will automatically be used as an input when specifying the parameter `--step recalibrate`.
 
 ##### Full samplesheet
 
@@ -225,7 +245,7 @@ patient,sample,cram,crai
 patient1,test_sample,test_mapped.cram,test_mapped.cram.crai
 ```
 
-The `Sarek`-generated `CSV` file is stored under `results/Preprocessing/CSV/recalibrated.csv` and will automatically be used as an input when specifying the parameter `--step variant_calling`.
+The `Sarek`-generated `CSV` file is stored under `results/csv/recalibrated.csv` and will automatically be used as an input when specifying the parameter `--step variant_calling`.
 
 ##### Full samplesheet
 
@@ -240,13 +260,28 @@ patient1,XX,1,relapse_sample,test3_mapped.cram,test3_mapped.cram.crai
 
 #### Start with annotation (`--step annotate`)
 
-Starting with annotation, is a special case in that it doesn't require an input sample sheet. The input files for Sarek can be specified using the path to a `VCF` file given to the `--input` command only with the annotation step (`--step annotate`).
+For starting from the annotation step, the `CSV` file must contain at least the columns `patient`, `sample`, `vcf`.
+
 As `Sarek` will use `bgzip` and `tabix` to compress and index the annotated `VCF` files, it expects the input `VCF` files to be sorted.
-Multiple `VCF` files can be specified, using a [glob path](https://docs.oracle.com/javase/tutorial/essential/io/fileOps.html#glob), if enclosed in quotes.
-For example:
 
-```bash
---step annotate --input "results/VariantCalling/*/{HaplotypeCaller,Manta,Mutect2,Strelka,TIDDIT}/*.vcf.gz"
+Example:
+
+```console
+patient,sample,vcf
+patient1,test_sample,test,vcf
+```
+
+The `Sarek`-generated `CSV` file is stored under `results/csv/variantcalled.csv` and will automatically be used as an input when specifying the parameter `--step annotation`.
+
+##### Full samplesheet
+
+In this example, all possible columns are used including the `variantcaller` information per sample:
+
+```console
+patient,sample,variantcaller,vcf
+test,sample3,strelka,sample3.variants.vcf.gz
+test,sample4_vs_sample3,manta,sample4_vs_sample3.diploid_sv.vcf.gz
+test,sample4_vs_sample3,manta,sample4_vs_sample3.somatic_sv.vcf.gz
 ```
 
 ### Updating the pipeline