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https://github.com/MillironX/nf-core_modules.git
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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>
88 lines
2 KiB
YAML
88 lines
2 KiB
YAML
name: chromap_chromap
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description: |
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Performs preprocessing and alignment of chromatin fastq files to
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fasta reference files using chromap.
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keywords:
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- chromap
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- alignment
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- map
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- fastq
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- bam
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- sam
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- hi-c
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- atac-seq
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- chip-seq
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- trimming
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- duplicate removal
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tools:
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- chromap:
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description: Fast alignment and preprocessing of chromatin profiles
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homepage: https://github.com/haowenz/chromap
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documentation: https://github.com/haowenz/chromap
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tool_dev_url: https://github.com/haowenz/chromap
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doi: ""
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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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- reads:
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type: file
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description: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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- fasta:
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type: file
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description: |
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The fasta reference file.
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- index:
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type: file
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description: |
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Chromap genome index files (*.index)
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- barcodes:
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type: file
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description: |
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Cell barcode files
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- whitelist:
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type: file
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description: |
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Cell barcode whitelist file
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- chr_order:
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type: file
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description: |
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Custom chromosome order
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- pairs_chr_order:
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type: file
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description: |
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Natural chromosome order for pairs flipping
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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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- bed:
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type: file
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description: BED file
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pattern: "*.bed.gz"
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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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- tagAlign:
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type: file
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description: tagAlign file
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pattern: "*.tagAlign.gz"
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- pairs:
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type: file
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description: pairs file
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pattern: "*.pairs.gz"
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authors:
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- "@mahesh-panchal"
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