Module/ichorcna/1.0 #178
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| Original file line number | Diff line number | Diff line change |
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| lcr-modules: | ||
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| ichorcna: | ||
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| inputs: | ||
| # Available wildcards: {seq_type} {genome_build} {sample_id} | ||
| sample_bam: "__UPDATE__" | ||
| sample_bai: "__UPDATE__" | ||
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| scratch_subdirectories: [] | ||
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| options: | ||
| readcounter: | ||
| chrs: | ||
| hg19: "1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y" | ||
| grch37: "1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y" | ||
| hs37d5: "1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y" | ||
| hg38: "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY" | ||
| grch38: "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY" | ||
| qual: 20 # only includes reads with mapping quality greater than 20 | ||
| binSize: 1000000 # set window size to compute coverage | ||
| # available binSizes are: 1000000, 500000, 50000, 10000 | ||
| run: | ||
| ichorCNA_libdir: "" | ||
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There was a problem hiding this comment. Are all these files in inst are being auto downloaded? They are probably then not needed in the config since you set the naming convention and the path to these. files in the snakelike rule There was a problem hiding this comment. For the chromosomes, I could use the function for the readCounter step since I need the command to look like: 'ichorCNA_libdir:' parameter is supposed to be set to where the github repo resides for ichorCNA (it'll use this to search for inst/extdata/ underneath that directory). I just left it in the config since it might be useful if someone needs to modify the path one day There was a problem hiding this comment. How is that vector being given to ichorCNA? There was a problem hiding this comment. In the command it would be --chrs "c('1', '2', '3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','X')" There was a problem hiding this comment. You could construct that in Python probably and then just add that as a "param" in your rule. |
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| ichorCNA_rscript: "{MODSDIR}/src/runIchorCNA.R" | ||
| # use panel matching same bin size (optional) | ||
| ichorCNA_normalPanel: | ||
| "1000000": "inst/extdata/HD_ULP_PoN_{genome_build}_1Mb_median_normAutosome_median.rds" | ||
| "500000": "inst/extdata/HD_ULP_PoN_{genome_build}_500kb_median_normAutosome_median.rds" | ||
| # must use gc wig file corresponding to same binSize (required) | ||
| ichorCNA_gcWig: | ||
| "1000000": "inst/extdata/gc_{genome_build}_1000kb.wig" | ||
| "500000": "inst/extdata/gc_{genome_build}_500kb.wig" | ||
| "50000": "inst/extdata/gc_{genome_build}_50kb.wig" | ||
| "10000": "inst/extdata/gc_{genome_build}_10kb.wig" | ||
| # must use map wig file corresponding to same binSize (required) | ||
| ichorCNA_mapWig: | ||
| "1000000": "inst/extdata/map_{genome_build}_1000kb.wig" | ||
| "500000": "inst/extdata/map_{genome_build}_500kb.wig" | ||
| "50000": "inst/extdata/map_{genome_build}_50kb.wig" | ||
| "10000": "inst/extdata/map_{genome_build}_10kb.wig" | ||
| # use bed file if sample has targeted regions, eg. exome data (optional) | ||
| ichorCNA_exons: NULL | ||
| ichorCNA_centromere: | ||
| grch37: "inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt" | ||
| hg19: "inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt" | ||
| hs37d5: "inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt" | ||
| grch38: "inst/extdata/GRCh38.GCA_000001405.2_centromere_acen.txt" | ||
| hg38: "inst/extdata/GRCh38.GCA_000001405.2_centromere_acen.txt" | ||
| ichorCNA_minMapScore: 0.75 | ||
| ichorCNA_chrs: | ||
| grch37: "c('1', '2', '3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','X')" | ||
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There was a problem hiding this comment. This looks very redundant with the chrs in the config near the top. What's the deal? There was a problem hiding this comment. Just input-syntax for two different programs (the first one is formatted for readCounter as part of hmmcopy_utils and this format is for ichorCNA (to be used in R)) There was a problem hiding this comment. Can this be moved to snakelike, instead of being in config? There, you can use file listing chromosomes generated by reference files (main_chromosomes.txt) or use function to generate chromosome names (there is example in sage module) There was a problem hiding this comment. Good suggestion. I agree it's better to embed anything that generates code (python, R etc) into the snakefile |
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| hg19: "c('1', '2', '3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','X')" | ||
| hs37d5: "c('1', '2', '3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','X')" | ||
| grch38: "c('chr1', 'chr2', 'chr3','chr4','chr5','chr6','chr7','chr8','chr9','chr10','chr11','chr12','chr13','chr14','chr15','chr16','chr17','chr18','chr19','chr20','chr21','chr22','chrX')" | ||
| hg38: "c('chr1', 'chr2', 'chr3','chr4','chr5','chr6','chr7','chr8','chr9','chr10','chr11','chr12','chr13','chr14','chr15','chr16','chr17','chr18','chr19','chr20','chr21','chr22','chrX')" | ||
| ichorCNA_fracReadsInChrYForMale: 0.002 # Threshold for fraction of reads in chrY to assign as male | ||
| ichorCNA_genomeStyle: # can set this to UCSC or NCBI | ||
| grch37: "NCBI" | ||
| hg19: "NCBI" | ||
| hs37d5: "NCBI" | ||
| grch38: "UCSC" | ||
| hg38: "UCSC" | ||
| # chrs used for training ichorCNA parameters, e.g. tumor fraction. | ||
| ichorCNA_chrTrain: | ||
| grch37: "c(1:22)" | ||
| hg19: "c(1:22)" | ||
| hs37d5: "c(1:22)" | ||
| grch38: "paste0('chr', c(1:22))" | ||
| hg38: "paste0('chr', c(1:22))" | ||
| # non-tumor fraction parameter restart values; higher values should be included for cfDNA | ||
| ichorCNA_normal: "c(0.5,0.6,0.7,0.8,0.9,0.95)" | ||
| # ploidy parameter restart values | ||
| ichorCNA_ploidy: "c(2,3,4)" | ||
| ichorCNA_estimateNormal: TRUE | ||
| ichorCNA_estimatePloidy: TRUE | ||
| ichorCNA_estimateClonality: TRUE | ||
| # states to use for subclonal CN | ||
| ichorCNA_scStates: "c(1,3)" | ||
| # set maximum copy number to use | ||
| ichorCNA_maxCN: 5 | ||
| # TRUE/FALSE to include homozygous deletion state # FALSE for low coverage libraries (ex. 0.1x) ; can turn on for higher coverage data (ex. >10x) | ||
| ichorCNA_includeHOMD: FALSE | ||
| # Exclude solutions if total length of subclonal CNAs > this fraction of the genome | ||
| ichorCNA_maxFracGenomeSubclone: 0.5 | ||
| # Exclude solutions if total length of subclonal CNAs > this fraction of total CNA length | ||
| ichorCNA_maxFracCNASubclone: 0.7 | ||
| # control segmentation - higher (e.g. 0.9999999) leads to higher specificity and fewer segments | ||
| # lower (e.g. 0.99) leads to higher sensitivity and more segments | ||
| ichorCNA_txnE: 0.9399999 | ||
| # control segmentation - higher (e.g. 10000000) leads to higher specificity and fewer segments | ||
| # lower (e.g. 100) leads to higher sensitivity and more segments | ||
| ichorCNA_txnStrength: 10000 | ||
| ichorCNA_plotFileType: "pdf" | ||
| ichorCNA_plotYlim: "c(-2,2)" | ||
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| conda_envs: | ||
| ichorcna: "{MODSDIR}/envs/ichorcna.env.yaml" | ||
| hmmcopy_utils: "{MODSDIR}/envs/hmmcopy_utils.env.yaml" | ||
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| threads: | ||
| readcounter: 4 | ||
| run: 4 | ||
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| resources: | ||
| readcounter: | ||
| mem_mb: 2000 | ||
| bam: 1 | ||
| run: | ||
| mem_mb: 2000 | ||
| bam: 1 | ||
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| pairing_config: | ||
| genome: | ||
| run_paired_tumours: False | ||
| run_unpaired_tumours_with: "no_normal" | ||
| run_paired_tumours_as_unpaired: True | ||
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| name: null | ||
| channels: | ||
| - conda-forge | ||
| - dranew | ||
| - bioconda | ||
| - defaults | ||
| - r | ||
| dependencies: | ||
| - _libgcc_mutex=0.1 | ||
| - _openmp_mutex=4.5 | ||
| - _r-mutex=1.0.1 | ||
| - binutils_impl_linux-64=2.35.1 | ||
| - binutils_linux-64=2.35 | ||
| - bioconductor-biocgenerics=0.36.0 | ||
| - bioconductor-genomeinfodb=1.26.0 | ||
| - bioconductor-genomeinfodbdata=1.2.4 | ||
| - bioconductor-genomicranges=1.42.0 | ||
| - bioconductor-hmmcopy=1.32.0 | ||
| - bioconductor-iranges=2.24.0 | ||
| - bioconductor-s4vectors=0.28.0 | ||
| - bioconductor-xvector=0.30.0 | ||
| - bioconductor-zlibbioc=1.36.0 | ||
| - bwidget=1.9.14 | ||
| - bzip2=1.0.8 | ||
| - ca-certificates=2020.12.5 | ||
| - cairo=1.16.0 | ||
| - curl=7.71.1 | ||
| - fontconfig=2.13.1 | ||
| - freetype=2.10.4 | ||
| - fribidi=1.0.10 | ||
| - gcc_impl_linux-64=9.3.0 | ||
| - gcc_linux-64=9.3.0 | ||
| - gettext=0.19.8.1 | ||
| - gfortran_impl_linux-64=9.3.0 | ||
| - gfortran_linux-64=9.3.0 | ||
| - graphite2=1.3.13 | ||
| - gsl=2.6 | ||
| - gxx_impl_linux-64=9.3.0 | ||
| - gxx_linux-64=9.3.0 | ||
| - harfbuzz=2.8.0 | ||
| - hmmcopy_utils=0.0.1 | ||
| - icu=68.1 | ||
| - jpeg=9d | ||
| - kernel-headers_linux-64=2.6.32 | ||
| - krb5=1.17.2 | ||
| - ld_impl_linux-64=2.35.1 | ||
| - libblas=3.8.0 | ||
| - libcblas=3.8.0 | ||
| - libcurl=7.71.1 | ||
| - libedit=3.1.20191231 | ||
| - libffi=3.3 | ||
| - libgcc-devel_linux-64=9.3.0 | ||
| - libgcc-ng=9.3.0 | ||
| - libgfortran-ng=9.3.0 | ||
| - libgfortran5=9.3.0 | ||
| - libglib=2.66.7 | ||
| - libgomp=9.3.0 | ||
| - libiconv=1.16 | ||
| - liblapack=3.8.0 | ||
| - libopenblas=0.3.10 | ||
| - libpng=1.6.37 | ||
| - libssh2=1.9.0 | ||
| - libstdcxx-devel_linux-64=9.3.0 | ||
| - libstdcxx-ng=9.3.0 | ||
| - libtiff=4.2.0 | ||
| - libuuid=2.32.1 | ||
| - libwebp-base=1.2.0 | ||
| - libxcb=1.13 | ||
| - libxml2=2.9.10 | ||
| - lz4-c=1.9.3 | ||
| - make=4.3 | ||
| - ncurses=6.2 | ||
| - openssl=1.1.1j | ||
| - pango=1.42.4 | ||
| - pcre=8.44 | ||
| - pcre2=10.36 | ||
| - pixman=0.40.0 | ||
| - pthread-stubs=0.4 | ||
| - r-base=4.0.3 | ||
| - r-bitops=1.0_6 | ||
| - r-data.table=1.14.0 | ||
| - r-getopt=1.20.3 | ||
| - r-ichorcna=0.2.0 | ||
| - r-optparse=1.6.6 | ||
| - r-plyr=1.8.6 | ||
| - r-rcpp=1.0.6 | ||
| - r-rcurl=1.98_1.2 | ||
| - readline=8.0 | ||
| - sed=4.8 | ||
| - sysroot_linux-64=2.12 | ||
| - tk=8.6.10 | ||
| - tktable=2.10 | ||
| - xorg-kbproto=1.0.7 | ||
| - xorg-libice=1.0.10 | ||
| - xorg-libsm=1.2.3 | ||
| - xorg-libx11=1.7.0 | ||
| - xorg-libxau=1.0.9 | ||
| - xorg-libxdmcp=1.1.3 | ||
| - xorg-libxext=1.3.4 | ||
| - xorg-libxrender=0.9.10 | ||
| - xorg-libxt=1.2.1 | ||
| - xorg-renderproto=0.11.1 | ||
| - xorg-xextproto=7.3.0 | ||
| - xorg-xproto=7.0.31 | ||
| - xz=5.2.5 | ||
| - zlib=1.2.11 | ||
| - zstd=1.4.9 | ||
| prefix: /projects/rmorin/projects/tumour_contam/envs/ichorcna |
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Ideally we wouldn't rely on the user to specify the chromosomes this way but I can live with this for now.