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https://github.com/MillironX/nf-core_modules.git
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Make variables consistent
This commit is contained in:
James Fellows Yates
parent
375b706a4f
commit
58e5c6aece
6 changed files with 17 additions and 17 deletions
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@ -10,7 +10,7 @@ process DIAMOND_BLASTP {
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input:
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tuple val(meta), path(fasta)
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path db
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val outext
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val out_ext
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val blast_columns
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output:
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@ -30,7 +30,7 @@ process DIAMOND_BLASTP {
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def columns = blast_columns ? "${blast_columns}" : ''
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switch ( outext ) {
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switch ( out_ext ) {
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case "blast": outfmt = 0; break
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case "xml": outfmt = 5; break
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case "txt": outfmt = 6; break
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@ -49,7 +49,7 @@ process DIAMOND_BLASTP {
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--query $fasta \\
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--outfmt ${outfmt} ${columns} \\
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$args \\
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--out ${prefix}.${outext}
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--out ${prefix}.${out_ext}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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@ -28,7 +28,7 @@ input:
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type: directory
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description: Directory containing the protein blast database
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pattern: "*"
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- outext:
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- out_ext:
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type: string
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description: |
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Specify the type of output file to be generated. `blast` corresponds to
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@ -40,7 +40,7 @@ input:
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type: string
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description: |
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Optional space separated list of DIAMOND tabular BLAST output keywords
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used for in conjunction with the 'txt' outext option (--outfmt 6). See
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used for in conjunction with the 'txt' out_ext option (--outfmt 6). See
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DIAMOND documnetation for more information.
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output:
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@ -10,7 +10,7 @@ process DIAMOND_BLASTX {
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input:
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tuple val(meta), path(fasta)
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path db
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val outext
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val out_ext
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val blast_columns
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output:
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@ -30,7 +30,7 @@ process DIAMOND_BLASTX {
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def columns = blast_columns ? "${blast_columns}" : ''
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switch ( outext ) {
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switch ( out_ext ) {
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case "blast": outfmt = 0; break
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case "xml": outfmt = 5; break
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case "txt": outfmt = 6; break
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@ -49,7 +49,7 @@ process DIAMOND_BLASTX {
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--query $fasta \\
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--outfmt ${outfmt} ${columns} \\
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$args \\
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--out ${prefix}.${outext}
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--out ${prefix}.${out_ext}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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@ -28,7 +28,7 @@ input:
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type: directory
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description: Directory containing the nucelotide blast database
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pattern: "*"
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- outext:
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- out_ext:
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type: string
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description: |
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Specify the type of output file to be generated. `blast` corresponds to
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@ -9,20 +9,20 @@ workflow test_diamond_blastp {
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db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
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fasta = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
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outext = 'txt'
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out_ext = 'txt'
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blast_columns = 'qseqid qlen'
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DIAMOND_MAKEDB ( db )
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DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext, blast_columns )
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DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
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}
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workflow test_diamond_blastp_daa {
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db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
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fasta = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
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outext = 'daa'
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out_ext = 'daa'
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blast_columns = []
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DIAMOND_MAKEDB ( db )
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DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext, blast_columns )
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DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
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}
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@ -9,20 +9,20 @@ workflow test_diamond_blastx {
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db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
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fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
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outext = 'txt'
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out_ext = 'txt'
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blast_columns = 'qseqid qlen'
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DIAMOND_MAKEDB ( db )
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DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext, blast_columns )
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DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
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}
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workflow test_diamond_blastx_daa {
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db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
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fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
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outext = 'daa'
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out_ext = 'daa'
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blast_columns = []
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DIAMOND_MAKEDB ( db )
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DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext, blast_columns )
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DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
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}
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