millironx/nf-core_modules
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nf-core_modules/tests/modules
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GCJMackenzie 08db860938
Update mergebam syntax and sample specific unmapped channel (#1238) 
* initial commit to setup branch

* workflow finished

* Update nextflow.config

* tumour to tumor, getpileup passed as nomral and tumor

* paired_somatic renamed to tumor_normal_somatic

* Apply suggestions from code review

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* Update subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* updated index names in meta.yml

* changed index file names in main script and test

* Apply suggestions from code review

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* Apply suggestions from code review

* fixed bug from changes

* Apply suggestions from code review

* modified yml to allow new subworkflow testing

* Update test.yml

* Update test.yml

* updated to follow the new mergebam syntax, also made unaligned input sample specific

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-01-27 15:30:27 +00:00
..
abacas Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
adapterremoval Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
agrvate Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
allelecounter Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
amps Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
arriba Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
artic Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
assemblyscan Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
ataqv/ataqv Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bakta Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bamaligncleaner Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bamtools/split Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bamutil/trimbam Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bandage/image Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bbmap Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
bcftools Remove bcftools and ivar module customisations (#1217) 2022-01-18 16:04:56 +00:00
bedtools Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
bismark Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
blast Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bowtie Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bowtie2 Bump software versions for viralrecon modules (#1198) 2022-01-07 17:52:39 +00:00
bwa Add new boolean sort_bam as input to be able to chose between sort and view in bwamem and bwamem2mem (#1125) 2021-12-08 14:31:27 +00:00
bwamem2 Add new boolean sort_bam as input to be able to chose between sort and view in bwamem and bwamem2mem (#1125) 2021-12-08 14:31:27 +00:00
bwameth Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
cat Editing the CAT/CAT module to handle single files (#1196) 2022-01-06 16:41:36 +00:00
cellranger Add bcl2fastq2 to cellranger dockerfile (#1115) 2022-01-25 19:58:22 +01:00
checkm/lineagewf Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
chromap Bump version 0.1.5 to chromap/chromap (#1223) 2022-01-20 19:00:20 +01:00
clonalframeml Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
cmseq/polymut Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
cnvkit/batch Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
cooler Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
csvtk Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
custom Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
cutadapt Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
damageprofiler Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
dastool Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
dedup Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
deeparg Add deeparg (#1234) 2022-01-26 15:19:16 +01:00
deeptools Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
deepvariant Update version & add intervals usage (#1214) 2022-01-17 16:40:31 +01:00
delly/call Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
diamond Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
dragmap feat: update dragmap to follow new bwa/mem + bwamem2/mem logic (#1146) 2021-12-08 23:19:37 +01:00
dragonflye Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
dshbio Update dsh-bio to version 2.0.7, add support for compressed GFA 1.0 format (#1207) 2022-01-17 09:24:40 +00:00
ectyper Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
emmtyper Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
ensemblvep greatly simplify syntax (#1121) 2021-12-07 11:18:12 +01:00
expansionhunter Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
fargene takes gunzip out of fargene main.nf (#1090) 2021-11-29 14:32:23 +01:00
fastani Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
fastp Bump software versions for viralrecon modules (#1198) 2022-01-07 17:52:39 +00:00
fastqc Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
fastqscan Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
fasttree Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
fgbio Added UMI sub-workflow (#1098) 2021-12-09 11:16:40 +01:00
filtlong Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
flash Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
freebayes Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
gatk4 Update mergebam syntax and sample specific unmapped channel (#1238) 2022-01-27 15:30:27 +00:00
genmap Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
genrich Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
gffread Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
glnexus Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
graphmap2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
gstama Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
gtdbtk/classifywf Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
gubbins Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
gunc Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
gunzip Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
hicap Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
hifiasm Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
hisat2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
hmmcopy hmmcopy/mapCounter (#1175) 2021-12-17 15:39:50 +00:00
hmmer/hmmalign Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
homer Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
idr Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
imputeme/vcftoprs Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
iqtree Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
ismapper Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
isoseq3 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
ivar Remove bcftools and ivar module customisations (#1217) 2022-01-18 16:04:56 +00:00
jupyternotebook Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
kallisto/index Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
kallistobustools Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
khmer/normalizebymedian Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
kleborate Fix kleborate inputs (#1172) 2021-12-22 11:39:35 +00:00
kraken2/kraken2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
krona Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
last Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
leehom Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
lima Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
lissero Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
lofreq Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
macrel/contigs Add new module macrel/contigs (#1109) 2021-12-09 13:17:50 +01:00
macs2/callpeak Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
malt Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
maltextract Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
manta Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
mapdamage2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
mash add module for mash dist (#1193) 2022-01-04 17:29:49 +01:00
mashtree Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
maxbin2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
medaka Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
megahit Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
meningotype Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
metabat2 Update metabat2 output channels and compression (#1111) 2021-12-09 15:00:32 +01:00
metaphlan3 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
methyldackel Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
minia Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
miniasm Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
minimap2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
mlst Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
mosdepth Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
msisensor Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
mtnucratio Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
multiqc Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
mummer Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
muscle Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
nanolyse Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
nanoplot Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
ncbigenomedownload Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
nextclade Bump Nextclade version to 1.10.1 (#1236) 2022-01-27 12:53:14 +00:00
ngmaster Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
nucmer Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
optitype Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
pairix Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
pairtools Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
pangolin Bump software versions for viralrecon modules (#1198) 2022-01-07 17:52:39 +00:00
paraclu Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
pbbam/pbmerge Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
pbccs Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
peddy Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
phyloflash Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
picard Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
pirate Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
plasmidid Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
plink Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
plink2/vcf Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
pmdtools/filter Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
porechop Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
preseq/lcextrap Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
prodigal Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
prokka Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
pycoqc Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
pydamage Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
qcat Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
qualimap/bamqc Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
quast Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
racon Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
rapidnj Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
rasusa Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
raxmlng Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
rmarkdownnotebook Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
roary Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
rsem Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
rseqc Provide BAI when running rseqc/tin (#1177) 2021-12-17 10:00:09 +00:00
salmon Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
samblaster Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
samtools Bump software versions for viralrecon modules (#1198) 2022-01-07 17:52:39 +00:00
scoary Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
seacr/callpeak Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
seqkit/split2 Update version & prefix (#1120) 2021-12-07 10:22:32 +01:00
seqsero2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
seqtk Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
sequenzautils Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
seqwish/induce Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
shovill Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
snpdists Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
snpeff greatly simplify syntax (#1121) 2021-12-07 11:18:12 +01:00
snpsift/split Added new module snpsift/split (#1031) 2021-12-17 09:08:14 +01:00
snpsites Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
spades Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
spatyper Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
sratools Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
staphopiasccmec Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
star Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
strelka Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
stringtie Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
subread/featurecounts Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
tabix Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
tbprofiler/profile Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
tiddit Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
trimgalore Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
ucsc ucsc/wigtobigwig: add meta map (#1199) 2022-01-11 21:31:37 +00:00
ultra/pipeline Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
unicycler Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
untar Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
unzip Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
variantbam Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
vcfanno New module/vcfanno (#1204) 2022-01-20 08:46:31 +00:00
vcflib/vcfuniq Add new vcflib/vcfuniq module (#1208) 2022-01-14 18:18:11 +00:00
vcftools Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
yara Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00