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aleksandrabliznina 4575e5455c
New last/split module to find split alignments. (#511) 
* New last/split module to find split alignments.

The `last-split` tool distributed with [LAST](https://gitlab.com/mcfrith/last)
finds split or spliced alignments in a MAF file that is produced with, for
example, LAST `lastal` command.

This new module is part of the work discribed in Issue #464. During this
development, we fix the versiob of LAST to 1219 to ensure consistency. We will
upgrade it later.

* Update software/last/split/main.nf

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-24 20:15:57 +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
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/split module to find split alignments. (#511) 2021-05-24 20:15:57 +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
nanolyse Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
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
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
picard Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
plasmidid Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
preseq/lcextrap Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
prodigal Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
prokka Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
pycoqc Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
qcat Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
qualimap Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
quast Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
rapidnj Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
rasusa Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
raxmlng Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
rsem Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
rseqc Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
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
seqwish/induce Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
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
sortmerna Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
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