millironx/nf-core_modules
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nf-core_modules/modules
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James A. Fellows Yates 01cc326c23
add Amps (#768) 
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Start work, continue once on non-mobile internet

* finished and working on conda

* Update modules/amps/main.nf

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Apply suggestions from code review

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-09-30 12:54:16 +02:00
..
abacas Fix version commands (#749) 2021-09-27 22:10:37 +01:00
adapterremoval Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
agrvate Fix version commands (#749) 2021-09-27 22:10:37 +01:00
allelecounter Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
amps add Amps (#768) 2021-09-30 12:54:16 +02:00
arriba Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
artic Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
bamaligncleaner Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
bandage/image Fix version commands (#749) 2021-09-27 22:10:37 +01:00
bbmap Fix version commands: round 3 (#754) 2021-09-28 14:37:47 +01:00
bcftools Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
bedtools Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
bismark Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
blast Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
bowtie remove cpu restrictions (#760) 2021-09-30 10:26:52 +02:00
bowtie2 remove cpu restrictions (#760) 2021-09-30 10:26:52 +02:00
bwa remove cpu restrictions (#760) 2021-09-30 10:26:52 +02:00
bwamem2 remove cpu restrictions (#760) 2021-09-30 10:26:52 +02:00
bwameth remove cpu restrictions (#760) 2021-09-30 10:26:52 +02:00
cat Fix flash and cat/fastq modules (#759) 2021-09-28 21:14:11 +01:00
chromap few version and test data config fixes (#758) 2021-09-28 20:42:04 +01:00
cnvkit Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
cooler Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
custom/dumpsoftwareversions Dump version for /custom/dumpsoftwareversions module itself (#764) 2021-09-30 09:00:33 +01:00
cutadapt Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
damageprofiler Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
deeptools Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
delly/call few version and test data config fixes (#758) 2021-09-28 20:42:04 +01:00
diamond Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
dragonflye Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
dshbio Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
ensemblvep few version and test data config fixes (#758) 2021-09-28 20:42:04 +01:00
expansionhunter few version and test data config fixes (#758) 2021-09-28 20:42:04 +01:00
fastani Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
fastp Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
fastqc Update fastqc to produce multi-version versions.yml (#665) 2021-09-24 10:01:54 +01:00
fasttree Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
fgbio few version and test data config fixes (#758) 2021-09-28 20:42:04 +01:00
flash Fix flash and cat/fastq modules (#759) 2021-09-28 21:14:11 +01:00
gatk4 Fix version commands (#749) 2021-09-27 22:10:37 +01:00
genmap Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
gffread Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
glnexus few version and test data config fixes (#758) 2021-09-28 20:42:04 +01:00
graphmap2 Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
gubbins Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
gunzip Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
hifiasm Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
hisat2 Fix version commands: round 3 (#754) 2021-09-28 14:37:47 +01:00
hmmer/hmmalign Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
homer Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
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 Fix yml ver (#756) 2021-09-28 18:33:07 +02:00
kallistobustools Fix yml ver (#756) 2021-09-28 18:33:07 +02:00
kleborate few version and test data config fixes (#758) 2021-09-28 20:42:04 +01:00
kraken2/kraken2 Fix version commands: round 3 (#754) 2021-09-28 14:37:47 +01:00
last Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
lib Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
lima New module: LIMA (#719) 2021-09-27 16:14:35 +01:00
lofreq Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
macs2/callpeak Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
malt Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
maltextract Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
mash/sketch Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
metaphlan3 Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
methyldackel Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
minia few version and test data config fixes (#758) 2021-09-28 20:42:04 +01:00
minimap2 Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
mosdepth Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
msisensor Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
multiqc Update fastqc to produce multi-version versions.yml (#665) 2021-09-24 10:01:54 +01:00
muscle Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
nanolyse Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
nanoplot Fix yml ver (#756) 2021-09-28 18:33:07 +02:00
nextclade Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
optitype Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
pairix Fix yml ver (#756) 2021-09-28 18:33:07 +02:00
pairtools Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
pangolin Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
pbccs Fix yml ver (#756) 2021-09-28 18:33:07 +02:00
phantompeakqualtools Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
picard Module new version reporting fixes (#753) 2021-09-28 10:51:19 +01:00
plasmidid Fix yml ver (#756) 2021-09-28 18:33:07 +02:00
plink/vcf Module new version reporting fixes (#753) 2021-09-28 10:51:19 +01:00
preseq/lcextrap Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
prodigal Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
prokka Module new version reporting fixes (#753) 2021-09-28 10:51:19 +01:00
pycoqc Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
pydamage Module new version reporting fixes (#753) 2021-09-28 10:51:19 +01:00
qcat Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
qualimap Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
quast Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
rapidnj Fix version commands: round 3 (#754) 2021-09-28 14:37:47 +01:00
rasusa Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
raxmlng Fix yml ver (#756) 2021-09-28 18:33:07 +02:00
rsem Fix version commands: round 3 (#754) 2021-09-28 14:37:47 +01:00
rseqc Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
salmon Fix version commands (#749) 2021-09-27 22:10:37 +01:00
samtools Fix version commands: round 3 (#754) 2021-09-28 14:37:47 +01:00
seacr/callpeak Fix version commands: round 3 (#754) 2021-09-28 14:37:47 +01:00
seqkit/split2 Fix version commands: round 3 (#754) 2021-09-28 14:37:47 +01:00
seqtk Fix version commands: round 3 (#754) 2021-09-28 14:37:47 +01:00
sequenzautils Fix version commands: round 3 (#754) 2021-09-28 14:37:47 +01:00
seqwish/induce Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
shovill Fix version commands: round 3 (#754) 2021-09-28 14:37:47 +01:00
snpdists Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
snpeff Module new version reporting fixes (#753) 2021-09-28 10:51:19 +01:00
snpsites Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
sortmerna Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
spades Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
staphopiasccmec Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
star Fix version commands: round 3 (#754) 2021-09-28 14:37:47 +01:00
strelka/germline Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
stringtie Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
subread/featurecounts fix more ver yml (#757) 2021-09-28 20:25:10 +01:00
tabix Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
tiddit/sv Fix version commands: round 3 (#754) 2021-09-28 14:37:47 +01:00
trimgalore Fix version commands (#749) 2021-09-27 22:10:37 +01:00
ucsc Fix version commands: round 3 (#754) 2021-09-28 14:37:47 +01:00
umitools Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
unicycler Fix version commands: round 3 (#754) 2021-09-28 14:37:47 +01:00
untar Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
unzip Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
variantbam Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
vcftools Module new version reporting fixes (#753) 2021-09-28 10:51:19 +01:00
yara Fix version commands: round 3 (#754) 2021-09-28 14:37:47 +01:00