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nf-core_modules/software
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Yuk Kei Wan faf77d6fee
add nanolyse module (from nanoseq modules) (#471) 
* add nanolyse modules

* add clean.fastq.gz path and md5sum

* fix errors

* remove unreproducible md5sum

* solve linting problem

* address PR suggestions

* GET_NANOLYSE_FASTA as a local module

* Update software/nanolyse/main.nf

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

* Update software/nanolyse/main.nf

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

* Update software/nanolyse/main.nf

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

* Update software/nanolyse/main.nf

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

* Update software/nanolyse/meta.yml

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

* Update software/nanolyse/meta.yml

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

* Update tests/software/nanolyse/test.yml

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

* Update tests/software/nanolyse/main.nf

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

* Update tests/software/nanolyse/main.nf

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

* update to the version from nf-core/tools-dev

* input and output files cannot have the same names

* Update test.yml

* Update software/nanolyse/main.nf

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

* Update tests/software/nanolyse/main.nf

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

* Update test.yml

* revert

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-05 11:20:09 +01:00
..
abacas Fixing abacas meta.yml file (#447) 2021-04-15 11:17:06 +01:00
adapterremoval Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
allelecounter Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
artic/guppyplex Add artic guppyplex (#455) 2021-04-27 15:57:34 +01:00
bandage/image Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
bcftools Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
bedtools Fixes for nanoseq modules (#479) 2021-04-30 15:57:43 +01:00
bismark Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
blast Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
bowtie Add default publish_dir for index processes (#428) 2021-04-10 20:49:09 +01:00
bowtie2 Add default publish_dir for index processes (#428) 2021-04-10 20:49:09 +01:00
bwa Add default publish_dir for index processes (#428) 2021-04-10 20:49:09 +01:00
bwamem2 Add default publish_dir for index processes (#428) 2021-04-10 20:49:09 +01:00
bwameth Add default publish_dir for index processes (#428) 2021-04-10 20:49:09 +01:00
cat/fastq Add default publish_dir for index processes (#428) 2021-04-10 20:49:09 +01:00
cnvkit Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
cutadapt Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
deeptools Finish deeptools modules (#442) 2021-04-13 21:48:43 +01:00
dshbio Update dsh-bio modules to version 2.0.4 (#482) 2021-05-04 14:28:44 +01:00
fastp minor typo (#451) 2021-04-15 19:45:23 +01:00
fastqc Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
fasttree Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
fgbio Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
flash Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
gatk4 remove deprecated test tags (#440) 2021-04-13 18:03:09 +01:00
gffread Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
graphmap2 Fixes for nanoseq modules (#479) 2021-04-30 15:57:43 +01:00
gubbins Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
gunzip Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
hisat2 Update modules required for rnaseq pipeline (#449) 2021-04-16 08:56:47 +01:00
hmmer/hmmalign New module to use hmmalign from HMMER to align sequences (#470) 2021-04-28 11:21:24 +01:00
homer/annotatepeaks Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
iqtree Iqtree (#435) 2021-04-12 17:01:26 +01:00
ivar Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
kallisto/index Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
kallistobustools Added kallistobustools/count (#409) 2021-04-30 07:27:17 +02:00
kraken2/run Add kraken2 pigz multi-tool container for compressing output fastq files (#434) 2021-04-12 18:47:34 +02:00
last/lastdb New last/lastdb module to index sequences before alignment. (#476) 2021-05-02 11:36:31 +01:00
lib Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
macs2/callpeak Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
mash/sketch 🏋️‍♀️ new submodule mash/sketch🕺 (#426) 2021-04-10 16:24:23 +01:00
methyldackel Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
minia Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
minimap2 Fixes for nanoseq modules (#479) 2021-04-30 15:57:43 +01:00
mosdepth Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
msisensor Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
multiqc Move test data to nf-core/test-datasets (#432) 2021-04-12 12:32:39 +01:00
nanolyse add nanolyse module (from nanoseq modules) (#471) 2021-05-05 11:20:09 +01:00
nanoplot Add artic guppyplex (#455) 2021-04-27 15:57:34 +01:00
optitype Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
pangolin Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
phantompeakqualtools Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
picard Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
plasmidid Bump plasmidid version (#460) 2021-04-26 12:40:38 +02:00
preseq/lcextrap Update modules required for rnaseq pipeline (#449) 2021-04-16 08:56:47 +01:00
prodigal Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
prokka Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
pycoqc Add pycoqc module (#424) 2021-04-12 10:52:14 +01:00
qcat Fixes for nanoseq modules (#479) 2021-04-30 15:57:43 +01:00
qualimap Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
quast Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
rapidnj Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
rasusa 🧸 Updated rasusa (#437) 2021-04-12 21:47:55 +01:00
raxmlng Raxmlng (#474) 2021-04-29 08:20:05 +01:00
rsem Add default publish_dir for index processes (#428) 2021-04-10 20:49:09 +01:00
rseqc Finish rseqc modules (#439) 2021-04-13 08:49:32 +01:00
salmon Add default publish_dir for index processes (#428) 2021-04-10 20:49:09 +01:00
samtools Update modules required for rnaseq pipeline (#449) 2021-04-16 08:56:47 +01:00
seacr/callpeak Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
seqkit/split2 Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
sequenzautils Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
seqwish/induce Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
shovill Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
snpsites output constant sites as a val so it can be passed into iqtree (#429) 2021-04-10 18:49:35 +01:00
sortmerna Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
spades Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
star Update modules required for rnaseq pipeline (#449) 2021-04-16 08:56:47 +01:00
strelka/germline Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
stringtie Add stringtie merge module (from nanoseq modules) (#475) 2021-05-03 07:18:51 +02:00
subread/featurecounts Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
tabix Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
tiddit/sv Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
trimgalore Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
ucsc Add ucsc/bedclip module (#450) 2021-04-15 22:04:59 +02:00
umitools Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
unicycler Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
untar Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
vcftools Update functions.nf to be more flexible for publishing by meta keys (#423) 2021-04-09 17:23:56 +01:00
yara Add default publish_dir for index processes (#428) 2021-04-10 20:49:09 +01:00