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Mahesh Binzer-Panchal 58134cb929
Chromap Module (#659) 
* Initialise chromap module

* Revert "Initialise chromap module"

This reverts commit 47c67ae231a6f221ef5b9b7b444b583b5406852b.

* Remake chromap base files with new layout

* Copy chromap

* Copy index

* Add compression

* Update padding

* Update container

* Update chromap input test data

* Add chromap chromap tests

* Add padding

* Update comment

* update yaml file

* Remove TODOs

* Add fasta input to yaml

* Update YAML

* Remove comment, update container

* Remove comments

* Import Chromap index

* Update test.yml

* Fix read input

* Update test.yml

* Add bcftools/concat module. (#641)

* draft for bcftools modules [ci skip]

* initial test for bcftools concat

* Update the params for testing

* fix tests

* Accomodate code review [ci skip]

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

* Update the meta file and open PR for review

* Update the keyword

* Update the tags for module [ci skip[

* add threads

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

* add module for dragonflye (#633)

* add module for dragonflye

* fix tests for dragonflye

* Update test.yml

* Update meta.yml

* Update main.nf

* Update main.nf

* Update modules/dragonflye/meta.yml

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>

* update typos. change quote from ' to ". (#652)

* Add bcftools/norm module (#655)

* Initial draft [ci skip]

* trigger first test

* update output file path

* Tests passing

* finishing touches for meta.yml and update checksum

* tweak checksum

* add threads to the module

* skip version info for matching test md5sum [ci skip]

* Add ref fasta and finalize the module

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>

* Expansionhunter (#666)


Please enter the commit message for your changes. Lines starting

* adds expansionhunter module

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* Update test.yml (#668)

* Specify in guidelines one should split CPUs when module has n > 1 tool (#660)

* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Describe CPU splitting

* Update README.md

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>

* More CPU examples

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>

* Add dsh-bio export-segments module (#631)

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>

* update: `BWA/ALN` (#653)

* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Remove reads from output channel following module guidelines. Should do a .join() based on $meta, to reassociate.

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>

* Update seqwish reported version to match bioconda version. (#678)

* Bbmap index (#683)

BBMap index module

* Initialise chromap module

* Revert "Initialise chromap module"

This reverts commit 47c67ae231a6f221ef5b9b7b444b583b5406852b.

* Remove unnecessary files

* Remove unnecessary files

* Update modules/chromap/index/main.nf

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

* Update modules/chromap/index/main.nf

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

* Update modules/chromap/chromap/main.nf

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

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

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

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

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

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

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

* Update modules/chromap/index/main.nf

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

* Remove pytest_software.yml

* Apply suggestions from code review

Co-authored-by: Abhinav Sharma <abhi18av@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: JIANHONG OU <jianhong@users.noreply.github.com>
Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Michael L Heuer <heuermh@acm.org>
Co-authored-by: Daniel Lundin <daniel.lundin@lnu.se>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-15 17:20:55 +01:00
..
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
allelecounter nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
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
bandage/image Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
bbmap Get rid of meta map from bbmap/index (#700) 2021-09-15 12:38:56 +02:00
bcftools Add bcftools/query module (#670) 2021-09-14 09:19:01 +02:00
bedtools Add bedtools/makewindows module (#658) 2021-09-07 14:36:06 -04:00
bismark Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
blast nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
bowtie Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
bowtie2 nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
bwa update: BWA/ALN (#653) 2021-08-17 15:55:54 +02:00
bwamem2 Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
bwameth Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
cat/fastq Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
chromap Chromap Module (#659) 2021-09-15 17:20:55 +01:00
cnvkit nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
cooler update typos. change quote from ' to ". (#652) 2021-08-16 11:57:22 +02:00
cutadapt nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
damageprofiler Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
deeptools nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
delly/call Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +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
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 Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
flash Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
gatk4 Mutect2 (#682) 2021-09-13 16:16:23 +01:00
genmap Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
gffread Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
graphmap2 Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +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
hifiasm Add hifiasm module (#596) 2021-07-20 21:50:22 +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 nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
ivar Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
kallisto/index Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
kallistobustools nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +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
lib Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
lofreq fix: lofreq/callparallel missing arg (#562) (#586) 2021-07-19 09:19:27 +01:00
macs2/callpeak Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
malt update: MALT build version bump (#699) 2021-09-15 16:46:29 +01:00
mash/sketch Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
metaphlan3 nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
methyldackel nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
minia Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
minimap2 nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
mosdepth nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
msisensor Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
multiqc nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +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 nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +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 Bump Pangolin to 3.1.7 (#593) 2021-07-20 12:25:36 +01:00
phantompeakqualtools Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
picard modify markduplicates module (#681) 2021-09-15 11:02:28 +02:00
plasmidid Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
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 nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +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
qcat Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
qualimap Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +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 nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
rsem Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
rseqc Require r-base>=3.5 for RSeqC Conda envs (#654) 2021-08-05 18:59:56 +01:00
salmon nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
samtools nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
seacr/callpeak Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
seqkit/split2 nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
seqtk Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
sequenzautils Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
seqwish/induce Update seqwish reported version to match bioconda version. (#678) 2021-08-26 15:33:38 -05:00
shovill nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +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
sortmerna 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
star Added PL tag in read group information for downstream analysis (#649) 2021-08-04 11:16:51 +02:00
strelka/germline Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
stringtie Add option -p to set the # of cpus on stringtie (#601) 2021-07-21 15:38:40 +02:00
subread/featurecounts Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
tabix nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
tiddit/sv Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
trimgalore nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
ucsc Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
umitools Add --paired flag to umitools dedup and bump to 1.1.2 (#583) 2021-07-16 14:21:08 +01:00
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 module: unzip (#642) 2021-08-02 09:40:57 +02:00
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 Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00