nf-core_modules/tests/software/last/mafconvert/main.nf

#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { LAST_MAFCONVERT } from '../../../../software/last/mafconvert/main.nf' addParams( options: [:] )

workflow test_last_mafconvert {
    
    input = [ [ id:'contigs.genome' ], // meta map
              file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) ]

    LAST_MAFCONVERT ( input, "psl" )
}
New last/mafconvert module to convert MAF alignments. (#527) * New last/mafconvert module to convert MAF alignments. The `maf-convert` tool distributed with [LAST](https://gitlab.com/mcfrith/last) reads alignmnts in [MAF](https://genome-asia.ucsc.edu/FAQ/FAQformat.html#format5) format and converts them in another format (axt, blast, blasttab, chain, gff, html, psl, sam, tab). This new module is part of the work described in Issue #464. During this development, we fix the versiob of LAST to 1219 to ensure consistency. We will upgrade it later. * Delete white space. * Update the function.nf file to the dev version. 2021-06-09 06:38:57 +00:00			`#!/usr/bin/env nextflow`

			`nextflow.enable.dsl = 2`

Update last module (#533) * Update LAST to version 1238. * Update functions.nf to the latest devel version. * Update test MD5sums after updating software version. * Make portable on MacOS * Allow input alignments to be uncompressed. While the strategy in this family of modules is to make all inputs and outputs compressed, this change might be useful to some users. As of LAST 2138, `last/split` does not allow its input to be compressed. * Search for .des file, that is guaranteed to be unique. Some LAST indexes have more than one .bck file and it makes the name detection crash. In this commit, I also standardise how the names are detected. * Use value input channel and optional output channels to handle formats. As discussed on Slack, it is preferred to use a value input channel instead of sneaking options through `params.args2` or `params.format` as we did. Likewise, optional output channels with clearly labeled format are preferred to 'catch-all' wildcards. 2021-06-14 11:27:27 +00:00			`include { LAST_MAFCONVERT } from '../../../../software/last/mafconvert/main.nf' addParams( options: [:] )`
New last/mafconvert module to convert MAF alignments. (#527) * New last/mafconvert module to convert MAF alignments. The `maf-convert` tool distributed with [LAST](https://gitlab.com/mcfrith/last) reads alignmnts in [MAF](https://genome-asia.ucsc.edu/FAQ/FAQformat.html#format5) format and converts them in another format (axt, blast, blasttab, chain, gff, html, psl, sam, tab). This new module is part of the work described in Issue #464. During this development, we fix the versiob of LAST to 1219 to ensure consistency. We will upgrade it later. * Delete white space. * Update the function.nf file to the dev version. 2021-06-09 06:38:57 +00:00
			`workflow test_last_mafconvert {`

			`input = [ [ id:'contigs.genome' ], // meta map`
			`file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) ]`

Update last module (#533) * Update LAST to version 1238. * Update functions.nf to the latest devel version. * Update test MD5sums after updating software version. * Make portable on MacOS * Allow input alignments to be uncompressed. While the strategy in this family of modules is to make all inputs and outputs compressed, this change might be useful to some users. As of LAST 2138, `last/split` does not allow its input to be compressed. * Search for .des file, that is guaranteed to be unique. Some LAST indexes have more than one .bck file and it makes the name detection crash. In this commit, I also standardise how the names are detected. * Use value input channel and optional output channels to handle formats. As discussed on Slack, it is preferred to use a value input channel instead of sneaking options through `params.args2` or `params.format` as we did. Likewise, optional output channels with clearly labeled format are preferred to 'catch-all' wildcards. 2021-06-14 11:27:27 +00:00			`LAST_MAFCONVERT ( input, "psl" )`
New last/mafconvert module to convert MAF alignments. (#527) * New last/mafconvert module to convert MAF alignments. The `maf-convert` tool distributed with [LAST](https://gitlab.com/mcfrith/last) reads alignmnts in [MAF](https://genome-asia.ucsc.edu/FAQ/FAQformat.html#format5) format and converts them in another format (axt, blast, blasttab, chain, gff, html, psl, sam, tab). This new module is part of the work described in Issue #464. During this development, we fix the versiob of LAST to 1219 to ensure consistency. We will upgrade it later. * Delete white space. * Update the function.nf file to the dev version. 2021-06-09 06:38:57 +00:00			`}`