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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>
79 lines
2.3 KiB
YAML
79 lines
2.3 KiB
YAML
name: last_mafconvert
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description: Converts MAF alignments in another format.
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keywords:
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- LAST
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- convert
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- alignment
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- MAF
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tools:
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- last:
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description: LAST finds & aligns related regions of sequences.
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homepage: https://gitlab.com/mcfrith/last
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documentation: https://gitlab.com/mcfrith/last/-/blob/main/doc/
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tool_dev_url: https://gitlab.com/mcfrith/last
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doi: ""
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licence: ["GPL v3-or-later"]
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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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- maf:
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type: file
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description: Multiple Aligment Format (MAF) file, optionally compressed with gzip
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pattern: "*.{maf.gz,maf}"
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- format:
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type: value
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description: Output format (one of axt, blast, blasttab, chain, gff, html, psl, sam, or tab)
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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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- axt_gz:
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type: file
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description: Gzipped pairwise alignment in Axt (Blastz) format (optional)
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pattern: "*.axt.gz"
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- blast_gz:
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type: file
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description: Gzipped pairwise alignment in blast format (optional)
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pattern: "*.blast.gz"
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- blasttab_gz:
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type: file
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description: Gzipped pairwise alignment in blasttab format (optional)
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pattern: "*.blasttab.gz"
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- chain_gz:
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type: file
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description: Gzipped pairwise alignment in UCSC chain format (optional)
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pattern: "*.chain.gz"
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- gff_gz:
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type: file
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description: Gzipped pairwise alignment in GFF format (optional)
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pattern: "*.gff.gz"
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- html_gz:
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type: file
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description: Gzipped pairwise alignment in HTML format (optional)
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pattern: "*.html.gz"
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- psl_gz:
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type: file
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description: Gzipped pairwise alignment in PSL (BLAT) format (optional)
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pattern: "*.psl.gz"
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- SAM:
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type: file
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description: Gzipped pairwise alignment in SAM format (optional)
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pattern: "*.sam.gz"
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- tab:
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type: file
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description: Gzipped pairwise alignment in TAB format (optional)
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pattern: "*.tab.gz"
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authors:
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- "@aleksandrabliznina"
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