mirror of
https://github.com/MillironX/nf-core_modules.git
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7daba6a13f
* add unzip alleles + loci * fix the partial absolute prefix path * exchanged deprecated function + added metrics * updated meta * tested logRCorrection + cram input * added BED for WES * added outputs + alleleCounter version * test samtools chr operations, fixed cancerit conda * ch formatting, fasta, bed input * comment out local tests * added metrics, bed, ref_fasta * rm print statement * added stub outputs * rm versions.yml * fix linting * rm fictitious md5sums for stub-run * try fixing top-level of stub versions.yml * ordered inputs alphabetically, ref_fasta -> fasta * rm R system command, adjust meta.yml * prettier yml
120 lines
4.6 KiB
YAML
120 lines
4.6 KiB
YAML
name: ascat
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description: copy number profiles of tumour cells.
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keywords:
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- bam
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- copy number
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- cram
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tools:
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- ascat:
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description: ASCAT is a method to derive copy number profiles of tumour cells, accounting for normal cell admixture and tumour aneuploidy. ASCAT infers tumour purity (the fraction of tumour cells) and ploidy (the amount of DNA per tumour cell), expressed as multiples of haploid genomes from SNP array or massively parallel sequencing data, and calculates whole-genome allele-specific copy number profiles (the number of copies of both parental alleles for all SNP loci across the genome).
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homepage: None
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documentation: https://github.com/VanLoo-lab/ascat/tree/master/man
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tool_dev_url: https://github.com/VanLoo-lab/ascat
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doi: "10.1093/bioinformatics/btaa538"
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licence: ["GPL v3"]
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input:
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- args:
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type: map
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description: |
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Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config. Parameters must be set between quotes. (optional) parameters can be removed from the map, if they are not set. For default values, please check the documentation above.
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```
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{
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[
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"gender": "XX",
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"genomeVersion": "hg19"
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"purity": (optional),
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"ploidy": (optional),
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"gc_files": (optional),
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"minCounts": (optional),
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"BED_file": (optional) but recommended for WES,
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"chrom_names": (optional),
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"min_base_qual": (optional),
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"min_map_qual": (optional),
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"ref_fasta": (optional),
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"skip_allele_counting_tumour": (optional),
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"skip_allele_counting_normal": (optional)
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]
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}
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```
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- input_normal:
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type: file
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description: BAM/CRAM file, must adhere to chr1, chr2, ...chrX notation
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For modifying chromosome notation in bam files please follow https://josephcckuo.wordpress.com/2016/11/17/modify-chromosome-notation-in-bam-file/.
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pattern: "*.{bam,cram}"
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- index_normal:
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type: file
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description: index for normal_bam/cram
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pattern: "*.{bai,crai}"
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- input_tumor:
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type: file
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description: BAM/CRAM file, must adhere to chr1, chr2, ...chrX notation
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pattern: "*.{bam,cram}"
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- index_tumor:
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type: file
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description: index for tumor_bam/cram
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pattern: "*.{bai,crai}"
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- allele_files:
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type: file
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description: allele files for ASCAT WGS. Can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS
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- loci_files:
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type: file
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description:
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loci files for ASCAT WGS. Loci files without chromosome notation can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS
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Make sure the chromosome notation matches the bam/cram input files. To add the chromosome notation to loci files (hg19/hg38) if necessary, you can run this command
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`if [[ $(samtools view <your_bam_file.bam> | head -n1 | cut -f3)\" == *\"chr\"* ]]; then for i in {1..22} X; do sed -i 's/^/chr/' G1000_loci_hg19_chr_${i}.txt; done; fi`
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- bed_file:
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type: file
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description: Bed file for ASCAT WES (optional, but recommended for WES)
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- fasta:
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type: file
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description: Reference fasta file (optional)
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- gc_file:
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type: file
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description: GC correction file (optional) - Used to do logR correction of the tumour sample(s) with genomic GC content
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- rt_file:
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type: file
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description: replication timing correction file (optional, provide only in combination with gc_file)
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- allelefreqs:
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type: file
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description: Files containing allee frequencies per chromosome
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pattern: "*{alleleFrequencies_chr*.txt}"
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- metrics:
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type: file
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description: File containing quality metrics
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pattern: "*.{metrics.txt}"
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- png:
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type: file
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description: ASCAT plots
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pattern: "*.{png}"
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- purityploidy:
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type: file
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description: File with purity and ploidy data
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pattern: "*.{purityploidy.txt}"
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- segments:
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type: file
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description: File with segments data
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pattern: "*.{segments.txt}"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@aasNGC"
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- "@lassefolkersen"
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- "@FriederikeHanssen"
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- "@maxulysse"
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- "@SusiJo"
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