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: | ||
| readCounterScript: "{MODSDIR}/src/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" | ||
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There was a problem hiding this comment. Ideally we wouldn't rely on the user to specify the chromosomes this way but I can live with this for now. |
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| 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 | ||
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There was a problem hiding this comment. Explain with a comment what this does. |
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| binSize: 1000000 # set window size to compute coverage | ||
| # available binSizes are: 1000000, 500000, 50000, 10000 | ||
| run: | ||
| ichorCNA_libdir: "{MODSDIR}/src/" | ||
| ichorCNA_rscript: "{MODSDIR}/src/runIchorCNA.R" | ||
| # use panel matching same bin size (optional) | ||
| ichorCNA_normalPanel: | ||
| "1000000": "{MODSDIR}/src/inst/extdata/HD_ULP_PoN_{genome_build}_1Mb_median_normAutosome_median.rds" | ||
| "500000": "{MODSDIR}/src/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": "{MODSDIR}/src/inst/extdata/gc_{genome_build}_1000kb.wig" | ||
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There was a problem hiding this comment. Does this genome_build naming match the one we use ? I assume it does since this was run in GAMBL, right? There was a problem hiding this comment. Yes, unfortunately ichorCNA's github repo is messy and inconsistent with their naming conventions. In my original version, I had to manually rename some of their reference files to fit this format. In the current version, there's one rule with a bunch of symlinks that renames the reference files so it would fit in downstream rules. |
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| "500000": "{MODSDIR}/src/inst/extdata/gc_{genome_build}_500kb.wig" | ||
| "50000": "{MODSDIR}/src/inst/extdata/gc_{genome_build}_50kb.wig" | ||
| "10000": "{MODSDIR}/src/inst/extdata/gc_{genome_build}_10kb.wig" | ||
| # must use map wig file corresponding to same binSize (required) | ||
| ichorCNA_mapWig: | ||
| "1000000": "{MODSDIR}/src/inst/extdata/map_{genome_build}_1000kb.wig" | ||
| "500000": "{MODSDIR}/src/inst/extdata/map_{genome_build}_500kb.wig" | ||
| "50000": "{MODSDIR}/src/inst/extdata/map_{genome_build}_50kb.wig" | ||
| "10000": "{MODSDIR}/src/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: "{MODSDIR}/src/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt" | ||
| hg19: "{MODSDIR}/src/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt" | ||
| hs37d5: "{MODSDIR}/src/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt" | ||
| grch38: "{MODSDIR}/src/inst/extdata/GRCh38.GCA_000001405.2_centromere_acen.txt" | ||
| hg38: "{MODSDIR}/src/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 | ||
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There was a problem hiding this comment. Can you briefly document this? |
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| 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)" | ||
| 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: 0.9999 | ||
| # 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" | ||
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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 | ||
| - 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 | ||
| - 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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add a newline after this
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Done