..
abacas
Move assembly test files from genome to illumina ( #441 )
2021-04-13 12:52:11 +02:00
adapterremoval
remove deprecated test tags ( #440 )
2021-04-13 18:03:09 +01:00
allelecounter
Update test data paths. ( #375 )
2021-03-24 18:18:01 +00:00
artic /guppyplex
Add artic guppyplex ( #455 )
2021-04-27 15:57:34 +01:00
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
Fixes for nanoseq modules ( #479 )
2021-04-30 15:57:43 +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
remove deprecated test tags ( #440 )
2021-04-13 18:03:09 +01:00
bowtie2
remove deprecated test tags ( #440 )
2021-04-13 18:03:09 +01:00
bwa
remove deprecated test tags ( #440 )
2021-04-13 18:03:09 +01:00
bwamem2
remove deprecated test tags ( #440 )
2021-04-13 18:03:09 +01:00
bwameth
Lint modules ci ( #389 )
2021-04-08 09:10:52 +01:00
cat /fastq
remove deprecated test tags ( #440 )
2021-04-13 18:03:09 +01:00
cnvkit
Update test data paths. ( #375 )
2021-03-24 18:18:01 +00:00
cutadapt
remove deprecated test tags ( #440 )
2021-04-13 18:03:09 +01:00
deeptools
Finish deeptools modules ( #442 )
2021-04-13 21:48:43 +01:00
dshbio
Update dsh-bio modules to version 2.0.4 ( #482 )
2021-05-04 14:28:44 +01:00
fastp
remove deprecated test tags ( #440 )
2021-04-13 18:03:09 +01:00
fastqc
remove deprecated test tags ( #440 )
2021-04-13 18:03:09 +01:00
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
remove deprecated test tags ( #440 )
2021-04-13 18:03:09 +01:00
gffread
Fixing a bunch of module tests ( #370 )
2021-03-24 17:36:29 +00:00
graphmap2
add graphmap index and align modules (from nanoseq modules) ( #468 )
2021-04-30 13:18:58 +01:00
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
remove deprecated test tags ( #440 )
2021-04-13 18:03:09 +01:00
hmmer /hmmalign
New module to use hmmalign from HMMER to align sequences ( #470 )
2021-04-28 11:21:24 +01:00
homer /annotatepeaks
Lint modules ci ( #389 )
2021-04-08 09:10:52 +01:00
iqtree
add new iqtree module ( #427 )
2021-04-12 09:45:56 +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
Added kallistobustools/count ( #409 )
2021-04-30 07:27:17 +02:00
kraken2 /run
Add kraken2 pigz multi-tool container for compressing output fastq files ( #434 )
2021-04-12 18:47:34 +02:00
last /lastdb
New last/lastdb module to index sequences before alignment. ( #476 )
2021-05-02 11:36:31 +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
Fixes for nanoseq modules ( #479 )
2021-04-30 15:57:43 +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
nanolyse
add nanolyse module (from nanoseq modules) ( #471 )
2021-05-05 11:20:09 +01:00
nanoplot
Nanoplot and sequencing_summary.txt for Nanopore test data ( #364 )
2021-04-09 08:31:38 +01:00
nextclade
Add Nextclade module ( #484 )
2021-05-06 15:48:15 +01:00
optitype
update tests for new config ( #384 )
2021-04-01 20:22:06 +01:00
pangolin
Add Nextclade module ( #484 )
2021-05-06 15:48:15 +01:00
picard
remove deprecated test tags ( #440 )
2021-04-13 18:03:09 +01:00
plasmidid
Bump plasmidid version ( #460 )
2021-04-26 12:40:38 +02:00
preseq /lcextrap
Update modules required for rnaseq pipeline ( #449 )
2021-04-16 08:56:47 +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
pycoqc
Add pycoqc module ( #424 )
2021-04-12 10:52:14 +01:00
qcat
Fixes for nanoseq modules ( #479 )
2021-04-30 15:57:43 +01:00
qualimap /bamqc
Lint modules ci ( #389 )
2021-04-08 09:10:52 +01:00
quast
remove deprecated test tags ( #440 )
2021-04-13 18:03:09 +01:00
rapidnj
add rapidnj module ( #421 )
2021-04-09 13:04:54 +01:00
rasusa
🧸 Updated rasusa ( #437 )
2021-04-12 21:47:55 +01:00
raxmlng
Raxmlng ( #474 )
2021-04-29 08:20:05 +01:00
rseqc
Finish rseqc modules ( #439 )
2021-04-13 08:49:32 +01:00
salmon
remove deprecated test tags ( #440 )
2021-04-13 18:03:09 +01:00
samtools
Update modules required for rnaseq pipeline ( #449 )
2021-04-16 08:56:47 +01:00
seacr /callpeak
Lint modules ci ( #389 )
2021-04-08 09:10:52 +01:00
seqkit /split2
remove deprecated test tags ( #440 )
2021-04-13 18:03:09 +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
remove deprecated test tags ( #440 )
2021-04-13 18:03:09 +01:00
snpsites
New Snpsites module ( #416 )
2021-04-09 08:00:33 +01:00
spades
remove deprecated test tags ( #440 )
2021-04-13 18:03:09 +01:00
star
Update modules required for rnaseq pipeline ( #449 )
2021-04-16 08:56:47 +01:00
strelka /germline
Lint modules ci ( #389 )
2021-04-08 09:10:52 +01:00
stringtie
Add stringtie merge module (from nanoseq modules) ( #475 )
2021-05-03 07:18:51 +02:00
subread /featurecounts
remove deprecated test tags ( #440 )
2021-04-13 18:03:09 +01:00
tabix
remove deprecated test tags ( #440 )
2021-04-13 18:03:09 +01:00
tiddit /sv
remove deprecated test tags ( #440 )
2021-04-13 18:03:09 +01:00
trimgalore
Fix a bunch of failing tests after switching to test config ( #378 )
2021-03-24 18:28:54 +00:00
ucsc
Add ucsc/bedclip module ( #450 )
2021-04-15 22:04:59 +02:00
unicycler
remove deprecated test tags ( #440 )
2021-04-13 18:03:09 +01:00
untar
Fix some module tests after switching to config data ( #386 )
2021-03-24 18:28:07 +00:00
vcftools
remove deprecated test tags ( #440 )
2021-04-13 18:03:09 +01:00
yara
remove deprecated test tags ( #440 )
2021-04-13 18:03:09 +01:00
b6e4ecabba