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nf-core_modules/modules
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Moritz E. Beber de997825de
Add a new module for fasterq-dump (#807) 
* chore: use template to create fasterq module

* feat: add fasterq-dump process module

* docs: provide input and output descriptions

* docs: add comment on `--temp`

* fix: use correct variable

* tests: define test output

* refactor: address review comments

* refactor: remove vdb-config input

* chore: add new test data to config

* tests: define single-end and paired-end cases

* refactor: choose specific output

* tests: do not expect single FASTQ for paired-end

* feat: add compression

* Apply suggestions from code review

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

* tests: revert the test data name

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-12 14:20:58 +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 New module: bamtools/split (#798) 2021-10-12 14:43:08 +02:00
bandage/image Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
bbmap Fix bug with SortMeRna not working on a single db file (#788) 2021-10-04 12:37:21 +01:00
bcftools Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
bedtools Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
bismark Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
blast Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
bowtie Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
bowtie2 Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
bwa Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
bwamem2 Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
bwameth Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
cat Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
chromap Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
cnvkit Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
cooler Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
csvtk/concat patch output extension in csvtk/concat (#797) 2021-10-05 22:15:08 +01:00
custom/dumpsoftwareversions Correct parsing versions with trailing zeros (#795) 2021-10-06 08:16:36 +02:00
cutadapt Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
damageprofiler Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
deeptools Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
delly/call Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
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 versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
ensemblvep Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
expansionhunter Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
fastani Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
fastp Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
fastqc Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
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
gatk4 Learnreadorientationmodel (#794) 2021-10-07 13:55:06 +01:00
genmap Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
gffread Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
glnexus Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
graphmap2 Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
gtdbtk/classifywf Add gtdbtk/classifywf module (#765) 2021-10-05 21:23:01 +01:00
gubbins Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
gunzip Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
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 Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
homer Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
iqtree Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
ismapper add ismapper module (#773) 2021-10-05 21:55:41 +01:00
isoseq3 New module: isoseq3/cluster (#801) 2021-10-07 10:06:02 +01:00
ivar Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
kallisto/index Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
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 Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
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 Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
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
metaphlan3 Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
methyldackel Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
minia Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
minimap2 Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
mlst added classic mlst module (#742) 2021-10-05 20:49:46 +01:00
mosdepth Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
msisensor Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
multiqc Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
muscle Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
nanolyse Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
nanoplot Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
nextclade Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
optitype Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
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 Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
pbbam/pbmerge New module: pbbam/pbmerge (#752) 2021-10-05 23:16:45 +01:00
pbccs Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
phantompeakqualtools Remove def software lines and emit versions channel as plural (#780) 2021-10-01 14:04:56 +01:00
picard Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +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/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 Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
qualimap Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
quast Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +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
roary add roary module (#776) 2021-10-05 22:08:47 +01:00
rsem Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
rseqc Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
salmon Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
samtools Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
seacr/callpeak Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
seqkit/split2 Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
seqtk Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
sequenzautils Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
seqwish/induce Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
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 Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
snpsites Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
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 Add a new module for fasterq-dump (#807) 2021-10-12 14:20:58 +01:00
staphopiasccmec Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
star Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
strelka/germline Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
stringtie Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
subread/featurecounts Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
tabix Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
tiddit/sv Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
trimgalore Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
ucsc Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
umitools Remove def software lines and emit versions channel as plural (#780) 2021-10-01 14:04:56 +01:00
unicycler Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
untar Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
unzip Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
variantbam Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
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