Anthony Underwood 6927f1d086 New Snpsites module (#416) ... * new gubbins module * new gubbins module * new gubbins module * Update software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gubbins/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * new gubbins module * new gubbins module * new gubbins module * new gubbins module * new gubbins module * new gubbins module * new gubbins module * Update tests/config/test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * new gubbins module * new gubbins module * new snpsites module * new snpsites module * new snpsites module * new snpsites module * adding fasttree module * correct trailing whitespace * using sarscov2 as a test dir * use sars-cov-2 alignment * remove old test alignment * new snpsites module * new snpsites module * new snpsites module * updated test file names * new snpsites module * revert to gubbins test on upstream * add new lines * renove whitespace * Apply suggestions from code review Co-authored-by: avantonder <avt@sanger.ac.uk> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: avantonder <ajv37@cam.ac.uk>		2021-04-09 08:00:33 +01:00
..
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	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/report: allow missing input data (#400)	2021-04-06 10:59:00 +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	Update test paths in bwa mappers (#387)	2021-03-25 09:24:21 +00:00
bwamem2	Update test paths in bwa mappers (#387)	2021-03-25 09:24:21 +00:00
bwameth	update bwameth container build to match conda version (#402)	2021-04-06 10:45:14 +01:00
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
fasttree	adding fasttree module (#412)	2021-04-08 18:15:23 +01:00
fgbio	New modules: Fgbio callmolecularconsensusreads and sortbam (#352)	2021-03-28 20:38:50 +01:00
flash	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
gatk4	gatk4 markduplicates (#356)	2021-03-26 23:25:40 +00:00
gffread	Fix nf-core modules lint tests (#275)	2021-03-16 17:16:47 +00:00
gubbins	new module: gubbins (#377)	2021-04-07 16:31:24 +01:00
gunzip	remove params section from meta.yml (#282)	2021-03-19 13:16:50 +01:00
hisat2	Add tests for hisat2 (#366)	2021-03-25 21:08:46 +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: fix version scraping (#401)	2021-04-06 10:59:33 +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
msisensor	Add module: nf-core hackathon #207 : new module: msisensor/msi (#343)	2021-03-25 16:46:00 -04:00
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	Version bumps and minor module updates (#406)	2021-04-06 13:38:41 +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
plasmidid	Add plasmidid module (#410)	2021-04-08 22:44:30 +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	Version bumps and minor module updates (#406)	2021-04-06 13:38:41 +01:00
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	PR for sequenzautils/bam2seqz (#395)	2021-04-01 07:08:27 +02:00
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
snpsites	New Snpsites module (#416)	2021-04-09 08:00:33 +01:00
sortmerna	Remove def from module options definition in main (#270)	2021-03-15 12:16:43 +00:00
spades	Version bumps and minor module updates (#406)	2021-04-06 13:38:41 +01:00
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	Add tests for subread #106 (#393)	2021-04-01 20:02:36 +01:00
tabix	Fix tabix/bgzip version command (#407)	2021-04-07 08:39:53 +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