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nf-core_modules/software
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Anthony Underwood 2ed9b6ae28
Raxmlng (#443) 
* new raxml module

* new raxml module

* pass in args for bootstrap and add test for support file

* remove unnecessary tag

* ensure tags meet guidleines

* Apply suggestions from code review

* Update to latest functions file

Co-authored-by: avantonder <avt@sanger.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-14 08:38:59 +01:00
..
abacas Add abacas module (#431) 2021-04-12 15:37:08 +01:00
adapterremoval Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
allelecounter Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
bandage/image Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
bcftools Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
bedtools Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
bismark Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
blast Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
bowtie Add default publish_dir for index processes (#428) 2021-04-10 20:49:09 +01:00
bowtie2 Add default publish_dir for index processes (#428) 2021-04-10 20:49:09 +01:00
bwa Add default publish_dir for index processes (#428) 2021-04-10 20:49:09 +01:00
bwamem2 Add default publish_dir for index processes (#428) 2021-04-10 20:49:09 +01:00
bwameth Add default publish_dir for index processes (#428) 2021-04-10 20:49:09 +01:00
cat/fastq Add default publish_dir for index processes (#428) 2021-04-10 20:49:09 +01:00
cnvkit Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
cutadapt Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
deeptools Finish deeptools modules (#442) 2021-04-13 21:48:43 +01:00
dsh Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
fastp Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
fastqc Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
fasttree Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
fgbio Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
flash Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
gatk4 remove deprecated test tags (#440) 2021-04-13 18:03:09 +01:00
gffread Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
gubbins Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
gunzip Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
hisat2 Add default publish_dir for index processes (#428) 2021-04-10 20:49:09 +01:00
homer/annotatepeaks Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
iqtree Iqtree (#435) 2021-04-12 17:01:26 +01:00
ivar Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
kallisto/index Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
kallistobustools/ref Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
kraken2/run Add kraken2 pigz multi-tool container for compressing output fastq files (#434) 2021-04-12 18:47:34 +02:00
lib Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
macs2/callpeak Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
mash/sketch 🏋️‍♀️ new submodule mash/sketch🕺 (#426) 2021-04-10 16:24:23 +01:00
methyldackel Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
minia Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
minimap2/align Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
mosdepth Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
msisensor Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
multiqc Move test data to nf-core/test-datasets (#432) 2021-04-12 12:32:39 +01:00
nanoplot Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
optitype Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
pangolin Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
phantompeakqualtools Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
picard Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
plasmidid Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
preseq/lcextrap Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
prodigal Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
prokka Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
pycoqc Add pycoqc module (#424) 2021-04-12 10:52:14 +01:00
qualimap Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
quast Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
rapidnj Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
rasusa 🧸 Updated rasusa (#437) 2021-04-12 21:47:55 +01:00
raxmlng Raxmlng (#443) 2021-04-14 08:38:59 +01:00
rsem Add default publish_dir for index processes (#428) 2021-04-10 20:49:09 +01:00
rseqc Finish rseqc modules (#439) 2021-04-13 08:49:32 +01:00
salmon Add default publish_dir for index processes (#428) 2021-04-10 20:49:09 +01:00
samtools Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
seacr/callpeak Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
seqkit/split2 Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
sequenzautils Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
seqwish/induce Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
shovill Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
snpsites output constant sites as a val so it can be passed into iqtree (#429) 2021-04-10 18:49:35 +01:00
sortmerna Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
spades Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
star Add default publish_dir for index processes (#428) 2021-04-10 20:49:09 +01:00
strelka/germline Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
stringtie Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
subread/featurecounts Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
tabix Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
tiddit/sv Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
trimgalore Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
ucsc Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
umitools Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
unicycler Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
untar Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
vcftools Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
yara Add default publish_dir for index processes (#428) 2021-04-10 20:49:09 +01:00