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alexandregilardet 94851901d5
add new module pmdtools/filter #847 (#963) 
* commit but won't be used because pmdtools should have a submodule

* added submodule pmdtools/filter

* removed pmdtools module created before deciding to design two submodules

* oops forgot to remove a TODO

* removed white space meta.yml, removed v in version and manually added submodule /filter to test

* Update pytest_modules.yml

* Update main.nf

added split_cpus for multi-tools module resources

* Update test.yml

added .pmd extension to match modules/ main.nf

* Update test.yml

update md5sum

* Update singularity and docker build in main.nf

From build 4 to 5 in order to match the conda one

* Update modules/pmdtools/filter/main.nf

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

* Update modules/pmdtools/filter/main.nf

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

* Update modules/pmdtools/filter/main.nf

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

* Update modules/pmdtools/filter/meta.yml

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

* Update modules/pmdtools/filter/meta.yml

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

* Update modules/pmdtools/filter/meta.yml

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

* Update modules/pmdtools/filter/meta.yml

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

* Update modules/pmdtools/filter/main.nf

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

* Update modules/pmdtools/filter/main.nf

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

* Update main.nf adding samtools version

we need both pmdtools and samtools versions

* Update main.nf remove .pmd extension

* Update test.yml md5sum

Because file extension changed

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-11-13 15:09:14 +00:00
..
abacas Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
adapterremoval Fix read indexing in AdapterRemoval module (#1051) 2021-11-10 12:21:12 +00:00
agrvate module for agrvate (#693) 2021-09-16 12:42:23 +02:00
allelecounter Add cram support to Allelecounter module (#1013) 2021-11-02 17:00:25 +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
assemblyscan add new assembly scan module (#971) 2021-10-29 10:01:23 +02:00
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 log to output from bbmap/align (#1050) 2021-11-10 10:27:52 +00:00
bcftools Add bcftools/index (#812) 2021-10-13 10:40:04 +02:00
bedtools Bedtools sort add extension choice input (#984) 2021-10-29 13:22:17 +01:00
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
cellranger/mkref 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 Chromap Module (#659) 2021-09-15 17:20:55 +01:00
cmseq/polymut Add new module: cmseq/polymut (#918) 2021-11-09 16:12:51 +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
emmtyper add emmtyper module (#1028) 2021-11-08 20:43:15 +01:00
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 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 Fix flash and cat/fastq modules (#759) 2021-09-28 21:14:11 +01:00
freebayes fix remove md5sum check (#1017) 2021-11-03 11:41:12 +01:00
gatk4 feat: update gatk4 from 4.2.0.0 to 4.2.3.0 (#1059) 2021-11-11 08:58:59 +01:00
genmap Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
genrich Refactor genrich to avoid params in main (#981) 2021-10-29 16:37:39 +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 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 nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
gunc New module: gunc run (+ gunc downloaddb) (#880) 2021-11-03 17:01:23 +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
hmmcopy readcounter module for hmmcopy (#1001) 2021-11-02 11:01:13 +00:00
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
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 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
khmer/normalizebymedian Khmer normalizebymedian (#985) 2021-10-29 13:23:34 +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
lissero add lissero module (#1026) 2021-11-08 20:52:07 +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
mapdamage2 Add new module Mapdamage2 (#975) 2021-11-09 14:05:23 +01:00
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
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 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 Add Racon module to nf-core/modules (#949) 2021-10-29 13:33:38 +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
mtnucratio Mtnucratio (#986) 2021-10-29 15:02:02 +02:00
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
ngmaster add ngmaster module (#1024) 2021-11-10 11:25:50 -07:00
optitype Updating test file for optitype (#782) 2021-10-28 14:24:52 +02:00
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 module: pbccs (#1018) 2021-11-11 14:19:26 +00:00
picard Picard/collecthsmetrics (#927) 2021-11-10 10:52:54 +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 Implement plink/extract module (#901) 2021-11-09 14:03:13 +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 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
racon Add Racon module to nf-core/modules (#949) 2021-10-29 13:33:38 +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
samblaster New module: Samblaster (#954) 2021-11-04 18:18:56 +01:00
samtools Add CRAM to samtools/index (#1049) 2021-11-10 10:30:48 +01:00
scoary add scoary module (#1034) 2021-11-06 16:34:39 +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
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 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