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nf-core_modules/software
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suzannejin 989fb7d5b7
modify test path - module gatk4 + added new module gatk4/haplotypecaller (#382) 
* new module: samtools/fastq

* solve conflict: pytest_software.yml

* solve linting conflicts

* solved EditorConfig linting problem

* Module samtools/fastq:
	* output compressed fastq.gz file(s)
	* add if conditionals for single/paired reads

* samtools/fastq: modified test.yml

* samtools/fastq: modified main.nf to avoid duplicated part of the script section

* fix README.md

* modify test path gatk4

* fix config

* Add new module gatk4/haplotypecaller

* solve check issues

* fix test.yml file

* fix test.yml gz.tbi

* Update software/gatk4/haplotypecaller/main.nf

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

* Update software/gatk4/haplotypecaller/main.nf

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

* Update software/gatk4/haplotypecaller/main.nf

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

* Update software/gatk4/haplotypecaller/meta.yml

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

* Update software/gatk4/haplotypecaller/meta.yml

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

* Update tests/software/gatk4/haplotypecaller/main.nf

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

* Apply suggestions from code review

Co-authored-by: suzannejin <suzanne.jin@crg.eu>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-26 12:46:46 +01:00
..
adapterremoval new module: AdapterRemoval (#309) 2021-03-22 17:16:04 +00:00
allelecounter Add alleleCounter module (#313) 2021-03-23 14:37:53 +01:00
bandage/image remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
bcftools remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
bedtools remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
bismark bismark: remove underscores from process names (#303) 2021-03-22 17:46:11 +01:00
blast remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
bowtie Add default output dir for modules that create indices, updated (#336) 2021-03-23 17:55:01 +00:00
bowtie2 Add default output dir for modules that create indices, updated (#336) 2021-03-23 17:55:01 +00:00
bwa Update test paths in bwa mappers (#387) 2021-03-25 09:24:21 +00:00
bwamem2 Update test paths in bwa mappers (#387) 2021-03-25 09:24:21 +00:00
bwameth Add default output dir for modules that create indices, updated (#336) 2021-03-23 17:55:01 +00:00
cat/fastq remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
cnvkit cnvkit module (#173) 2021-03-22 15:27:30 -07:00
cutadapt remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
deeptools Remove def from module options definition in main (#270) 2021-03-15 12:16:43 +00:00
dsh remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
fastp remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
fastqc remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
flash Re-organise all test data (#354) 2021-03-24 09:53:41 +00:00
gatk4 modify test path - module gatk4 + added new module gatk4/haplotypecaller (#382) 2021-03-26 12:46:46 +01:00
gffread Fix nf-core modules lint tests (#275) 2021-03-16 17:16:47 +00:00
gunzip remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
hisat2 Add tests for hisat2 (#366) 2021-03-25 21:08:46 +00:00
homer/annotatepeaks Homer (#330) 2021-03-23 11:24:54 -07:00
ivar remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
kallisto/index Add module kallisto/index (#357) 2021-03-24 12:25:39 +00:00
kraken2/run Add kraken2 run module (#266) 2021-03-18 13:08:06 +00:00
lib style(#77): Fix editorconfig errors 2020-12-17 17:50:24 -06:00
macs2/callpeak Remove def from module options definition in main (#270) 2021-03-15 12:16:43 +00:00
methyldackel methyldackel: bump version to 0.5.2 (#305) 2021-03-22 17:46:28 +01:00
minia remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
minimap2/align remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
mosdepth remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
msisensor Add module: nf-core hackathon #207 : new module: msisensor/msi (#343) 2021-03-25 16:46:00 -04:00
multiqc remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
optitype Add in OptiType (configbuilder, type) module(s) (#301) 2021-03-23 16:48:05 +01:00
pangolin remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
phantompeakqualtools Remove def from module options definition in main (#270) 2021-03-15 12:16:43 +00:00
picard add picard_collectwgsmetrics (#304) 2021-03-22 17:05:59 +01:00
preseq/lcextrap Remove def from module options definition in main (#270) 2021-03-15 12:16:43 +00:00
prodigal Prodigal (#333) 2021-03-23 11:03:58 -07:00
prokka Add process label to prokka (#350) 2021-03-24 04:54:52 +00:00
qualimap remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
quast remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
rsem Add default output dir for modules that create indices, updated (#336) 2021-03-23 17:55:01 +00:00
rseqc Remove def from module options definition in main (#270) 2021-03-15 12:16:43 +00:00
salmon Add default output dir for modules that create indices, updated (#336) 2021-03-23 17:55:01 +00:00
samtools modified the samtools/fastq module (#339) 2021-03-23 17:43:52 +00:00
seacr/callpeak remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
seqkit/split2 remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
sequenzautils/gcwiggle PR for sequenzautils/gcwiggle (#345) 2021-03-24 05:03:03 +00:00
seqwish/induce remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
shovill Update shovill module (#337) 2021-03-24 04:57:41 +00:00
sortmerna Remove def from module options definition in main (#270) 2021-03-15 12:16:43 +00:00
spades Add spades module (#277) 2021-03-18 13:48:38 +00:00
star Add default output dir for modules that create indices, updated (#336) 2021-03-23 17:55:01 +00:00
strelka/germline Re-organise all test data (#354) 2021-03-24 09:53:41 +00:00
stringtie Remove def from module options definition in main (#270) 2021-03-15 12:16:43 +00:00
subread/featurecounts Remove def from module options definition in main (#270) 2021-03-15 12:16:43 +00:00
tabix remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
tiddit/sv remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
trimgalore remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
ucsc ucsc_bed12tobigbed (previous pull request had conflicts) (#302) 2021-03-24 04:55:49 +00:00
umitools Remove def from module options definition in main (#270) 2021-03-15 12:16:43 +00:00
unicycler Adding unicycler module (#307) 2021-03-22 18:14:24 +01:00
untar remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
vcftools add vcftools module (#334) 2021-03-24 04:54:23 +00:00
yara Add YARA module (#353) 2021-03-24 17:14:52 +01:00