millironx/nf-core_modules
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nf-core_modules/software
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Robert A. Petit III c2aa95cb6c
add prokka module (#298) 
* add prokka module

* adjust test outputs

* fix prokka command

* adjust test outputs

* handle optional input

* update pytest

* update pytest

* adjust test outputs

* adjust test outputs

* switch to lists for optional inputs, add md5sums for non-timestamped outputs

* add optional prodigal training file

* add optional prodigal training info to meta yaml
2021-03-23 02:51:23 -07:00
..
adapterremoval new module: AdapterRemoval (#309) 2021-03-22 17:16:04 +00:00
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 remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
bowtie2 remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
bwa remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
bwamem2 remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
bwameth remove params section from meta.yml (#282) 2021-03-19 13:16:50 +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
gatk4 add gatk4/fastqtosam #198 (#311) 2021-03-22 18:26:02 +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 Fix nf-core modules lint tests (#275) 2021-03-16 17:16:47 +00:00
homer/annotatepeaks Remove def from module options definition in main (#270) 2021-03-15 12:16:43 +00:00
ivar remove params section from meta.yml (#282) 2021-03-19 13:16:50 +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: 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
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
prokka add prokka module (#298) 2021-03-23 02:51:23 -07:00
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 Remove def from module options definition in main (#270) 2021-03-15 12:16:43 +00:00
rseqc Remove def from module options definition in main (#270) 2021-03-15 12:16:43 +00:00
salmon remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
samtools add samtools merge (#296) 2021-03-22 13:48:23 +01:00
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
seqwish/induce remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
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 remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
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/bedgraphtobigwig Remove def from module options definition in main (#270) 2021-03-15 12:16:43 +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