Mark-S-Hill 889465cb2b update test data paths (#373) ... * update test data paths * Update test md5sums * gatk test fixes & update variantfiltration main * few extra fixes after review * fix suspected format error * Update software/gatk4/variantfiltration/main.nf * Update software/gatk4/variantfiltration/main.nf * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>		2021-03-24 18:14:11 +00:00
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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	remove params section from meta.yml (#282)	2021-03-19 13:16:50 +01:00
bcftools	remove params section from meta.yml (#282)	2021-03-19 13:16:50 +01:00
bedtools	remove params section from meta.yml (#282)	2021-03-19 13:16:50 +01:00
bismark	bismark: remove underscores from process names (#303)	2021-03-22 17:46:11 +01:00
blast	remove params section from meta.yml (#282)	2021-03-19 13:16:50 +01:00
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	remove params section from meta.yml (#282)	2021-03-19 13:16:50 +01:00
cnvkit	cnvkit module (#173)	2021-03-22 15:27:30 -07:00
cutadapt	remove params section from meta.yml (#282)	2021-03-19 13:16:50 +01:00
deeptools	Remove def from module options definition in main (#270)	2021-03-15 12:16:43 +00:00
dsh	remove params section from meta.yml (#282)	2021-03-19 13:16:50 +01:00
fastp	remove params section from meta.yml (#282)	2021-03-19 13:16:50 +01:00
fastqc	remove params section from meta.yml (#282)	2021-03-19 13:16:50 +01:00
flash	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
gatk4	update test data paths (#373)	2021-03-24 18:14:11 +00:00
gffread	Fix nf-core modules lint tests (#275)	2021-03-16 17:16:47 +00:00
gunzip	remove params section from meta.yml (#282)	2021-03-19 13:16:50 +01:00
hisat2	Add default output dir for modules that create indices, updated (#336)	2021-03-23 17:55:01 +00:00
homer/annotatepeaks	Homer (#330)	2021-03-23 11:24:54 -07:00
ivar	remove params section from meta.yml (#282)	2021-03-19 13:16:50 +01:00
kallisto/index	Add module kallisto/index (#357)	2021-03-24 12:25:39 +00:00
kraken2/run	Add kraken2 run module (#266)	2021-03-18 13:08:06 +00:00
lib	style(#77): Fix editorconfig errors	2020-12-17 17:50:24 -06:00
macs2/callpeak	Remove def from module options definition in main (#270)	2021-03-15 12:16:43 +00:00
methyldackel	methyldackel: bump version to 0.5.2 (#305)	2021-03-22 17:46:28 +01:00
minia	remove params section from meta.yml (#282)	2021-03-19 13:16:50 +01:00
minimap2/align	remove params section from meta.yml (#282)	2021-03-19 13:16:50 +01:00
mosdepth	remove params section from meta.yml (#282)	2021-03-19 13:16:50 +01:00
multiqc	remove params section from meta.yml (#282)	2021-03-19 13:16:50 +01:00
optitype	Add in OptiType (configbuilder, type) module(s) (#301)	2021-03-23 16:48:05 +01:00
pangolin	remove params section from meta.yml (#282)	2021-03-19 13:16:50 +01:00
phantompeakqualtools	Remove def from module options definition in main (#270)	2021-03-15 12:16:43 +00:00
picard	add picard_collectwgsmetrics (#304)	2021-03-22 17:05:59 +01:00
preseq/lcextrap	Remove def from module options definition in main (#270)	2021-03-15 12:16:43 +00:00
prodigal	Prodigal (#333)	2021-03-23 11:03:58 -07:00
prokka	Add process label to prokka (#350)	2021-03-24 04:54:52 +00:00
qualimap	remove params section from meta.yml (#282)	2021-03-19 13:16:50 +01:00
quast	remove params section from meta.yml (#282)	2021-03-19 13:16:50 +01:00
rsem	Add default output dir for modules that create indices, updated (#336)	2021-03-23 17:55:01 +00:00
rseqc	Remove def from module options definition in main (#270)	2021-03-15 12:16:43 +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	remove params section from meta.yml (#282)	2021-03-19 13:16:50 +01:00
seqkit/split2	remove params section from meta.yml (#282)	2021-03-19 13:16:50 +01:00
sequenzautils/gcwiggle	PR for sequenzautils/gcwiggle (#345)	2021-03-24 05:03:03 +00:00
seqwish/induce	remove params section from meta.yml (#282)	2021-03-19 13:16:50 +01:00
shovill	Update shovill module (#337)	2021-03-24 04:57:41 +00:00
sortmerna	Remove def from module options definition in main (#270)	2021-03-15 12:16:43 +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	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
stringtie	Remove def from module options definition in main (#270)	2021-03-15 12:16:43 +00:00
subread/featurecounts	Remove def from module options definition in main (#270)	2021-03-15 12:16:43 +00:00
tabix	remove params section from meta.yml (#282)	2021-03-19 13:16:50 +01:00
tiddit/sv	remove params section from meta.yml (#282)	2021-03-19 13:16:50 +01:00
trimgalore	remove params section from meta.yml (#282)	2021-03-19 13:16:50 +01:00
ucsc	ucsc_bed12tobigbed (previous pull request had conflicts) (#302)	2021-03-24 04:55:49 +00:00
umitools	Remove def from module options definition in main (#270)	2021-03-15 12:16:43 +00:00
unicycler	Adding unicycler module (#307)	2021-03-22 18:14:24 +01:00
untar	remove params section from meta.yml (#282)	2021-03-19 13:16:50 +01:00
vcftools	add vcftools module (#334)	2021-03-24 04:54:23 +00:00
yara	Add YARA module (#353)	2021-03-24 17:14:52 +01:00