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emnilsson 9402595711
New module seqtk/mergepe (#951) 
* First step into creating a seqtk/mergepe module to interleave fastQ input

* First rewrite of main.nf to make the module perform the desired (interleave/merge of pe reads) task

* Modifications to test the new seqtk/mergepe module.

* Improving the seqtk/mergepe module to output single end reads as well, and making sure tests work

* Modified so that gzip uses -n and that single read entries are symlinked with ln -s instead of copied, therefore updated test.yml as well.

* Fix trailing whitespaces

Co-authored-by: Daniel Lundin <daniel.lundin@lnu.se>
2021-10-28 16:53:33 +02:00
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abacas Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
adapterremoval Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
agrvate Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
allelecounter Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +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
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
bandage/image Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
bbmap Fix bug with SortMeRna not working on a single db file (#788) 2021-10-04 12:37:21 +01:00
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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
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csvtk/concat patch output extension in csvtk/concat (#797) 2021-10-05 22:15:08 +01:00
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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 Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
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fasttree Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +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 Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
freebayes New module: freebayes (#818) 2021-10-20 15:19:31 +02:00
gatk4 Createsomaticpanelofnormals (#859) 2021-10-23 19:30:14 +01:00
genmap Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
genrich New module: genrich (#877) 2021-10-22 12:22:02 +02:00
gffread Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
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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 Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
gunzip Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
hicap add hicap module (#772) 2021-10-05 21:42:09 +01:00
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
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lib Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
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maltextract Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
manta adding new manta/germline + manta/tumoronly modules (#906) 2021-10-27 18:24:48 +02:00
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
megahit Add MEGAHIT (#810) 2021-10-12 16:06:06 +01:00
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mlst added classic mlst module (#742) 2021-10-05 20:49:46 +01:00
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paraclu add paraclu (#909) 2021-10-27 15:48:49 +02:00
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pbccs Update of pbccs (#835) 2021-10-23 19:09:41 +01:00
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pirate add pirate module (#777) 2021-10-05 22:28:25 +01:00
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plink/vcf Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
porechop add porechop module (#914) 2021-10-28 13:21:36 +02:00
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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
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samtools add new module samtools/depth (#950) 2021-10-28 12:53:21 +02:00
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seqkit/split2 Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
seqtk New module seqtk/mergepe (#951) 2021-10-28 16:53:33 +02:00
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shovill Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
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sortmerna Fix sortmerna docker container pointer (#791) 2021-10-05 12:05:37 +02:00
spades Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
spatyper add spatyper module (#784) 2021-10-05 22:21:35 +01:00
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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 strelka, by enabling BP if Manta candidates are present (#923) 2021-10-27 17:49:54 +02:00
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subread/featurecounts Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
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ucsc New module: ucsc/liftover (#868) 2021-10-21 18:04:15 +02:00
umitools added meta.yml for umitools (#860) 2021-10-23 17:30:10 +01:00
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