millironx/nf-core_modules
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nf-core_modules/tests/modules
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James A. Fellows Yates e971f538a9
Module new version reporting fixes (#753) 
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Fix IQ tree

* Fix picard markdup and merge sam

* Fix plink/vcf version

* Fix plink version output

* Fix prokka version command

* Fix pydamage

* Try fixing markduplicates

* Fix snpEff

* Fix vcftools version

* Fix pydamage and filtersamreads test run

* Fix MarkDuplicates tests

* Add missing unsorted checks

* Remove MD5 sym due to stochasicity in BAM file
2021-09-28 10:51:19 +01:00
..
abacas Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
adapterremoval Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
agrvate module for agrvate (#693) 2021-09-16 12:42:23 +02:00
allelecounter Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
arriba Added module arriba (#611) 2021-07-22 15:19:42 +01:00
artic Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
bamaligncleaner Add module: bamaligncleaner (#676) 2021-09-15 10:31:49 +02:00
bandage/image Fix version commands (#749) 2021-09-27 22:10:37 +01:00
bbmap Fix version commands (#749) 2021-09-27 22:10:37 +01:00
bcftools Add bcftools/query module (#670) 2021-09-14 09:19:01 +02:00
bedtools Add bedtools/makewindows module (#658) 2021-09-07 14:36:06 -04:00
bismark Fix version commands (#749) 2021-09-27 22:10:37 +01:00
blast nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
bowtie Fix version commands (#749) 2021-09-27 22:10:37 +01:00
bowtie2 Fix version commands (#749) 2021-09-27 22:10:37 +01:00
bwa Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
bwamem2 Fix version commands (#749) 2021-09-27 22:10:37 +01:00
bwameth Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
cat Refactor cat/cat module (#723) 2021-09-21 11:17:00 +01:00
chromap Chromap Module (#659) 2021-09-15 17:20:55 +01:00
cnvkit Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
cooler Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
cutadapt Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
damageprofiler Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
deeptools nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
delly/call Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
diamond Diamond (#710) 2021-09-23 09:13:04 +01:00
dragonflye add module for dragonflye (#633) 2021-08-16 11:51:30 +02:00
dshbio Add dsh-bio export-segments module (#631) 2021-08-17 15:53:41 +02:00
ensemblvep Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
expansionhunter Expansionhunter (#666) 2021-08-16 17:47:42 +02:00
fastani module fastani (#695) 2021-09-21 20:20:26 +01:00
fastp enhance module fastp: add save_merged (#598) (#614) 2021-07-23 10:44:00 +01:00
fastqc Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
fasttree Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
fgbio Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
flash Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
gatk4 Update for mutect2: add output channel for stats file (#716) 2021-09-17 09:56:56 +01:00
genmap Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
gffread Fix bug in gffread (#686) 2021-09-15 19:55:08 +01:00
glnexus Add glnexus (#729) 2021-09-22 13:31:01 +01:00
graphmap2 Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
gubbins nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
gunzip Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
hifiasm Add hifiasm module (#596) 2021-07-20 21:50:22 +01:00
hisat2 nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
hmmer/hmmalign Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
homer Homer Modules (#75) 2021-09-08 15:40:34 +00:00
iqtree Module new version reporting fixes (#753) 2021-09-28 10:51:19 +01:00
ivar Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
kallisto/index Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
kallistobustools nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
kleborate Add module kleborate (#711) 2021-09-21 20:45:42 +01:00
kraken2/kraken2 Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
last nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
lima New module: LIMA (#719) 2021-09-27 16:14:35 +01:00
lofreq fix: lofreq/callparallel missing arg (#562) (#586) 2021-07-19 09:19:27 +01:00
malt update: MALT build version bump (#699) 2021-09-15 16:46:29 +01:00
maltextract add: MALTEXTRACT (#725) 2021-09-21 19:57:27 +01:00
mash/sketch Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
metaphlan3 Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
methyldackel Fix version commands (#749) 2021-09-27 22:10:37 +01:00
minia Fix version commands (#749) 2021-09-27 22:10:37 +01:00
minimap2 nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
mosdepth Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
msisensor Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
multiqc Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
muscle Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
nanolyse Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
nanoplot Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
nextclade Update Nextclade to output all files by default (#638) 2021-07-28 19:49:50 +01:00
optitype Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
pairix Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
pairtools Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
pangolin Update pangolin to 3.1.11 (#721) 2021-09-20 19:59:05 +01:00
pbccs new module: pbccs (#688) 2021-09-16 11:48:18 +01:00
picard Module new version reporting fixes (#753) 2021-09-28 10:51:19 +01:00
plasmidid Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
plink/vcf Adding plink/vcf module (#656) 2021-09-14 08:51:40 +02:00
preseq/lcextrap Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
prodigal Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
prokka Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
pycoqc Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
pydamage Module new version reporting fixes (#753) 2021-09-28 10:51:19 +01:00
qcat Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
qualimap/bamqc Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
quast Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
rapidnj Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
rasusa Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
raxmlng Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
rsem Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
rseqc Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
salmon Fix version commands (#749) 2021-09-27 22:10:37 +01:00
samtools Fix version commands (#749) 2021-09-27 22:10:37 +01:00
seacr/callpeak Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
seqkit/split2 Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
seqtk Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
sequenzautils Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
seqwish/induce Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
shovill Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
snpdists module: snp-dists (#697) 2021-09-15 16:36:49 +01:00
snpeff Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
snpsites Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
spades nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
staphopiasccmec add staphopia-sccmec module (#702) 2021-09-15 17:24:11 +01:00
star Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
strelka/germline Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
stringtie Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
subread/featurecounts Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
tabix nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
tiddit/sv Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
trimgalore Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
ucsc Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
unicycler Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
untar Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
unzip Unzip update (#730) 2021-09-22 11:02:32 +01:00
variantbam Add variantbam (#618) 2021-07-26 19:07:29 +01:00
vcftools Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
yara Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00