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nf-core_modules/tests/modules
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James A. Fellows Yates e27553b989
Add module: dedup (#907) 
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* feat: add megahit module, currently decompressed output

* Update main.nf

* Update tests/modules/megahit/test.yml

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>

* Apply suggestions from code review

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

* feat: compress all outputs, remove md5sums due to gz stochasicity

* fix: wrong conda channel for pigz

* fix: broken singleend tests and update meta.yml

* Missed one

* Apply suggestions from code review

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

* fix: pigz formatting

* Apply suggestions from code review

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

* Apply suggestions from code review

* Add dedup (tests and version not working)

* Fix dedup and tests

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
2021-10-28 12:10:21 +02:00
..
abacas Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
adapterremoval Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
agrvate module for agrvate (#693) 2021-09-16 12:42:23 +02:00
allelecounter Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
amps add Amps (#768) 2021-09-30 12:54:16 +02:00
arriba Added module arriba (#611) 2021-07-22 15:19:42 +01:00
artic Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
bamaligncleaner Add module: bamaligncleaner (#676) 2021-09-15 10:31:49 +02:00
bamtools/split Update module: bamtools/split (#885) 2021-10-23 19:39:27 +01:00
bandage/image Fix version commands (#749) 2021-09-27 22:10:37 +01:00
bbmap Add bbmap/bbsplit module (#771) 2021-09-30 13:37:35 +01:00
bcftools Add bcftools/index (#812) 2021-10-13 10:40:04 +02:00
bedtools Add bedtools/makewindows module (#658) 2021-09-07 14:36:06 -04:00
bismark Fix version commands (#749) 2021-09-27 22:10:37 +01:00
blast nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
bowtie Fix version commands (#749) 2021-09-27 22:10:37 +01:00
bowtie2 Fix version commands (#749) 2021-09-27 22:10:37 +01:00
bwa Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
bwamem2 Fix version commands (#749) 2021-09-27 22:10:37 +01:00
bwameth Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
cat Fix flash and cat/fastq modules (#759) 2021-09-28 21:14:11 +01:00
checkm/lineagewf New module: checkm/lineagewf (#899) 2021-10-26 21:54:10 +01:00
chromap Chromap Module (#659) 2021-09-15 17:20:55 +01:00
cnvkit Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
cooler Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
csvtk/concat add csvtk/concat module (#785) 2021-10-05 21:48:47 +01:00
custom/dumpsoftwareversions Correct parsing versions with trailing zeros (#795) 2021-10-06 08:16:36 +02:00
cutadapt Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
damageprofiler fix: reduce number of required input files for damage profiler (#612) 2021-10-20 10:02:30 +02:00
dedup Add module: dedup (#907) 2021-10-28 12:10:21 +02:00
deeptools nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
delly/call few version and test data config fixes (#758) 2021-09-28 20:42:04 +01:00
diamond Diamond (#710) 2021-09-23 09:13:04 +01:00
dragonflye add module for dragonflye (#633) 2021-08-16 11:51:30 +02:00
dshbio Add dsh-bio export-segments module (#631) 2021-08-17 15:53:41 +02:00
ensemblvep Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
expansionhunter Expansionhunter (#666) 2021-08-16 17:47:42 +02:00
fastani module fastani (#695) 2021-09-21 20:20:26 +01:00
fastp enhance module fastp: add save_merged (#598) (#614) 2021-07-23 10:44:00 +01:00
fastqc Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
fasttree Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
fgbio Rewritten module fgbio/fastqtobam (#916) 2021-10-27 19:06:06 +02:00
filtlong add filtlong (#919) 2021-10-27 17:00:11 +02:00
flash Fix flash and cat/fastq modules (#759) 2021-09-28 21:14:11 +01:00
freebayes Check only for file being generated (#879) 2021-10-21 11:32:05 +02:00
gatk4 Createsomaticpanelofnormals (#859) 2021-10-23 19:30:14 +01:00
genmap Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
genrich New module: genrich (#877) 2021-10-22 12:22:02 +02:00
gffread Fix bug in gffread (#686) 2021-09-15 19:55:08 +01:00
glnexus Add glnexus (#729) 2021-09-22 13:31:01 +01:00
graphmap2 Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
gstama New module: gstama/merge (#813) 2021-10-23 19:00:39 +01:00
gtdbtk/classifywf Add gtdbtk/classifywf module (#765) 2021-10-05 21:23:01 +01:00
gubbins nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
gunzip Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
hicap add hicap module (#772) 2021-10-05 21:42:09 +01:00
hifiasm few version and test data config fixes (#758) 2021-09-28 20:42:04 +01:00
hisat2 nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
hmmer/hmmalign Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
homer Homer Modules (#75) 2021-09-08 15:40:34 +00:00
iqtree Module new version reporting fixes (#753) 2021-09-28 10:51:19 +01:00
ismapper add ismapper module (#773) 2021-10-05 21:55:41 +01:00
isoseq3 Update isoseq3/cluster (#856) 2021-10-14 11:07:53 +01:00
ivar Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
jupyternotebook Notebook modules (#617) 2021-10-24 20:51:56 +02:00
kallisto/index Fix yml ver (#756) 2021-09-28 18:33:07 +02:00
kallistobustools Fix yml ver (#756) 2021-09-28 18:33:07 +02:00
kleborate Add module kleborate (#711) 2021-09-21 20:45:42 +01:00
kraken2/kraken2 Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
last nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
lima New module: LIMA (#719) 2021-09-27 16:14:35 +01:00
lofreq fix: lofreq/callparallel missing arg (#562) (#586) 2021-07-19 09:19:27 +01:00
malt update: MALT build version bump (#699) 2021-09-15 16:46:29 +01:00
maltextract add: MALTEXTRACT (#725) 2021-09-21 19:57:27 +01:00
manta adding new manta/germline + manta/tumoronly modules (#906) 2021-10-27 18:24:48 +02:00
mash/sketch Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
mashtree add mashtree module (#767) 2021-10-05 21:27:30 +01:00
maxbin2 New module: maxbin2 (#895) 2021-10-26 22:07:33 +01:00
megahit Add MEGAHIT (#810) 2021-10-12 16:06:06 +01:00
metaphlan3 Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
methyldackel Fix version commands (#749) 2021-09-27 22:10:37 +01:00
minia Fix version commands (#749) 2021-09-27 22:10:37 +01:00
minimap2 nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
mlst added classic mlst module (#742) 2021-10-05 20:49:46 +01:00
mosdepth Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
msisensor Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
multiqc Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
muscle Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
nanolyse Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
nanoplot Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
nextclade Update Nextclade to output all files by default (#638) 2021-07-28 19:49:50 +01:00
optitype Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
pairix Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
pairtools Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
pangolin Update pangolin to 3.1.11 (#721) 2021-09-20 19:59:05 +01:00
paraclu add paraclu (#909) 2021-10-27 15:48:49 +02:00
pbbam/pbmerge New module: pbbam/pbmerge (#752) 2021-10-05 23:16:45 +01:00
pbccs Update of pbccs (#835) 2021-10-23 19:09:41 +01:00
picard Module new version reporting fixes (#753) 2021-09-28 10:51:19 +01:00
pirate add pirate module (#777) 2021-10-05 22:28:25 +01:00
plasmidid Fix yml ver (#756) 2021-09-28 18:33:07 +02:00
plink/vcf Adding plink/vcf module (#656) 2021-09-14 08:51:40 +02:00
preseq/lcextrap Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
prodigal Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
prokka Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
pycoqc Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
pydamage Pydamage analyzer update (#863) 2021-10-18 15:24:49 +02:00
qcat Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
qualimap/bamqc Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
quast Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
rapidnj Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
rasusa Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
raxmlng Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
rmarkdownnotebook Notebook modules (#617) 2021-10-24 20:51:56 +02:00
roary add roary module (#776) 2021-10-05 22:08:47 +01:00
rsem Update checksum modules using human GTF (#900) 2021-10-26 23:09:04 +01:00
rseqc Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
salmon Fix version commands (#749) 2021-09-27 22:10:37 +01:00
samtools Subworkflow Infrastructure (#662) 2021-10-08 16:02:42 +01:00
seacr/callpeak I accidently deleted a branch before the PR merged for PR 800 (#881) 2021-10-21 12:28:59 +01:00
seqkit/split2 Fix version commands: round 3 (#754) 2021-09-28 14:37:47 +01:00
seqtk Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
sequenzautils Fix version commands: round 3 (#754) 2021-09-28 14:37:47 +01:00
seqwish/induce Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
shovill Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
snpdists module: snp-dists (#697) 2021-09-15 16:36:49 +01:00
snpeff Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
snpsites Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
spades nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
spatyper add spatyper module (#784) 2021-10-05 22:21:35 +01:00
sratools Add a new module for fasterq-dump (#807) 2021-10-12 14:20:58 +01:00
staphopiasccmec add staphopia-sccmec module (#702) 2021-09-15 17:24:11 +01:00
star Update checksum modules using human GTF (#900) 2021-10-26 23:09:04 +01:00
strelka Update strelka, by enabling BP if Manta candidates are present (#923) 2021-10-27 17:49:54 +02:00
stringtie Update checksum modules using human GTF (#900) 2021-10-26 23:09:04 +01:00
subread/featurecounts fix more ver yml (#757) 2021-09-28 20:25:10 +01:00
tabix nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
tiddit Add TIDDIT cov (#822) 2021-10-13 12:59:35 +02:00
trimgalore Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
ucsc New module: ucsc/liftover (#868) 2021-10-21 18:04:15 +02:00
unicycler Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
untar Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
unzip Unzip update (#730) 2021-09-22 11:02:32 +01:00
variantbam Add variantbam (#618) 2021-07-26 19:07:29 +01:00
vcftools Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
yara fix more ver yml (#757) 2021-09-28 20:25:10 +01:00