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e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
114 lines
4.2 KiB
YAML
114 lines
4.2 KiB
YAML
name: mapdamage2
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description: Computational framework for tracking and quantifying DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.
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keywords:
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- ancient DNA
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- DNA damage
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- NGS
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- damage patterns
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- bam
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tools:
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- mapdamage2:
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description: Tracking and quantifying damage patterns in ancient DNA sequences
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homepage: http://ginolhac.github.io/mapDamage/
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documentation: https://ginolhac.github.io/mapDamage/
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tool_dev_url: https://github.com/ginolhac/mapDamage
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doi: "10.1093/bioinformatics/btt193"
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licence: ["MIT"]
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input:
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- meta:
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type: map
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description: Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
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- bam:
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type: file
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description: BAM file
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pattern: "*.{bam}"
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- fasta:
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type: file
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description: Fasta file, the reference the input BAM was mapped against
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pattern: "*.{fasta}"
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output:
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- meta:
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type: map
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description: Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
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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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- runtime_log:
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type: file
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description: Log file with a summary of command lines used and timestamps.
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pattern: "Runtime_log.txt"
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- fragmisincorporation_plot:
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type: file
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description: A pdf file that displays both fragmentation and misincorporation patterns.
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pattern: "Fragmisincorporation_plot.pdf"
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- length_plot:
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type: file
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description: A pdf file that displays length distribution of singleton reads per strand and cumulative frequencies of C->T at 5'-end and G->A at 3'-end are also displayed per strand.
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pattern: "Length_plot.pdf"
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- misincorporation:
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type: file
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description: Contains a table with occurrences for each type of mutations and relative positions from the reads ends.
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pattern: "misincorporation.txt"
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- pctot_freq:
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type: file
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description: Contains frequencies of Cytosine to Thymine mutations per position from the 5'-ends.
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pattern: "5pCtoT_freq.txt"
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- pgtoa_freq:
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type: file
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description: Contains frequencies of Guanine to Adenine mutations per position from the 3'-ends.
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pattern: "3pGtoA_freq.txt"
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- dnacomp:
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type: file
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description: Contains a table of the reference genome base composition per position, inside reads and adjacent regions.
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pattern: "dnacomp.txt"
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- lgdistribution:
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type: file
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description: Contains a table with read length distributions per strand.
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pattern: "lgdistribution.txt"
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- stats_out_mcmc_hist:
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type: file
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description: A MCMC histogram for the damage parameters and log likelihood.
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pattern: "Stats_out_MCMC_hist.pdf"
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- stats_out_mcmc_iter:
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type: file
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description: Values for the damage parameters and log likelihood in each MCMC iteration.
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pattern: "Stats_out_MCMC_iter.csv"
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- stats_out_mcmc_trace:
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type: file
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description: A MCMC trace plot for the damage parameters and log likelihood.
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pattern: "Stats_out_MCMC_trace.pdf"
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- stats_out_mcmc_iter_summ_stat:
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type: file
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description: Summary statistics for the damage parameters estimated posterior distributions.
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pattern: "Stats_out_MCMC_iter_summ_stat.csv"
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- stats_out_mcmc_post_pred:
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type: file
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description: Empirical misincorporation frequency and posterior predictive intervals from the fitted model.
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pattern: "Stats_out_MCMC_post_pred.pdf"
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- stats_out_mcmc_correct_prob:
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type: file
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description: Position specific probability of a C->T and G->A misincorporation is due to damage.
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pattern: "Stats_out_MCMC_correct_prob.csv"
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- dnacomp_genome:
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type: file
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description: Contains the global reference genome base composition (computed by seqtk).
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pattern: "dnacomp_genome.csv"
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- rescaled:
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type: file
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description: Rescaled BAM file, where likely post-mortem damaged bases have downscaled quality scores.
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pattern: "*.{bam}"
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- fasta:
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type: file
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description: Allignments in a FASTA file, only if flagged by -d.
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pattern: "*.{fasta}"
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- folder:
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type: folder
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description: Folder created when --plot-only, --rescale and --stats-only flags are passed.
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pattern: "*/"
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authors:
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- "@darcy220606"
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