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nf-core_modules/tests/software
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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 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 Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
blast Lint modules ci (#389) 2021-04-08 09:10:52 +01:00
bowtie remove deprecated test tags (#440) 2021-04-13 18:03:09 +01:00
bowtie2 remove deprecated test tags (#440) 2021-04-13 18:03:09 +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 Update test data paths. (#375) 2021-03-24 18:18:01 +00:00
cutadapt Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
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 Intervallisttools (#491) 2021-05-12 11:44:36 +02:00
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 remove deprecated test tags (#440) 2021-04-13 18:03:09 +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/run Add kraken2 pigz multi-tool container for compressing output fastq files (#434) 2021-04-12 18:47:34 +02:00
last New last/train module to train alignment parameters. (#492) 2021-05-19 08:37:08 +01:00
mash/sketch 🏋️‍♀️ new submodule mash/sketch🕺 (#426) 2021-04-10 16:24:23 +01:00
methyldackel Lint modules ci (#389) 2021-04-08 09:10:52 +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 Update and check tests are running for all modules (#420) 2021-04-09 13:47:05 +01:00
multiqc Fix some module test after adapting test config approach (#379) 2021-03-24 18:29:41 +00:00
nanolyse add nanolyse module (from nanoseq modules) (#471) 2021-05-05 11:20:09 +01:00
nanoplot Nanoplot and sequencing_summary.txt for Nanopore test data (#364) 2021-04-09 08:31:38 +01:00
nextclade Add Nextclade module (#484) 2021-05-06 15:48:15 +01:00
optitype update tests for new config (#384) 2021-04-01 20:22:06 +01:00
pangolin Add Nextclade module (#484) 2021-05-06 15:48:15 +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
rseqc Finish rseqc modules (#439) 2021-04-13 08:49:32 +01:00
salmon remove deprecated test tags (#440) 2021-04-13 18:03:09 +01:00
samtools Update modules required for rnaseq pipeline (#449) 2021-04-16 08:56:47 +01:00
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/sample Update comments with new style (#497) 2021-05-12 14:56:46 +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 Lint modules ci (#389) 2021-04-08 09:10:52 +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 remove deprecated test tags (#440) 2021-04-13 18:03:09 +01:00
tiddit/sv remove deprecated test tags (#440) 2021-04-13 18:03:09 +01:00
trimgalore Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
ucsc Add ucsc/bedclip module (#450) 2021-04-15 22:04:59 +02:00
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