nf-core_modules

mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-12-22 02:58:17 +00:00

History

Florian Wuennemann 0f53c3b96b Added kallistobustools/ref (#408 ) * Added kallistobustools/ref. Local tests all passing with Docker. Linting passed. Test data currently in /tests/data/delete_me * Removed trailing whitespace line 29 * Moved workflow from meta to options. * Update main.nf * Forgot to remove previous testing input channel for workflow. * Apply suggestions from code review Applied changes suggested by @drpatelh Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Added gtf to meta.yml. * Apply suggestions from code review Adding @drpatelh suggested changes. Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Moved workflow to input value. Fixed tests. * Update tests/software/kallistobustools/ref/test.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>		2021-04-09 09:41:41 +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
kallistobustools/ref	Added kallistobustools/ref (#408 )	2021-04-09 09:41:41 +01:00
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
nanoplot	Nanoplot and sequencing_summary.txt for Nanopore test data (#364 )	2021-04-09 08:31:38 +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