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nf-core_modules/modules
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Sébastien Guizard 481d3c811d
New module: gstama/collapse (#809) 
* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 📦 NEW: Add galgal6 chr30 test data

* 📦 NEW: Add gd-tama module

* 🐛 FIX (TEMP): Update singularity container address

* 📦 NEW: Add bamtools module

* 📦 NEW: Rewrite and rename module (gstama => gstama/collapse)

* 👌 IMPROVE: ignore test data

* 👌 IMPROVE: Remove junk files

* 👌 IMPROVE: Update output

* 👌 IMPROVE: Add channel for publishing tama's metadata outputs

* 👌 IMPROVE: Update process label

* 🐛 FIX: Use depot.galxyproject.org url for singularity

* 👌 IMPROVE: autoselect running mode

* 🐛 FIX: correct gstama collapse bash test

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update tama package and label

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Update test

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 📦 NEW: Add galgal6 chr30 test data

* 📦 NEW: Add gd-tama module

* 🐛 FIX (TEMP): Update singularity container address

* 📦 NEW: Add bamtools module

* 📦 NEW: Rewrite and rename module (gstama => gstama/collapse)

* 👌 IMPROVE: ignore test data

* 👌 IMPROVE: Update output

* 👌 IMPROVE: Add channel for publishing tama's metadata outputs

* 👌 IMPROVE: Update process label

* 🐛 FIX: Use depot.galxyproject.org url for singularity

* 👌 IMPROVE: autoselect running mode

* 🐛 FIX: correct gstama collapse bash test

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update tama package and label

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Update test

* 👌 IMPROVE: delete unnecessary files

* 👌 IMPROVE: Update + clean

- Remove unnecessary files
- Update to new versions.yml file
- Better output channels

* 👌 IMPROVE: Update meta.yml and output channels

* 👌 IMPROVE: Remove useless files

* 👌 IMPROVE: Remove automatic MODE setup

* 👌 IMPROVE: Applied @jfy133 code modification suggestions

* Update modules/gstama/collapse/meta.yml

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

* 🐛 FIX: Add missing fasta option in meta.yml

* 🐛 FIX: Fix typo

* 🐛 FIX: Update package version

* Update main.nf

* Update meta.yml

* Update modules/gstama/collapse/meta.yml

* Apply suggestions from code review

* Update tests/modules/gstama/collapse/main.nf

* Update main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-23 18:55:28 +01:00
..
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 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
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 Filtermutectcalls (#796) 2021-10-23 18:45:19 +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/collapse New module: gstama/collapse (#809) 2021-10-23 18:55:28 +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
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
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 Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
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
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