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abenjakabenjak
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update main to be compatible in wf. update readme
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‎facets/README.md‎

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@@ -6,35 +6,21 @@ Read more: [https://github.com/mskcc/facets/](https://github.com/mskcc/facets/)
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## Usage
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The typical command for running the pipeline is as follows:
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```
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nextflow run wes-postproc/modules/facets --input input.txt -profile cluster,singularity
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```
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Mandatory arguments:
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```
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--input Tab delimited file (no header), with paths to following files:
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tumor_ID normal_ID tumor.bam normal.bam target.dbsnp
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--pileup Pileup file produced by snp-pileup (.bc.gz)
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--out_prefix Output prefix
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```
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Optional arguments:
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```
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--snp_pileup Full path to the folder containing the snp_pileup files (you might want to use this when re-running facets)
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--summaryPrefix Prefix for the summary files [all.geneCN]
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--q (snp-pileup) Sets the minimum threshold for mapping quality [1]
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--Q (snp-pileup) Sets the minimum threshold for base quality [13]
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--r (snp-pileup) Comma separated list of minimum read counts for a position to be output [25,0]
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--d (snp-pileup) Sets the maximum depth [1000]
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--genome Genome build (b37, GRCh37, hg19, mm9, mm10, GRCm38, hg38). [hg38]
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--seed [1234]
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--snp_nbhd Window size [250]
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--minNDepth Minimum depth in normal to keep the position [25]
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--maxNDepth Maximum depth in normal to keep the position [1000]
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--pre_cval Pre-processing critical value [cval1 - 50]
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--cval1 Critical value for estimating diploid log Ratio [200]
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--cval2 Starting critical value for segmentation (increases by 25 until success) [cval1 - 50]
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--max_cval Maximum critical value for segmentation (increases by 25 until success) [5000]
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--minNDepth Minimum depth in normal to keep the position [5]
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--maxNDepth Maximum depth in normal to keep the position [500]
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--pre_cval Pre-processing critical value [80]
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--cval Critical value for estimating diploid log Ratio [200]
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--min_nhet Minimum number of heterozygote snps in a segment used for bivariate t-statistic during clustering of segment [25]
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--unmatched Is it unmatched? [FALSE]
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--minGC Min GC of position [0]
@@ -43,41 +29,24 @@ Optional arguments:
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## Output
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```
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./facets_out/snp_pileup .................. pileup files for every sample.
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{tumor_id}__{normal_id}__q{params.q}_Q{params.Q}_d{params.maxNDepth}_r{params.r}.bc.gz
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./facets_out/cval1{params.cval1} .......... FACETS results for every sample.
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{tumor_id}__{normal_id}.cncf.pdf ...... genome-wide profile. Figures:
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log-ratio: logR with chromosomes alternating in blue and gray. The green line indicates the median logR in the sample. The purple line indicates the logR of the diploid state.
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log-odds-ratio: Segment means are ploted in red lines.
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copy number (em): plots the total (black) and minor (red) copy number for each segment.
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cf-em: shows the associated cellular fraction (cf). Dark blue indicates high cf. Light blue indicates low cf. Beige indicates a normal segment (total=2,minor=1).
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{tumor_id}__{normal_id}.cncf.txt ...... FACETS result table. The columns are:
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chrom: the chromosome to which the segment belongs.seg: the segment number.
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num.mark: the number of SNPs in the segment.
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nhet: the number of SNPs that are deemed heterozygous.
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cnlr.median: the median log-ratio of the segment.
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mafR: the log-odds-ratio summary for the segment (close to zero means the alleles are in balance).
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segclust: the segment cluster to which segment belongs.
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cnlr.median.clust: the median log-ratio of the segment cluster.
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mafR.clust: the log-odds-ratio summary for the segment cluster.
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cf.em: the cellular fraction of the segment.
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tcn.em: the total copy number of the segment.
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lcn.em: the minor copy number of the segment.
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{tumor_id}__{normal_id}.logR.pdf ...... genome-wide profile log-ratio only.
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{tumor_id}__{normal_id}.out ........... result summary file and log
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{tumor_id}__{normal_id}.Rdata ......... FACETS R session
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.cncf.pdf ...... genome-wide profile. Figures:
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log-ratio: logR with chromosomes alternating in blue and gray. The green line indicates the median logR in the sample. The purple line indicates the logR of the diploid state.
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log-odds-ratio: Segment means are ploted in red lines.
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copy number (em): plots the total (black) and minor (red) copy number for each segment.
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cf-em: shows the associated cellular fraction (cf). Dark blue indicates high cf. Light blue indicates low cf. Beige indicates a normal segment (total=2,minor=1).
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.cncf.txt ...... FACETS result table. The columns are:
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chrom: the chromosome to which the segment belongs.seg: the segment number.
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num.mark: the number of SNPs in the segment.
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nhet: the number of SNPs that are deemed heterozygous.
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cnlr.median: the median log-ratio of the segment.
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mafR: the log-odds-ratio summary for the segment (close to zero means the alleles are in balance).
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segclust: the segment cluster to which segment belongs.
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cnlr.median.clust: the median log-ratio of the segment cluster.
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mafR.clust: the log-odds-ratio summary for the segment cluster.
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cf.em: the cellular fraction of the segment.
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tcn.em: the total copy number of the segment.
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lcn.em: the minor copy number of the segment.
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.out ........... result summary file and log
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.Rdata ......... FACETS R session
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```
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## Fetching the singularity container
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```
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bash scripts/fetch_image.sh
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```
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## Fetching resource files
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```
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bash scripts/fetch_resources.sh
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```

‎facets/main.nf‎

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@@ -49,7 +49,7 @@ params.publish_dir = "" // set to empty string will disable publishDir
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params.help = null
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// tool specific parmas go here, add / change as needed
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params.tumor_id = null
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params.out_prefix = null
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params.pileup = null
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params.genome = 'hg38'
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params.snp_nbhd = 500
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nextflow run facets/main.nf --pileup <snp-pileup.bc.gz>
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Mandatory arguments:
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--tumor_id Tumor ID
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--pileup Pileup file produced by snp-pileup (.bc.gz)
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--out_prefix Output prefix
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Optional arguments:
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--genome Genome build (b37, GRCh37, hg19, mm9, mm10, GRCm38, hg38). [${params.genome}]
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if (params.help) exit 0, helpMessage()
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// Validate inputs
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if(params.out_prefix == null) error "Missing mandatory '--out_prefix' parameter"
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log.info ""
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log.info "tumor_id=${params.tumor_id}"
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log.info "pileup=${params.out_prefix}"
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log.info "pileup=${params.pileup}"
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log.info "genome=${params.genome}"
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log.info ""
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// Validate inputs
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if(params.tumor_id == null) error "Missing mandatory '--tumor_id' parameter"
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if(params.pileup == null) error "Missing mandatory '--pileup' parameter"
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process facets {
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container "${params.container ?: container[params.container_registry ?: default_container_registry]}:${params.container_version ?: version}"
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publishDir "${params.publish_dir}/${task.process.replaceAll(':', '_')}", mode: "copy", enabled: params.publish_dir
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shell:
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'''
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#run facets
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facetsRun.R --seed !{params.seed} --minNDepth !{params.minNDepth} --maxNDepth !{params.maxNDepth} --snp_nbhd !{params.snp_nbhd} --minGC !{params.minGC} --maxGC !{params.maxGC} --cval !{params.cval} --pre_cval !{params.pre_cval} --genome !{params.genome} --min_nhet !{params.min_nhet} --outPrefix !{params.tumor_id} --tumorName !{params.tumor_id} !{pileup}
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facetsRun.R --seed !{params.seed} --minNDepth !{params.minNDepth} --maxNDepth !{params.maxNDepth} --snp_nbhd !{params.snp_nbhd} --minGC !{params.minGC} --maxGC !{params.maxGC} --cval !{params.cval} --pre_cval !{params.pre_cval} --genome !{params.genome} --min_nhet !{params.min_nhet} --outPrefix !{params.out_prefix} --tumorName !{params.out_prefix} !{pileup}
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#fetch results (cncf and plot can be missing from facets results, but if produced both will be available)
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facetsResults.sh -s !{params.tumor_id}.out $(if [[ -f !{params.tumor_id}.cncf.txt && -f !{params.tumor_id}.cncf.pdf ]]; then echo -c !{params.tumor_id}.cncf.txt -p !{params.tumor_id}.cncf.pdf; fi)
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facetsResults.sh -s !{params.out_prefix}.out $(if [[ -f !{params.out_prefix}.cncf.txt && -f !{params.out_prefix}.cncf.pdf ]]; then echo -c !{params.out_prefix}.cncf.txt -p !{params.out_prefix}.cncf.pdf; fi)
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'''
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}
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‎facets/tests/checker.nf‎

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@@ -48,7 +48,7 @@ params.container_version = ""
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params.container = ""
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// tool specific parmas go here, add / change as needed
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params.tumor_id = ""
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params.out_prefix = ""
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params.pileup = ""
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params.genome = ""
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params.expected_output = ""
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workflow checker {
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take:
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pileup
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tumor_id
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out_prefix
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genome
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expected_output
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workflow {
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checker(
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file(params.pileup),
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params.tumor_id,
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params.out_prefix,
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params.genome,
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file(params.expected_output)
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)

‎facets/tests/test-job-1.json‎

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{
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"pileup": "input/test.bc.gz",
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"tumor_id": "test",
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"out_prefix": "test",
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"genome": "hg19",
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"expected_output": "expected/expected.out",
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"publish_dir": "outdir",

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