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nf-core_modules/tests/software
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Charles Plessy ca321ce69d
New module last/postmask to filter alignment files (#526) 
The `last-postmask` tool distributed with [LAST](https://gitlab.com/mcfrith/last)
filters alignments in a MAF file to remove those with too many masked
(lower-case) positions compared with their score.

As other filter modules like `last/split`, its output file risks to
overwrite its input file as their names are constructed from the sample
ID when multiple filters are chained in the pipeline.  I added a check
that gives a clearer error message in this case.  Please let me know
what you think about; I can add this test to the existing LAST modules
as well.

This new module is part of the work discribed in Issue #464. During this
development, we fix the version of LAST to 1219 to ensure consistency.
We will upgrade it later.
2021-06-08 11:14:08 +02:00
..
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
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 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 module last/postmask to filter alignment files (#526) 2021-06-08 11:14:08 +02:00
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
pairix add software/pairix (#508) 2021-05-25 21:22:57 +01:00
pairtools Pairtools sort (#524) 2021-05-27 18:25:23 +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 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/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 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