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nf-core_modules/tests/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 Move assembly test files from genome to illumina (#441) 2021-04-13 12:52:11 +02:00
adapterremoval remove deprecated test tags (#440) 2021-04-13 18:03:09 +01:00
allelecounter Update test data paths. (#375) 2021-03-24 18:18:01 +00:00
artic Add artic minion (#486) 2021-05-07 16:37:35 +01:00
bandage/image Lint modules ci (#389) 2021-04-08 09:10:52 +01:00
bbmap/bbduk Bbmap/bbduk (#487) 2021-05-10 11:45:52 +01:00
bcftools Lint modules ci (#389) 2021-04-08 09:10:52 +01:00
bedtools Fixes for nanoseq modules (#479) 2021-04-30 15:57:43 +01:00
bismark Fix 459 (#534) 2021-06-14 12:24:59 +01:00
blast Lint modules ci (#389) 2021-04-08 09:10:52 +01:00
bowtie Fix linting failures (#552) 2021-07-01 19:50:14 +01:00
bowtie2 Fix linting failures (#552) 2021-07-01 19:50:14 +01:00
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 Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
cat/fastq remove deprecated test tags (#440) 2021-04-13 18:03:09 +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 Finish deeptools modules (#442) 2021-04-13 21:48:43 +01:00
dshbio Update dsh-bio modules to version 2.0.4 (#482) 2021-05-04 14:28:44 +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 adding fasttree module (#412) 2021-04-08 18:15:23 +01:00
fgbio Update and check tests are running for all modules (#420) 2021-04-09 13:47:05 +01:00
flash update tests for new config (#384) 2021-04-01 20:22:06 +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 Fixing a bunch of module tests (#370) 2021-03-24 17:36:29 +00:00
graphmap2 add graphmap index and align modules (from nanoseq modules) (#468) 2021-04-30 13:18:58 +01:00
gubbins Update gubbins module to use new files (#417) 2021-04-09 07:54:11 +01:00
gunzip Update test data paths. (#375) 2021-03-24 18:18:01 +00:00
hisat2 Fix linting failures (#552) 2021-07-01 19:50:14 +01:00
hmmer/hmmalign New module to use hmmalign from HMMER to align sequences (#470) 2021-04-28 11:21:24 +01:00
homer/annotatepeaks Lint modules ci (#389) 2021-04-08 09:10:52 +01:00
iqtree add new iqtree module (#427) 2021-04-12 09:45:56 +01:00
ivar Lint modules ci (#389) 2021-04-08 09:10:52 +01:00
kallisto/index Lint modules ci (#389) 2021-04-08 09:10:52 +01:00
kallistobustools Added kallistobustools/count (#409) 2021-04-30 07:27:17 +02:00
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
lofreq Lofreq filter (#559) 2021-07-05 10:24:45 +01:00
mash/sketch 🏋️‍♀️ new submodule mash/sketch🕺 (#426) 2021-04-10 16:24:23 +01:00
metaphlan3 Add metaphlan3 module (#543) 2021-06-25 08:15:15 +02:00
methyldackel Fix 459 (#534) 2021-06-14 12:24:59 +01:00
minia Fixing a bunch of module tests (#370) 2021-03-24 17:36:29 +00:00
minimap2 Fixes for nanoseq modules (#479) 2021-04-30 15:57:43 +01:00
mosdepth update tests for new config (#384) 2021-04-01 20:22:06 +01:00
msisensor Fix 459 (#534) 2021-06-14 12:24:59 +01:00
multiqc Fix some module test after adapting test config approach (#379) 2021-03-24 18:29:41 +00:00
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 Nanoplot and sequencing_summary.txt for Nanopore test data (#364) 2021-04-09 08:31:38 +01:00
nextclade Bump new nextclade version (0.14.4) (#532) 2021-06-09 14:12:21 +01:00
optitype update tests for new config (#384) 2021-04-01 20:22:06 +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 Pangolin bump new version (3.0.5) (#531) 2021-06-09 14:11:59 +01:00
picard remove deprecated test tags (#440) 2021-04-13 18:03:09 +01:00
plasmidid Bump plasmidid version (#460) 2021-04-26 12:40:38 +02:00
preseq/lcextrap Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
prodigal Update test data paths. (#375) 2021-03-24 18:18:01 +00:00
prokka Update test data paths. (#375) 2021-03-24 18:18:01 +00:00
pycoqc Add pycoqc module (#424) 2021-04-12 10:52:14 +01:00
qcat Fixes for nanoseq modules (#479) 2021-04-30 15:57:43 +01:00
qualimap/bamqc Lint modules ci (#389) 2021-04-08 09:10:52 +01:00
quast remove deprecated test tags (#440) 2021-04-13 18:03:09 +01:00
rapidnj add rapidnj module (#421) 2021-04-09 13:04:54 +01:00
rasusa 🧸 Updated rasusa (#437) 2021-04-12 21:47:55 +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 Lint modules ci (#389) 2021-04-08 09:10:52 +01:00
seqkit/split2 remove deprecated test tags (#440) 2021-04-13 18:03:09 +01:00
seqtk Feat seqtk update (#503) 2021-06-14 12:23:15 +01:00
sequenzautils Update and check tests are running for all modules (#420) 2021-04-09 13:47:05 +01:00
seqwish/induce Lint modules ci (#389) 2021-04-08 09:10:52 +01:00
shovill remove deprecated test tags (#440) 2021-04-13 18:03:09 +01:00
snpsites Snpsites (#480) 2021-05-06 16:05:07 +01:00
spades remove deprecated test tags (#440) 2021-04-13 18:03:09 +01:00
star Update modules required for rnaseq pipeline (#449) 2021-04-16 08:56:47 +01:00
strelka/germline Modules TLC (#551) 2021-07-01 16:13:01 +01:00
stringtie Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
subread/featurecounts remove deprecated test tags (#440) 2021-04-13 18:03:09 +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 add additional ucsc tools (#506) 2021-05-20 15:39:33 -04:00
unicycler remove deprecated test tags (#440) 2021-04-13 18:03:09 +01:00
untar Fix some module tests after switching to config data (#386) 2021-03-24 18:28:07 +00:00
vcftools remove deprecated test tags (#440) 2021-04-13 18:03:09 +01:00
yara remove deprecated test tags (#440) 2021-04-13 18:03:09 +01:00