nf-core_modules/modules/mapdamage2/meta.yml
Matthias Hörtenhuber e745e167c1
Fix formatting in yaml files, add yamllint config (#1279)
* 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>
2022-02-15 11:15:27 +00:00

114 lines
4.2 KiB
YAML

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