Anthony Underwood 212177d479 output constant sites as a val so it can be passed into iqtree (#429) ... * output constant sites as a val as well as a file so it can be passed into iqtree * Using an env variable because that's far safer! * Update software/snpsites/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>		2021-04-10 18:49:35 +01:00
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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	Update functions.nf to be more flexible for publishing by meta keys (#423)	2021-04-09 17:23:56 +01:00
bowtie2	Update functions.nf to be more flexible for publishing by meta keys (#423)	2021-04-09 17:23:56 +01:00
bwa	Update functions.nf to be more flexible for publishing by meta keys (#423)	2021-04-09 17:23:56 +01:00
bwamem2	Update functions.nf to be more flexible for publishing by meta keys (#423)	2021-04-09 17:23:56 +01:00
bwameth	Update functions.nf to be more flexible for publishing by meta keys (#423)	2021-04-09 17:23:56 +01:00
cat/fastq	Update functions.nf to be more flexible for publishing by meta keys (#423)	2021-04-09 17:23:56 +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	Update functions.nf to be more flexible for publishing by meta keys (#423)	2021-04-09 17:23:56 +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	Update functions.nf to be more flexible for publishing by meta keys (#423)	2021-04-09 17:23:56 +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	Update functions.nf to be more flexible for publishing by meta keys (#423)	2021-04-09 17:23:56 +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
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	Update functions.nf to be more flexible for publishing by meta keys (#423)	2021-04-09 17:23:56 +01:00
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	Update functions.nf to be more flexible for publishing by meta keys (#423)	2021-04-09 17:23:56 +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
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	Update functions.nf to be more flexible for publishing by meta keys (#423)	2021-04-09 17:23:56 +01:00
rsem	Update functions.nf to be more flexible for publishing by meta keys (#423)	2021-04-09 17:23:56 +01:00
rseqc	Update functions.nf to be more flexible for publishing by meta keys (#423)	2021-04-09 17:23:56 +01:00
salmon	Update functions.nf to be more flexible for publishing by meta keys (#423)	2021-04-09 17:23:56 +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	Update functions.nf to be more flexible for publishing by meta keys (#423)	2021-04-09 17:23:56 +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	Update functions.nf to be more flexible for publishing by meta keys (#423)	2021-04-09 17:23:56 +01:00