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nf-core_modules/tests/software
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Mei Wu 3f4eccbf0f
Delly/call (#565) 
* testing works but need to fix paths and add exclude list

* edited meta file and removed TODOs

* left over TODOs

* test passed, final push

* resolving initial comments

* Update software/delly/call/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-06 12:54:14 +01:00
..
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 Fix linting failures (#552) 2021-07-01 19:50:14 +01:00
bowtie2 Fix linting failures (#552) 2021-07-01 19:50:14 +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 Modules TLC (#551) 2021-07-01 16:13:01 +01:00
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
damageprofiler damageprofiler (#545) 2021-06-30 09:46:24 +02:00
deeptools Finish deeptools modules (#442) 2021-04-13 21:48:43 +01:00
delly/call Delly/call (#565) 2021-07-06 12:54:14 +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 Modules TLC (#551) 2021-07-01 16:13:01 +01:00
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 Fix linting failures (#552) 2021-07-01 19:50:14 +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/kraken2 Modules TLC (#551) 2021-07-01 16:13:01 +01:00
last Input a triple (id, fasta, params) to last/lastal (#563) 2021-07-06 09:35:04 +01:00
lofreq Lofreq call (#564) 2021-07-06 10:41:00 +01:00
mash/sketch 🏋️‍♀️ new submodule mash/sketch🕺 (#426) 2021-04-10 16:24:23 +01:00
metaphlan3 Add metaphlan3 module (#543) 2021-06-25 08:15:15 +02:00
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
muscle update muscle (#542) 2021-06-28 08:20:02 +02:00
nanolyse Modules TLC (#551) 2021-07-01 16:13:01 +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 select (#523) 2021-06-23 15:58:31 +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
rsem Fix rsem (#555) 2021-07-02 13:09:48 +02:00
rseqc fix rseqc/junctionsaturation (#553) 2021-07-02 13:31:09 +02:00
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 Modules TLC (#551) 2021-07-01 16:13:01 +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 Add modules bgziptabix (#544) 2021-06-25 10:52:02 +02:00
tiddit/sv Modules TLC (#551) 2021-07-01 16:13:01 +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