..
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
Add artic minion ( #486 )
2021-05-07 16:37:35 +01:00
bandage /image
Lint modules ci ( #389 )
2021-04-08 09:10:52 +01:00
bbmap /bbduk
Bbmap/bbduk ( #487 )
2021-05-10 11:45:52 +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
Fix 459 ( #534 )
2021-06-14 12:24:59 +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
Fix number of cpus for modules with piped tools ( #499 )
2021-05-18 09:52:00 +02:00
bwamem2
Fix number of cpus for modules with piped tools ( #499 )
2021-05-18 09:52:00 +02:00
bwameth
Update comments with new style ( #497 )
2021-05-12 14:56:46 +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
cooler
Cooler digest ( #517 )
2021-06-09 11:39:22 +02:00
cutadapt
Update comments with new style ( #497 )
2021-05-12 14:56:46 +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
Update comments with new style ( #497 )
2021-05-12 14:56:46 +01:00
fastqc
Update comments with new style ( #497 )
2021-05-12 14:56:46 +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
Intervallisttools ( #491 )
2021-05-12 11:44:36 +02:00
genmap
add genmap/mappability ( #509 )
2021-05-25 22:12:10 +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
Update last module ( #533 )
2021-06-14 12:27:27 +01:00
mash /sketch
🏋️♀️ new submodule mash/sketch 🕺 ( #426 )
2021-04-10 16:24:23 +01:00
methyldackel
Fix 459 ( #534 )
2021-06-14 12:24:59 +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
Fix 459 ( #534 )
2021-06-14 12:24:59 +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
Bump new nextclade version (0.14.4) ( #532 )
2021-06-09 14:12:21 +01:00
optitype
update tests for new config ( #384 )
2021-04-01 20:22:06 +01:00
pairix
add software/pairix ( #508 )
2021-05-25 21:22:57 +01:00
pairtools
Pairtools restrict ( #522 )
2021-06-10 19:39:35 +02:00
pangolin
Pangolin bump new version (3.0.5) ( #531 )
2021-06-09 14:11:59 +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 comments with new style ( #497 )
2021-05-12 14:56:46 +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
Update comments with new style ( #497 )
2021-05-12 14:56:46 +01:00
rseqc
Finish rseqc modules ( #439 )
2021-04-13 08:49:32 +01:00
salmon
Update salmon/quant to provide '--libType A' option ( #536 )
2021-06-17 15:13:47 +02:00
samtools
Update samtools from 1.10 to 1.12 ( #530 )
2021-06-07 13:07:32 +02:00
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
seqtk
Feat seqtk update ( #503 )
2021-06-14 12:23:15 +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
Snpsites ( #480 )
2021-05-06 16:05:07 +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
Update comments with new style ( #497 )
2021-05-12 14:56:46 +01:00
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
Update comments with new style ( #497 )
2021-05-12 14:56:46 +01:00
ucsc
add additional ucsc tools ( #506 )
2021-05-20 15:39:33 -04:00
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
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