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nf-core_modules/software
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Charles Plessy 45f2f1ee5f
Input a triple (id, fasta, params) to last/lastal (#563) 
The `last/lastal` submodule takes query sequences to align to a target
index, and optionally takes one set of alignment parameters (including a
score matrix) computed by the `last/train` module for each of the
sequences.

In the previous implementation the sequences and the alignment
parameters were provided in different channels, causing them to be
sometimes desynchronised.

In the patched implementation, `last/lastal` takes a 3-tuple as
input to ensure synchronicity.  To produce this tuple in a pipeline,
one can use the `join` command as in the following example.

     LAST_TRAIN  ( query,
                   target )
     LAST_LASTAL ( query.join(LAST_TRAIN.out.param_file),
                   target )

In case no parameter file is computed one can pass a dummy file
to the module as follows:

     LAST_LASTAL ( query.map { row -> [ row[0], row[1], [] ] },
                   target )
2021-07-06 09:35:04 +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 Modules TLC (#551) 2021-07-01 16:13:01 +01:00
cooler Cooler digest (#517) 2021-06-09 11:39:22 +02:00
cutadapt Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
damageprofiler damageprofiler (#545) 2021-06-30 09:46:24 +02:00
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 do not add "." in prefix when suffix is set (#550) 2021-07-01 11:14:58 +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 Modules TLC (#551) 2021-07-01 16:13:01 +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/kraken2 Modules TLC (#551) 2021-07-01 16:13:01 +01:00
last Input a triple (id, fasta, params) to last/lastal (#563) 2021-07-06 09:35:04 +01:00
lib Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
lofreq Lofreq filter (#559) 2021-07-05 10:24:45 +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
metaphlan3 Add metaphlan3 module (#543) 2021-06-25 08:15:15 +02:00
methyldackel Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
minia Modules TLC (#551) 2021-07-01 16:13:01 +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
muscle update muscle (#542) 2021-06-28 08:20:02 +02:00
nanolyse Modules TLC (#551) 2021-07-01 16:13:01 +01:00
nanoplot Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
nextclade Bump new nextclade version (0.14.4) (#532) 2021-06-09 14:12:21 +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 select (#523) 2021-06-23 15:58:31 +02:00
pangolin Modules TLC (#551) 2021-07-01 16:13:01 +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 Fix rsem (#555) 2021-07-02 13:09:48 +02:00
rseqc fix rseqc/junctionsaturation (#553) 2021-07-02 13:31:09 +02:00
salmon Update salmon/quant to provide '--libType A' option (#536) 2021-06-17 15:13:47 +02:00
samtools Update samtools from 1.10 to 1.12 (#530) 2021-06-07 13:07:32 +02:00
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 Feat seqtk update (#503) 2021-06-14 12:23:15 +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 Modules TLC (#551) 2021-07-01 16:13:01 +01:00
stringtie Modules TLC (#551) 2021-07-01 16:13:01 +01:00
subread/featurecounts Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
tabix Add modules bgziptabix (#544) 2021-06-25 10:52:02 +02:00
tiddit/sv Modules TLC (#551) 2021-07-01 16:13:01 +01:00
trimgalore Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
ucsc Modules TLC (#551) 2021-07-01 16:13:01 +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