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nf-core_modules/modules
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Maxime Borry 72c94dbed9
Add new module: Das Tool (#1004) 
* add pydamage module

* remove TODOs

* split module by subcommands

* update version parsing

* remove forgotten TODOs

* update module names

* remove old holistic module

* Update modules/pydamage/analyze/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add keywords

* update resource requirement

* Update modules/pydamage/filter/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/pydamage/filter/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* merge from upstream

* update pydamage from upstream

* add freebayes

* update pydamage test from upstream

* fix meta.yml

* update functions.nf

* update test.yml

* update version parsing

* update version parsing

* fix indentation

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add optional inputs

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add bed test

* add metabat2 module

* only freebayes

* remove metabat2

* update md5sum because of vcf including date of the day

* add keyword

* rescue conflicted files

* attempt to fix ECLint

* add pytest workflow for metabat

* remove -

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add optional inputs/outpus

* remove trailing whitespace

* compressing and removing not reproducible md5sums

* follow symlinks while decompressing

* add dastool/scaffolds2bin

* add dastool

* remove non reproducible md5sum check for compressed files

* Update tests/modules/metabat2/metabat2/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update tests/modules/metabat2/metabat2/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* split tests

* export env variable

* remove metabat2 from PR

* fix linting errors

* remove traling whitespace

* Update modules/metabat2/jgisummarizebamcontigdepths/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* answer PR comments and switch to bgzip

* PR review updates

* update from PR review

* update test files

* add bacillus fragilis alignments

* switch tests to bacillus fragilis

* add string check

* update test string

* add pr comment answer

* last fixes for PR review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-19 08:33:29 +01:00
..
abacas Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
adapterremoval Fix read indexing in AdapterRemoval module (#1051) 2021-11-10 12:21:12 +00:00
agrvate Update agrvate version (#970) 2021-11-15 16:06:02 +01:00
allelecounter Add cram support to Allelecounter module (#1013) 2021-11-02 17:00:25 +01:00
amps Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
arriba Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
artic Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
assemblyscan add new assembly scan module (#971) 2021-10-29 10:01:23 +02:00
ataqv/ataqv Add new module 'ataqv/ataqv' (#998) 2021-11-15 12:51:40 +00:00
bamaligncleaner Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
bamtools/split Update module: bamtools/split (#885) 2021-10-23 19:39:27 +01:00
bamutil/trimbam Add bamutil/trimbam (#1060) 2021-11-15 16:44:12 +00:00
bandage/image Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
bbmap Add log to output from bbmap/align (#1050) 2021-11-10 10:27:52 +00:00
bcftools Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
bedtools Bedtools sort add extension choice input (#984) 2021-10-29 13:22:17 +01:00
bismark Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
blast Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
bowtie Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
bowtie2 Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
bwa Bwa index (#1040) 2021-11-15 11:26:01 +00:00
bwamem2 Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
bwameth bwameth: Add touch command to fix problem with bwameth rejecting older files (#1037) 2021-11-06 16:05:04 +01:00
cat Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
cellranger new module cellranger mkref (#896) 2021-10-28 13:33:57 +02:00
checkm/lineagewf New module: checkm/lineagewf (#899) 2021-10-26 21:54:10 +01:00
chromap Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
clonalframeml add clonalframeml module (#974) 2021-11-15 19:43:53 +00:00
cmseq/polymut Add new module: cmseq/polymut (#918) 2021-11-09 16:12:51 +01:00
cnvkit Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
cooler Cooler cload (#634) 2021-11-15 21:43:55 +00:00
csvtk Added new module csvtk/split (#1014) 2021-11-15 18:29:55 +00:00
custom Add module get_chrom_sizes (#1063) 2021-11-15 19:22:12 +00:00
cutadapt Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
damageprofiler fix: reduce number of required input files for damage profiler (#612) 2021-10-20 10:02:30 +02:00
dastool Add new module: Das Tool (#1004) 2021-11-19 08:33:29 +01:00
dedup Add module: dedup (#907) 2021-10-28 12:10:21 +02:00
deeptools Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
delly/call Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
diamond Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
dragonflye Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
dshbio Update dsh-bio to 2.0.6. (#1075) 2021-11-16 11:37:27 +00:00
emmtyper add emmtyper module (#1028) 2021-11-08 20:43:15 +01:00
ensemblvep Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
expansionhunter Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
fargene new module fargene (#1068) 2021-11-15 16:42:48 +00:00
fastani Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
fastp Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
fastqc Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
fastqscan add module for fastq-scan (#935) 2021-11-15 15:41:36 +01:00
fasttree Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
fgbio Fgbio group reads by umi (#952) 2021-10-29 14:00:54 +02:00
filtlong add filtlong (#919) 2021-10-27 17:00:11 +02:00
flash Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
freebayes Merge freebayes subtools (#1015) 2021-11-03 11:22:06 +01:00
gatk4 Update in GATK4 variantfiltration: Added vcf_index to vcf tuple; output to vcf.gz format. (#1083) 2021-11-18 21:47:40 +01:00
genmap Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
genrich Refactor genrich to avoid params in main (#981) 2021-10-29 16:37:39 +02:00
gffread Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
glnexus Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
graphmap2 Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
gstama Update: gstama/collapse (#1057) 2021-11-11 14:57:55 +00:00
gtdbtk/classifywf Add gtdbtk/classifywf module (#765) 2021-10-05 21:23:01 +01:00
gubbins Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
gunc New module: gunc run (+ gunc downloaddb) (#880) 2021-11-03 17:01:23 +01:00
gunzip Imputeme (#882) 2021-11-05 10:25:54 +01:00
hicap [fix] hicap module allow optional outputs (#937) 2021-11-16 09:23:07 +00:00
hifiasm Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
hisat2 Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
hmmcopy readcounter module for hmmcopy (#1001) 2021-11-02 11:01:13 +00:00
hmmer/hmmalign Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
homer Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
idr Add IDR module (#908) 2021-10-30 10:52:13 +02:00
imputeme/vcftoprs Imputeme (#882) 2021-11-05 10:25:54 +01:00
iqtree Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
ismapper Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
isoseq3 Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
ivar Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
jupyternotebook Notebook modules (#617) 2021-10-24 20:51:56 +02:00
kallisto/index Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
kallistobustools Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
khmer/normalizebymedian Khmer normalizebymedian (#985) 2021-10-29 13:23:34 +02:00
kleborate Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
kraken2/kraken2 Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
kronatools add Kronatools KTImportTaxonomy (#928) 2021-11-15 17:40:46 +00:00
last Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
leehom Add leehom module (#1052) 2021-11-15 15:26:06 +01:00
lib Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
lima Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
lissero add lissero module (#1026) 2021-11-08 20:52:07 +01:00
lofreq Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
macs2/callpeak Macs2 calllpeak (#1038) 2021-11-15 18:17:40 +01:00
malt Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
maltextract Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
manta Update to allow cram + update needed to use the gatk4 modules in sarek (#976) 2021-10-29 13:01:05 +02:00
mapdamage2 Add new module Mapdamage2 (#975) 2021-11-09 14:05:23 +01:00
mash/sketch Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +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
medaka Add Medaka module (#992) 2021-11-15 17:26:37 +00:00
megahit Add MEGAHIT (#810) 2021-10-12 16:06:06 +01:00
meningotype add meningotype module (#1022) 2021-11-06 16:44:26 +01:00
metabat2 New module: metabat2 (#875) 2021-11-08 21:08:26 +01:00
metaphlan3 Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
methyldackel Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
minia Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
miniasm Add Miniasm module (#962) 2021-11-15 17:50:56 +00:00
minimap2 Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
mlst added classic mlst module (#742) 2021-10-05 20:49:46 +01:00
mosdepth Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
msisensor Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
mtnucratio Mtnucratio (#986) 2021-10-29 15:02:02 +02:00
multiqc Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
mummer Initial commit mummer module (#940) 2021-11-15 16:53:41 +01:00
muscle Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
nanolyse Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
nanoplot Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
ncbigenomedownload add ncbi-genome-download module (#980) 2021-11-15 18:32:53 +00:00
nextclade Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
ngmaster add ngmaster module (#1024) 2021-11-10 11:25:50 -07:00
nucmer add new nucmer module (#945) 2021-11-15 22:05:34 +00:00
optitype Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
pairix Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
pairtools Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
pangolin Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
paraclu add paraclu (#909) 2021-10-27 15:48:49 +02:00
pbbam/pbmerge Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
pbccs Update module: pbccs (#1018) 2021-11-11 14:19:26 +00:00
phantompeakqualtools Remove def software lines and emit versions channel as plural (#780) 2021-10-01 14:04:56 +01:00
picard Fix picard markduplicates (#1084) 2021-11-18 21:54:14 +01:00
pirate add pirate module (#777) 2021-10-05 22:28:25 +01:00
plasmidid Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
plink Implement plink/extract module (#901) 2021-11-09 14:03:13 +00:00
plink2/vcf New module: plink2/vcf (#1006) 2021-11-15 13:55:18 +00:00
pmdtools/filter add new module pmdtools/filter #847 (#963) 2021-11-13 15:09:14 +00:00
porechop add porechop module (#914) 2021-10-28 13:21:36 +02:00
preseq/lcextrap Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
prodigal Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
prokka Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
pycoqc Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
pydamage Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
qcat Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
qualimap Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
quast Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
racon Add Racon module to nf-core/modules (#949) 2021-10-29 13:33:38 +01:00
rapidnj Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
rasusa Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
raxmlng Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +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 Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
rseqc Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
salmon Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
samblaster New module: Samblaster (#954) 2021-11-04 18:18:56 +01:00
samtools Add thread option to samtools modules (#1069) 2021-11-18 22:24:47 +01:00
scoary add scoary module (#1034) 2021-11-06 16:34:39 +01:00
seacr/callpeak Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
seqkit/split2 Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
seqsero2 add seqsero2 module (#1016) 2021-11-04 07:49:30 +00:00
seqtk New module seqtk/mergepe (#951) 2021-10-28 16:53:33 +02:00
sequenzautils Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
seqwish/induce Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
shovill Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
snpdists Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
snpeff Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
snpsites Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
sortmerna Fix sortmerna docker container pointer (#791) 2021-10-05 12:05:37 +02:00
spades Change Spades input (#1039) 2021-11-15 11:53:07 +00:00
spatyper Update main.nf (#938) 2021-11-15 15:47:41 +01:00
sratools Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
staphopiasccmec Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
star Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
strelka Update to allow cram + update needed to use the gatk4 modules in sarek (#976) 2021-10-29 13:01:05 +02:00
stringtie Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
subread/featurecounts Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
tabix Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
tbprofiler/profile add module for tbprofiler (#947) 2021-11-15 15:35:55 +01:00
tiddit Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
trimgalore Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
ucsc New module: ucsc/liftover (#868) 2021-10-21 18:04:15 +02:00
ultra/pipeline New module: Ultra (#871) 2021-11-15 15:57:58 +00:00
umitools added meta.yml for umitools (#860) 2021-10-23 17:30:10 +01:00
unicycler Unicycler with long read input (#1041) 2021-11-15 11:48:56 +00:00
untar Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
unzip Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
variantbam Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
vcftools Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
yara Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00