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nf-core_modules/tests/software
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Harshil Patel 5e18e36895
Update and check tests are running for all modules (#420) 
* Fixes for PR 371

* Fix tags

* Add md5sum

* Add md5sums for stringtie

* Fix tests for modules where subtool = build

* Fix pytest_software name conflicts

* Change _ to / in test.yml tags

* Nope...that didnt work

* Fix sequenzautils/bam2seqz tests
2021-04-09 13:47:05 +01:00
..
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
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