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Add warn of default being used

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This commit is contained in:
James Fellows Yates 2022-05-02 12:41:24 +02:00
parent 67b074382e
commit bd3bfe0817
3 changed files with 11 additions and 1 deletions
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5
modules/diamond/blastp/main.nf
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@ -38,6 +38,11 @@ process DIAMOND_BLASTP {
case "sam": outfmt = 101; break case "sam": outfmt = 101; break
case "tsv": outfmt = 102; break case "tsv": outfmt = 102; break
case "paf": outfmt = 103; break case "paf": outfmt = 103; break
default:
outfmt = '6';
out_ext = 'txt';
log.warn("Unknown output file format provided (${out_ext}): selecting DIAMOND default of tabular BLAST output (txt)");
break
} }
""" """
DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'` DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'`

5
modules/diamond/blastx/main.nf
View file

@ -38,6 +38,11 @@ process DIAMOND_BLASTX {
case "sam": outfmt = 101; break case "sam": outfmt = 101; break
case "tsv": outfmt = 102; break case "tsv": outfmt = 102; break
case "paf": outfmt = 103; break case "paf": outfmt = 103; break
default:
outfmt = '6';
out_ext = 'txt';
log.warn("Unknown output file format provided (${out_ext}): selecting DIAMOND default of tabular BLAST output (txt)");
break
} }
""" """
DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'` DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'`

2
tests/modules/diamond/blastx/main.nf
View file

@ -9,7 +9,7 @@ workflow test_diamond_blastx {
db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ] db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ] fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
out_ext = 'txt' out_ext = 'tfdfdt'
blast_columns = 'qseqid qlen' blast_columns = 'qseqid qlen'
DIAMOND_MAKEDB ( db ) DIAMOND_MAKEDB ( db )