JIANHONG OU 18440df87a add genmap/mappability (#509) ... * add genmap/mappability * Add index module. Remove -w parameter from mappability module. * change the output of genmap/index * fix the lint error which can not handle stageAs. * Apply suggestions from code review * Update main.nf * Update test.yml * Update main.nf * Update test.yml * Update tests/software/genmap/mappability/main.nf * Update software/genmap/mappability/main.nf * Update software/genmap/mappability/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>		2021-05-25 22:12:10 +01:00
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abacas	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
adapterremoval	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
allelecounter	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
artic	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
bandage/image	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
bbmap/bbduk	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
bcftools	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
bedtools	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
bismark	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
blast	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
bowtie	Fix number of cpus for modules with piped tools (#499)	2021-05-18 09:52:00 +02:00
bowtie2	Fix number of cpus for modules with piped tools (#499)	2021-05-18 09:52:00 +02:00
bwa	Fix number of cpus for modules with piped tools (#499)	2021-05-18 09:52:00 +02:00
bwamem2	Fix number of cpus for modules with piped tools (#499)	2021-05-18 09:52:00 +02:00
bwameth	Fix number of cpus for modules with piped tools (#499)	2021-05-18 09:52:00 +02:00
cat/fastq	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
cnvkit	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
cutadapt	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
deeptools	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
dshbio	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
fastp	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
fastqc	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
fasttree	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
fgbio	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
flash	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
gatk4	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
genmap	add genmap/mappability (#509)	2021-05-25 22:12:10 +01:00
gffread	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
graphmap2	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
gubbins	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
gunzip	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
hisat2	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
hmmer/hmmalign	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
homer/annotatepeaks	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
iqtree	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
ivar	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
kallisto/index	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
kallistobustools	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
kraken2/run	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
last	New last/lastal module to align query sequences on a target index (#510)	2021-05-25 22:10:48 +01:00
lib	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
macs2/callpeak	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
mash/sketch	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
methyldackel	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
minia	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
minimap2	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
mosdepth	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
msisensor	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
multiqc	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
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nanoplot	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
nextclade	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
optitype	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
pairix	add software/pairix (#508)	2021-05-25 21:22:57 +01:00
pangolin	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
phantompeakqualtools	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
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salmon	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
samtools	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
seacr/callpeak	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
seqkit/split2	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
seqtk/sample	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
sequenzautils	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
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shovill	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
snpsites	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
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spades	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
star	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
strelka/germline	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
stringtie	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
subread/featurecounts	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
tabix	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
tiddit/sv	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
trimgalore	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
ucsc	add additional ucsc tools (#506)	2021-05-20 15:39:33 -04:00
umitools	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
unicycler	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
untar	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
vcftools	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
yara	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00