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James A. Fellows Yates bd2baa1e7c
New module: maxbin2 (#895) 
* 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

* Added, just need to finish tests once we have bacterial data

* Add prelim test data

* Fix version reporting

* Add tests based on proposed test-dataset

* Finalise new testdata

* Fix md5sum issue by removing it...

* Update main.nf

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
2021-10-26 22:07:33 +01:00
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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
bcftools Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
bedtools Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
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 Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
bwamem2 Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
bwameth Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
cat Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
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
cnvkit Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
cooler Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
csvtk/concat patch output extension in csvtk/concat (#797) 2021-10-05 22:15:08 +01:00
custom/dumpsoftwareversions Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
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
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 Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
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
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
fasttree Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
fgbio Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
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
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 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
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
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
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
last Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +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
lofreq Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
macs2/callpeak Remove def software lines and emit versions channel as plural (#780) 2021-10-01 14:04:56 +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
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
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
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
multiqc Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
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
nextclade Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
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
pbbam/pbmerge Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
pbccs Update of pbccs (#835) 2021-10-23 19:09:41 +01:00
phantompeakqualtools Remove def software lines and emit versions channel as plural (#780) 2021-10-01 14:04:56 +01:00
picard Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
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/vcf Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
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
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
samtools Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
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
seqtk Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
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 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
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 Add strelka/somatic module (#866) 2021-10-18 22:34:23 +01:00
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
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
umitools added meta.yml for umitools (#860) 2021-10-23 17:30:10 +01:00
unicycler Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
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