Charles Plessy f7ebc2fc48 New last/dotplot module for pairwise similarity plots (#529) ... * New last/dotplot module for pairwise similarity plots The `last-dotplot` tool takes a pairwise alignment in [MAF](http://genome.ucsc.edu/FAQ/FAQformat.html#format5) format, possibly compressed with gzip, or in a tabular format produced by the `maf-convert` tool, and produces a similarity dot-plot of the two sequences in one of the graphical formats supported by the Python Imaging Library. A the tool guesses the output format by the file extension of the file, which is constructed by the module at run time, I have used the `args2` option to convey this information to the module. This new module is part of the work described in Issue #464. During this development, we fix the version of LAST to 1219 to ensure consistency (hence please ignore lint's version warning). * Update the functions.nf file to the dev branch. https://raw.githubusercontent.com/nf-core/tools/dev/nf_core/module-template/software/functions.nf		2021-06-08 11:13:51 +02:00
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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
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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/dotplot module for pairwise similarity plots (#529)	2021-06-08 11:13:51 +02:00
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
pairtools	Pairtools sort (#524)	2021-05-27 18:25:23 +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
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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 samtools from 1.10 to 1.12 (#530)	2021-06-07 13:07:32 +02:00
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seqkit/split2	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
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strelka/germline	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
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subread/featurecounts	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
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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
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yara	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00