Thanh Lee ec15bae344 🏋️‍♀️ new submodule mash/sketch🕺 (#426) ... * new submodule mash/sketch * fixed submodule naming * OK, tag is diff to keyword * OK another round 🤣 * removed TODO comments * updated as per review comments 🙆‍♂️ * updated functions.nf 😁 * Update software/mash/sketch/main.nf * Update main.nf Removed blank line at the 12th Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>		2021-04-10 16:24:23 +01:00
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adapterremoval	Update restructured paths (#380)	2021-03-24 18:26:54 +00:00
allelecounter	Update test data paths. (#375)	2021-03-24 18:18:01 +00:00
bandage/image	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
bcftools	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
bedtools	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
bismark	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
blast	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
bowtie	Update and check tests are running for all modules (#420)	2021-04-09 13:47:05 +01:00
bowtie2	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
bwa	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
bwamem2	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
bwameth	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
cat/fastq	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
cnvkit	Update test data paths. (#375)	2021-03-24 18:18:01 +00:00
cutadapt	Update test data paths. (#375)	2021-03-24 18:18:01 +00:00
dsh	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
fastp	modify fastp tests (#367)	2021-03-24 17:08:59 +01:00
fastqc	Use a config containing all test data for module tests (#365)	2021-03-24 13:07:37 +00:00
fasttree	adding fasttree module (#412)	2021-04-08 18:15:23 +01:00
fgbio	Update and check tests are running for all modules (#420)	2021-04-09 13:47:05 +01:00
flash	update tests for new config (#384)	2021-04-01 20:22:06 +01:00
gatk4	Update and check tests are running for all modules (#420)	2021-04-09 13:47:05 +01:00
gffread	Fixing a bunch of module tests (#370)	2021-03-24 17:36:29 +00:00
gubbins	Update gubbins module to use new files (#417)	2021-04-09 07:54:11 +01:00
gunzip	Update test data paths. (#375)	2021-03-24 18:18:01 +00:00
hisat2	Update and check tests are running for all modules (#420)	2021-04-09 13:47:05 +01:00
homer/annotatepeaks	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
ivar	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
kallisto/index	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
kallistobustools/ref	Added kallistobustools/ref (#408)	2021-04-09 09:41:41 +01:00
kraken2/run	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
mash/sketch	🏋️‍♀️ new submodule mash/sketch🕺 (#426)	2021-04-10 16:24:23 +01:00
methyldackel	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
minia	Fixing a bunch of module tests (#370)	2021-03-24 17:36:29 +00:00
minimap2/align	Update and check tests are running for all modules (#420)	2021-04-09 13:47:05 +01:00
mosdepth	update tests for new config (#384)	2021-04-01 20:22:06 +01:00
msisensor	Update and check tests are running for all modules (#420)	2021-04-09 13:47:05 +01:00
multiqc	Fix some module test after adapting test config approach (#379)	2021-03-24 18:29:41 +00:00
nanoplot	Nanoplot and sequencing_summary.txt for Nanopore test data (#364)	2021-04-09 08:31:38 +01:00
optitype	update tests for new config (#384)	2021-04-01 20:22:06 +01:00
pangolin	Version bumps and minor module updates (#406)	2021-04-06 13:38:41 +01:00
picard	Update and check tests are running for all modules (#420)	2021-04-09 13:47:05 +01:00
plasmidid	Add plasmidid module (#410)	2021-04-08 22:44:30 +01:00
preseq/lcextrap	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
prodigal	Update test data paths. (#375)	2021-03-24 18:18:01 +00:00
prokka	Update test data paths. (#375)	2021-03-24 18:18:01 +00:00
qualimap/bamqc	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
quast	update tests for new config (#384)	2021-04-01 20:22:06 +01:00
rapidnj	add rapidnj module (#421)	2021-04-09 13:04:54 +01:00
rasusa	new module: rasusa (#413)	2021-04-09 13:10:32 +01:00
salmon	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
samtools	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
seacr/callpeak	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
seqkit/split2	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
sequenzautils	Update and check tests are running for all modules (#420)	2021-04-09 13:47:05 +01:00
seqwish/induce	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
shovill	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
snpsites	New Snpsites module (#416)	2021-04-09 08:00:33 +01:00
spades	Version bumps and minor module updates (#406)	2021-04-06 13:38:41 +01:00
star	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
strelka/germline	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
stringtie	Update and check tests are running for all modules (#420)	2021-04-09 13:47:05 +01:00
subread/featurecounts	Update and check tests are running for all modules (#420)	2021-04-09 13:47:05 +01:00
tabix	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
tiddit/sv	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
trimgalore	Fix a bunch of failing tests after switching to test config (#378)	2021-03-24 18:28:54 +00:00
ucsc	Update and check tests are running for all modules (#420)	2021-04-09 13:47:05 +01:00
unicycler	update tests for new config (#384)	2021-04-01 20:22:06 +01:00
untar	Fix some module tests after switching to config data (#386)	2021-03-24 18:28:07 +00:00
vcftools	Fixing vcftools and bismark tests (#383)	2021-03-25 09:12:08 +00:00
yara	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00