nf-core_modules/software
Charles Plessy 207930139a
New last/lastal module to align query sequences on a target index (#510)
* New last/lastal to align query sequences on a target index

`lastal` is the main program of the [LAST](https://gitlab.com/mcfrith/last)
suite.  It align query DNA sequences in FASTA or FASTQ format to a
target index of DNA or protein sequences.  The index is produced by
the `lastdb` program (module `last/lastdb`).  The score matrix for
evaluating the alignment can be chosen among preset ones or computed
iteratively by the `last-train` program (module `last/train`).  For
this reason, the `last/lastal` module proposed here has one input
channel containing an optional file, that has to be dummy when not used.

The LAST aligner outputs MAF files that can be very large (up to
hundreds of gigabytes), therefore this module unconditionally compresses
its output with gzip.

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 ignore lint's version warning).

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Un-hardcode the path to the LAST index.

Among multiple alternatives I have chosen the following command to
detect the sample name of the index, because it fails in situations
where there is no index files in the index folder, and in situations
were there are two indexes files in the folder.  Not failing would
result in feeding garbage information in the INDEX_NAME variable.

    basename \$(ls $index/*.bck) .bck

In case of missing file, a clear error message is given by `ls`.  In
case of more than one file, the error message of `basename` is more
cryptic, unfortunately.  (`basename: extra operand ‘.bck’`)

Alternatives that do not fail if there is no .bck file:

    basename $index/*bck .bck
    find $index -name '*bck' | sed 's/.bck//'

Alternatives that do not fail if there are more than one .bck file:

    basename -s .bck $index/*bck
    ls $index/*.bck | xargs basename -s .bck
    find $index -name '*bck' | sed 's/.bck//'

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-25 22:10:48 +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/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
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
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
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