millironx/nf-core_modules
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nf-core_modules/modules
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James A. Fellows Yates 8a2f01c416
module: bwa/samse (#626) 
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Add bwa/aln module

* Also output reads as required with SAI

* Add bwa samse

* Fix container paths

* remove TODO comment

* Updated based on code from from @grst on bwa/sampe

* Clarify output docs
2021-08-02 15:21:23 +02:00
..
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
bandage/image Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
bbmap/bbduk Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
bcftools nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
bedtools Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
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 module: bwa/samse (#626) 2021-08-02 15:21:23 +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
cnvkit nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
cooler Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
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
dshbio Update dsh-bio to 2.0.5 (#628) 2021-07-27 15:32:18 +01:00
ensemblvep Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +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 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 fix: update to gatk4.2.0.0 (#575) 2021-07-16 11:26:28 +02:00
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/annotatepeaks Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
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
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 nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
plasmidid Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
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 Fix tyop in output for rseqc/junctionannotation (#592) 2021-07-20 11:27:47 +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 nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
shovill nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +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 an optional output junction channel in STAR (#621) 2021-07-26 19:03:30 +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