suzannejin d6850f8312 modified the samtools/fastq module (#339) ... * 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 Co-authored-by: suzannejin <suzanne.jin@crg.eu>		2021-03-23 17:43:52 +00:00
..
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	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
bcftools	Exchange VCF data by sarscov2 data (#261)	2021-03-09 10:04:08 +01:00
bedtools	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
bismark	bismark: remove underscores from process names (#303)	2021-03-22 17:46:11 +01:00
blast	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
bowtie	Fix bowtie builds (#273)	2021-03-15 15:39:42 +01:00
bowtie2	Fix bowtie builds (#273)	2021-03-15 15:39:42 +01:00
bwa	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
bwamem2	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
bwameth	Remove def from module options definition in main (#270)	2021-03-15 12:16:43 +00:00
cat/fastq	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
cnvkit	cnvkit module (#173)	2021-03-22 15:27:30 -07:00
cutadapt	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
dsh	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
fastp	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
fastqc	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
gatk4	Add gatk4/baserecalibrator (#327)	2021-03-23 18:32:37 +01:00
gffread	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
gunzip	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
ivar	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
kraken2/run	Add kraken2 run module (#266)	2021-03-18 13:08:06 +00:00
methyldackel	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
minia	Adding minia for viralrecon (#267)	2021-03-17 12:54:15 +01:00
minimap2/align	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
mosdepth	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
multiqc	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
optitype	Add in OptiType (configbuilder, type) module(s) (#301)	2021-03-23 16:48:05 +01:00
pangolin	add task.cpus to pangolin (#263)	2021-03-10 09:02:23 +01:00
picard	add picard_collectwgsmetrics (#304)	2021-03-22 17:05:59 +01:00
preseq/lcextrap	Fix preseq tests	2021-02-03 17:28:44 +00:00
prokka	add prokka module (#298)	2021-03-23 02:51:23 -07:00
qualimap/bamqc	Remove def from module options definition in main (#270)	2021-03-15 12:16:43 +00:00
quast	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
salmon	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
samtools	modified the samtools/fastq module (#339)	2021-03-23 17:43:52 +00:00
seacr/callpeak	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
seqkit/split2	Remove def from module options definition in main (#270)	2021-03-15 12:16:43 +00:00
seqwish/induce	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
spades	Add spades module (#277)	2021-03-18 13:48:38 +00:00
star	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
stringtie	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
tabix	Exchange VCF data by sarscov2 data (#261)	2021-03-09 10:04:08 +01:00
tiddit/sv	Update main.nf (#314)	2021-03-22 17:16:43 +00:00
trimgalore	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00
ucsc/bedgraphtobigwig	Change path to tests	2021-02-03 16:44:56 +00:00
unicycler	Adding unicycler module (#307)	2021-03-22 18:14:24 +01:00
untar	Converge test data usage (#249)	2021-03-04 10:10:57 +00:00