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* add atlas/pmd * update atlas/pmd tests * Add atlas/PMD module * Remove comment * Run Prettier * Incorporate Review by @jfy133 Co-authored-by: maxibor <maxime.borry@gmail.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
83 lines
2.5 KiB
YAML
83 lines
2.5 KiB
YAML
name: "atlas_pmd"
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description: Estimate the post-mortem damage patterns of DNA
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keywords:
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- ancient DNA
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- post mortem damage
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- bam
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tools:
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- "atlas":
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description: "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity"
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homepage: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
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documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
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tool_dev_url: "https://bitbucket.org/wegmannlab/atlas"
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doi: "10.1101/105346"
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licence: "['GPL v3']"
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- bam:
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type: file
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description: Single input BAM file
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pattern: "*.bam"
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- bai:
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type: file
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description: The BAI file for the input BAM file
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pattern: "*.bai"
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- fasta:
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type: file
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description: The reference genome provided as FASTA file
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pattern: "*.fasta"
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- fai:
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type: file
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description: The FAI file for the reference genome FASTA file
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pattern: "*.fai"
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- pool_rg_txt:
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type: file
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description: |
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Optional. Provide the names of read groups that should be merged for PMD estimation.
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All read groups that should be pooled listed on one line, separated by any white space.
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Other read groups will be recalibrated separately.
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pattern: "*.txt"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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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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- empiric:
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type: file
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description: A list of pmd patterns estimated with the empirical method for each readgroup
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pattern: "*_PMD_input_Empiric.txt"
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- exponential:
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type: file
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description: A list of pmd patterns estimated with the exponential method for each readgroup
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pattern: "*_PMD_input_Exponential.txt"
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- counts:
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type: file
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description: |
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The counts of all possible transitions for each read position
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(or up to a certain position, see specific command length)
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pattern: "*_PMD_Table_counts.txt"
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- table:
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type: file
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description: |
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For all possible transitions the ratio of the transition counts,
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which are taken from the _counts.txt table, over the total amount
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of the base that was mutated, for each position and readgroup
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pattern: "*_PMD_Table.txt"
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authors:
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- "@maxibor"
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- "@merszym"
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