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Module/ichorcna/1.0 #178
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Module/ichorcna/1.0 #178
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d8ba998
Add initial draft of ichorcna version 1.0
Jwong684 7e7dbc7
Merge branch 'master' of https://github.com/LCR-BCCRC/lcr-modules int…
Jwong684 e357f09
Updated ichorcna config and smk framework
Jwong684 a8f558b
Working version of ichorcna
Jwong684 3cbe645
removed the README (unnecessary download instructions)
Jwong684 80edb57
ichorCNA working module
Jwong684 874bb89
overhaul ichorcna - address all PR; ichorcna and dependencies are dow…
Jwong684 0466b04
Added a chr- function for readCounter
Jwong684 ad9c362
ichorCNA changed chrom input for R too
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,107 @@ | ||
| 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: | ||
| 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: "" | ||
| 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_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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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,108 @@ | ||
| 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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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
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For the chromosomes, I could use the function for the readCounter step since I need the command to look like:
"1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y"
but for the ichorCNA step, it needs to be in R-vector format:
"c('1', '2', '3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','X')"
Wouldn't it be simpler to keep it like this in the config? Otherwise, I'd need to make a function to include c( ), and ' '
'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
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How is that vector being given to ichorCNA?
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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')"
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You could construct that in Python probably and then just add that as a "param" in your rule.
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Done