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nf-core_modules/tests/software
History
arontommi 86bb832fae
Strelka germline (#340) 
* nf-core template created

* boilerplate and sarek_dsl2 code merged

* adding an option to give it args

* bai got away

* seperating vcf files and vcf index files into seperate streams

* some minor spacefixes

* adding standard information about the module

* removing typos

* some basic tests based on tiddit tests

* removed the bed parameter, should be provided via options.args instead

* removing typos

* adding indexed bam file instead

* Adding changing out fasta with reference to deal with empty fasta input

* adding the correct fasta

* removing the empty test

* adding the correct data to the testoutput and removing the md5sum since
it constantly changes

* adding  target_bed to input

* adding info on target bed

* adding target bed to test

* adding more files to the test

* adding meta for target bed test

* adding a test for target_bed

* typo

* fixing pytest with master
2021-03-24 05:07:29 +00:00
..
adapterremoval new module: AdapterRemoval (#309) 2021-03-22 17:16:04 +00:00
allelecounter Add alleleCounter module (#313) 2021-03-23 14:37:53 +01:00
bandage/image Converge test data usage (#249) 2021-03-04 10:10:57 +00:00
bcftools Exchange VCF data by sarscov2 data (#261) 2021-03-09 10:04:08 +01:00
bedtools Converge test data usage (#249) 2021-03-04 10:10:57 +00:00
bismark bismark: remove underscores from process names (#303) 2021-03-22 17:46:11 +01:00
blast Converge test data usage (#249) 2021-03-04 10:10:57 +00:00
bowtie Add default output dir for modules that create indices, updated (#336) 2021-03-23 17:55:01 +00:00
bowtie2 Add default output dir for modules that create indices, updated (#336) 2021-03-23 17:55:01 +00:00
bwa Add default output dir for modules that create indices, updated (#336) 2021-03-23 17:55:01 +00:00
bwamem2 Add default output dir for modules that create indices, updated (#336) 2021-03-23 17:55:01 +00:00
bwameth Add default output dir for modules that create indices, updated (#336) 2021-03-23 17:55:01 +00:00
cat/fastq Converge test data usage (#249) 2021-03-04 10:10:57 +00:00
cnvkit cnvkit module (#173) 2021-03-22 15:27:30 -07:00
cutadapt Converge test data usage (#249) 2021-03-04 10:10:57 +00:00
dsh Converge test data usage (#249) 2021-03-04 10:10:57 +00:00
fastp Converge test data usage (#249) 2021-03-04 10:10:57 +00:00
fastqc Converge test data usage (#249) 2021-03-04 10:10:57 +00:00
flash add flash module (#341) 2021-03-24 05:05:45 +00:00
gatk4 Add gatk4/baserecalibrator (#327) 2021-03-23 18:32:37 +01:00
gffread Converge test data usage (#249) 2021-03-04 10:10:57 +00:00
gunzip Converge test data usage (#249) 2021-03-04 10:10:57 +00:00
homer/annotatepeaks Homer (#330) 2021-03-23 11:24:54 -07:00
ivar Converge test data usage (#249) 2021-03-04 10:10:57 +00:00
kraken2/run Add kraken2 run module (#266) 2021-03-18 13:08:06 +00:00
methyldackel Converge test data usage (#249) 2021-03-04 10:10:57 +00:00
minia Adding minia for viralrecon (#267) 2021-03-17 12:54:15 +01:00
minimap2/align Converge test data usage (#249) 2021-03-04 10:10:57 +00:00
mosdepth Converge test data usage (#249) 2021-03-04 10:10:57 +00:00
multiqc Converge test data usage (#249) 2021-03-04 10:10:57 +00:00
optitype Add in OptiType (configbuilder, type) module(s) (#301) 2021-03-23 16:48:05 +01:00
pangolin add task.cpus to pangolin (#263) 2021-03-10 09:02:23 +01:00
picard add picard_collectwgsmetrics (#304) 2021-03-22 17:05:59 +01:00
preseq/lcextrap Fix preseq tests 2021-02-03 17:28:44 +00:00
prodigal Prodigal (#333) 2021-03-23 11:03:58 -07:00
prokka add prokka module (#298) 2021-03-23 02:51:23 -07:00
qualimap/bamqc Remove def from module options definition in main (#270) 2021-03-15 12:16:43 +00:00
quast Converge test data usage (#249) 2021-03-04 10:10:57 +00:00
salmon Add default output dir for modules that create indices, updated (#336) 2021-03-23 17:55:01 +00:00
samtools modified the samtools/fastq module (#339) 2021-03-23 17:43:52 +00:00
seacr/callpeak Converge test data usage (#249) 2021-03-04 10:10:57 +00:00
seqkit/split2 Remove def from module options definition in main (#270) 2021-03-15 12:16:43 +00:00
sequenzautils/gcwiggle PR for sequenzautils/gcwiggle (#345) 2021-03-24 05:03:03 +00:00
seqwish/induce Converge test data usage (#249) 2021-03-04 10:10:57 +00:00
shovill Update shovill module (#337) 2021-03-24 04:57:41 +00:00
spades Add spades module (#277) 2021-03-18 13:48:38 +00:00
star Add default output dir for modules that create indices, updated (#336) 2021-03-23 17:55:01 +00:00
strelka/germline Strelka germline (#340) 2021-03-24 05:07:29 +00:00
stringtie Converge test data usage (#249) 2021-03-04 10:10:57 +00:00
tabix Exchange VCF data by sarscov2 data (#261) 2021-03-09 10:04:08 +01:00
tiddit/sv Update main.nf (#314) 2021-03-22 17:16:43 +00:00
trimgalore Converge test data usage (#249) 2021-03-04 10:10:57 +00:00
ucsc ucsc_bed12tobigbed (previous pull request had conflicts) (#302) 2021-03-24 04:55:49 +00:00
unicycler Adding unicycler module (#307) 2021-03-22 18:14:24 +01:00
untar Converge test data usage (#249) 2021-03-04 10:10:57 +00:00
vcftools add vcftools module (#334) 2021-03-24 04:54:23 +00:00