aleksandrabliznina b592cea30b New last/train module to train alignment parameters. (#492) ... * New last/train module to train alignment parameters. The last-train command creates a parameter file that will be used by last/lastal module for sequence alignment. It takes indexed sequences and query sequences as input and we use the metadata of both to create an id of the parameter output file. Submission of the LAST modules is discussed in more details in the issue #464. For consistancy, we use LAST version 1219 for this whole development and will upgrade later. * Corrected files according to the nf-core v1.14 standards. * Fixed function.nf file for the last-train module. * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Find index name. * Correct after the input channels were changed. * Use double underscore as a name separator. Single underscores can happen in ids, therefore, we would like to keep two underscores. * Remove extra spaces. * Fixed the passing of the "score matrix" line. * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/last/train/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>		2021-05-19 08:37:08 +01:00
..
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/train module to train alignment parameters. (#492)	2021-05-19 08:37:08 +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	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
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