Anthony Underwood 63b3975292 Update gubbins module to use new files (#417) ... * new gubbins module * new gubbins module * new gubbins module * Update software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gubbins/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * new gubbins module * new gubbins module * new gubbins module * new gubbins module * new gubbins module * new gubbins module * new gubbins module * Update tests/config/test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * new gubbins module * new gubbins module * new snpsites module * new snpsites module * new snpsites module * new snpsites module * adding fasttree module * correct trailing whitespace * using sarscov2 as a test dir * use sars-cov-2 alignment * remove old test alignment * new snpsites module * new snpsites module * new snpsites module * updated test file names * new snpsites module * remove snpsites from gubbins branch * remove redundant test_fas alignment * update md5 sums Co-authored-by: avantonder <avt@sanger.ac.uk> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: avantonder <ajv37@cam.ac.uk>		2021-04-09 07:54:11 +01:00
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alignment	Update gubbins module to use new files (#417)	2021-04-09 07:54:11 +01:00
bed	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
db	Fix some module tests after switching to config data (#386)	2021-03-24 18:28:07 +00:00
gcwiggle	PR for sequenzautils/bam2seqz (#395)	2021-04-01 07:08:27 +02:00
contigs.fasta	Add plasmidid module (#410)	2021-04-08 22:44:30 +01:00
genome.dict	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
genome.fasta	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
genome.fasta.fai	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
genome.gff3	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
genome.gff3.gz	update tests for new config (#384)	2021-04-01 20:22:06 +01:00
genome.gtf	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
genome.sizes	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
transcriptome.fasta	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
transcriptome.paf	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00