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nf-core_modules/modules/last/lastal/meta.yml

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New last/lastal module to align query sequences on a target index (#510) * New last/lastal to align query sequences on a target index `lastal` is the main program of the [LAST](https://gitlab.com/mcfrith/last) suite. It align query DNA sequences in FASTA or FASTQ format to a target index of DNA or protein sequences. The index is produced by the `lastdb` program (module `last/lastdb`). The score matrix for evaluating the alignment can be chosen among preset ones or computed iteratively by the `last-train` program (module `last/train`). For this reason, the `last/lastal` module proposed here has one input channel containing an optional file, that has to be dummy when not used. The LAST aligner outputs MAF files that can be very large (up to hundreds of gigabytes), therefore this module unconditionally compresses its output with gzip. This new module is part of the work described in Issue #464. During this development, we fix the version of LAST to 1219 to ensure consistency (hence ignore lint's version warning). * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Un-hardcode the path to the LAST index. Among multiple alternatives I have chosen the following command to detect the sample name of the index, because it fails in situations where there is no index files in the index folder, and in situations were there are two indexes files in the folder. Not failing would result in feeding garbage information in the INDEX_NAME variable. basename \$(ls $index/*.bck) .bck In case of missing file, a clear error message is given by `ls`. In case of more than one file, the error message of `basename` is more cryptic, unfortunately. (`basename: extra operand ‘.bck’`) Alternatives that do not fail if there is no .bck file: basename $index/*bck .bck find $index -name '*bck' | sed 's/.bck//' Alternatives that do not fail if there are more than one .bck file: basename -s .bck $index/*bck ls $index/*.bck | xargs basename -s .bck find $index -name '*bck' | sed 's/.bck//' Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-25 21:10:48 +00:00
name: last_lastal
description: Find suitable score parameters for sequence alignment
keywords:
- LAST
- align
- fastq
- fasta
tools:
- last:
description: LAST finds & aligns related regions of sequences.
homepage: https://gitlab.com/mcfrith/last
documentation: https://gitlab.com/mcfrith/last/-/blob/main/doc/last-train.rst
tool_dev_url: https://gitlab.com/mcfrith/last
doi: ""
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
licence: ["GPL v3-or-later"]
New last/lastal module to align query sequences on a target index (#510) * New last/lastal to align query sequences on a target index `lastal` is the main program of the [LAST](https://gitlab.com/mcfrith/last) suite. It align query DNA sequences in FASTA or FASTQ format to a target index of DNA or protein sequences. The index is produced by the `lastdb` program (module `last/lastdb`). The score matrix for evaluating the alignment can be chosen among preset ones or computed iteratively by the `last-train` program (module `last/train`). For this reason, the `last/lastal` module proposed here has one input channel containing an optional file, that has to be dummy when not used. The LAST aligner outputs MAF files that can be very large (up to hundreds of gigabytes), therefore this module unconditionally compresses its output with gzip. This new module is part of the work described in Issue #464. During this development, we fix the version of LAST to 1219 to ensure consistency (hence ignore lint's version warning). * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Un-hardcode the path to the LAST index. Among multiple alternatives I have chosen the following command to detect the sample name of the index, because it fails in situations where there is no index files in the index folder, and in situations were there are two indexes files in the folder. Not failing would result in feeding garbage information in the INDEX_NAME variable. basename \$(ls $index/*.bck) .bck In case of missing file, a clear error message is given by `ls`. In case of more than one file, the error message of `basename` is more cryptic, unfortunately. (`basename: extra operand ‘.bck’`) Alternatives that do not fail if there is no .bck file: basename $index/*bck .bck find $index -name '*bck' | sed 's/.bck//' Alternatives that do not fail if there are more than one .bck file: basename -s .bck $index/*bck ls $index/*.bck | xargs basename -s .bck find $index -name '*bck' | sed 's/.bck//' Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-25 21:10:48 +00:00
input:
- index:
type: directory
description: Directory containing the files of the LAST index
pattern: "lastdb/"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- fastx:
type: file
description: FASTA/FASTQ file
pattern: "*.{fasta,fastq}"
- param_file:
type: file
description: Trained parameter file
pattern: "*.par"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
Update versions key in meta.yml for all modules (#787)
2021-10-03 07:20:26 +00:00
- versions:
New last/lastal module to align query sequences on a target index (#510) * New last/lastal to align query sequences on a target index `lastal` is the main program of the [LAST](https://gitlab.com/mcfrith/last) suite. It align query DNA sequences in FASTA or FASTQ format to a target index of DNA or protein sequences. The index is produced by the `lastdb` program (module `last/lastdb`). The score matrix for evaluating the alignment can be chosen among preset ones or computed iteratively by the `last-train` program (module `last/train`). For this reason, the `last/lastal` module proposed here has one input channel containing an optional file, that has to be dummy when not used. The LAST aligner outputs MAF files that can be very large (up to hundreds of gigabytes), therefore this module unconditionally compresses its output with gzip. This new module is part of the work described in Issue #464. During this development, we fix the version of LAST to 1219 to ensure consistency (hence ignore lint's version warning). * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Un-hardcode the path to the LAST index. Among multiple alternatives I have chosen the following command to detect the sample name of the index, because it fails in situations where there is no index files in the index folder, and in situations were there are two indexes files in the folder. Not failing would result in feeding garbage information in the INDEX_NAME variable. basename \$(ls $index/*.bck) .bck In case of missing file, a clear error message is given by `ls`. In case of more than one file, the error message of `basename` is more cryptic, unfortunately. (`basename: extra operand ‘.bck’`) Alternatives that do not fail if there is no .bck file: basename $index/*bck .bck find $index -name '*bck' | sed 's/.bck//' Alternatives that do not fail if there are more than one .bck file: basename -s .bck $index/*bck ls $index/*.bck | xargs basename -s .bck find $index -name '*bck' | sed 's/.bck//' Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-25 21:10:48 +00:00
type: file
Update versions key in meta.yml for all modules (#787)
2021-10-03 07:20:26 +00:00
description: File containing software versions
Bulk update modules to use versions.yml (#739) * New functions.nf * Convert code to create versions.yml * Update meta.yml * update output channel * Fix more meta.yml * Manually update remaining modules * remove superflous echo * Fix misformatted meta.yml files * Fix yaml, was list instead of dict * fix version for bcftools Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-27 08:41:24 +00:00
pattern: "versions.yml"
New last/lastal module to align query sequences on a target index (#510) * New last/lastal to align query sequences on a target index `lastal` is the main program of the [LAST](https://gitlab.com/mcfrith/last) suite. It align query DNA sequences in FASTA or FASTQ format to a target index of DNA or protein sequences. The index is produced by the `lastdb` program (module `last/lastdb`). The score matrix for evaluating the alignment can be chosen among preset ones or computed iteratively by the `last-train` program (module `last/train`). For this reason, the `last/lastal` module proposed here has one input channel containing an optional file, that has to be dummy when not used. The LAST aligner outputs MAF files that can be very large (up to hundreds of gigabytes), therefore this module unconditionally compresses its output with gzip. This new module is part of the work described in Issue #464. During this development, we fix the version of LAST to 1219 to ensure consistency (hence ignore lint's version warning). * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Un-hardcode the path to the LAST index. Among multiple alternatives I have chosen the following command to detect the sample name of the index, because it fails in situations where there is no index files in the index folder, and in situations were there are two indexes files in the folder. Not failing would result in feeding garbage information in the INDEX_NAME variable. basename \$(ls $index/*.bck) .bck In case of missing file, a clear error message is given by `ls`. In case of more than one file, the error message of `basename` is more cryptic, unfortunately. (`basename: extra operand ‘.bck’`) Alternatives that do not fail if there is no .bck file: basename $index/*bck .bck find $index -name '*bck' | sed 's/.bck//' Alternatives that do not fail if there are more than one .bck file: basename -s .bck $index/*bck ls $index/*.bck | xargs basename -s .bck find $index -name '*bck' | sed 's/.bck//' Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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- maf:
type: file
description: Gzipped MAF (Multiple Alignment Format) file
pattern: "*.{maf.gz}"
authors:
- "@charles-plessy"
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