Yuk Kei Wan 16e8d21477 Nanoplot and sequencing_summary.txt for Nanopore test data (#364) ... * add nanoplot * add Nanopore 100 read subset bam and fastq * add nanoplot module and sequencing_summary.txt * Update pytest_software.yml * Update main.nf * test directory path * testing one output file * Update main.nf * fix typo * remove path to test outputs (it worked locally) * use test_data.config in test * add meta.yml * allowing either summary.txt or fastq.gz inputs * fix linting and test.yml * test whether github check can catch the output * add summary.txt test output paths * check Nanoplot-report.html output		2021-04-09 08:31:38 +01:00
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adapterremoval	Update restructured paths (#380)	2021-03-24 18:26:54 +00:00
allelecounter	Update test data paths. (#375)	2021-03-24 18:18:01 +00:00
bandage/image	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
bcftools	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
bedtools	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
bismark	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
blast	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
bowtie	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
bowtie2	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
bwa	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
bwamem2	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
bwameth	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
cat/fastq	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
cnvkit	Update test data paths. (#375)	2021-03-24 18:18:01 +00:00
cutadapt	Update test data paths. (#375)	2021-03-24 18:18:01 +00:00
dsh	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
fastp	modify fastp tests (#367)	2021-03-24 17:08:59 +01:00
fastqc	Use a config containing all test data for module tests (#365)	2021-03-24 13:07:37 +00:00
fasttree	adding fasttree module (#412)	2021-04-08 18:15:23 +01:00
fgbio	New modules: Fgbio callmolecularconsensusreads and sortbam (#352)	2021-03-28 20:38:50 +01:00
flash	update tests for new config (#384)	2021-04-01 20:22:06 +01:00
gatk4	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
gffread	Fixing a bunch of module tests (#370)	2021-03-24 17:36:29 +00:00
gubbins	Update gubbins module to use new files (#417)	2021-04-09 07:54:11 +01:00
gunzip	Update test data paths. (#375)	2021-03-24 18:18:01 +00:00
hisat2	Add tests for hisat2 (#366)	2021-03-25 21:08:46 +00:00
homer/annotatepeaks	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
ivar	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
kallisto/index	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
kraken2/run	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
methyldackel	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
minia	Fixing a bunch of module tests (#370)	2021-03-24 17:36:29 +00:00
minimap2/align	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
mosdepth	update tests for new config (#384)	2021-04-01 20:22:06 +01:00
msisensor	Add module: nf-core hackathon #207 : new module: msisensor/msi (#343)	2021-03-25 16:46:00 -04:00
multiqc	Fix some module test after adapting test config approach (#379)	2021-03-24 18:29:41 +00:00
nanoplot	Nanoplot and sequencing_summary.txt for Nanopore test data (#364)	2021-04-09 08:31:38 +01:00
optitype	update tests for new config (#384)	2021-04-01 20:22:06 +01:00
pangolin	Version bumps and minor module updates (#406)	2021-04-06 13:38:41 +01:00
picard	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
plasmidid	Add plasmidid module (#410)	2021-04-08 22:44:30 +01:00
preseq/lcextrap	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
prodigal	Update test data paths. (#375)	2021-03-24 18:18:01 +00:00
prokka	Update test data paths. (#375)	2021-03-24 18:18:01 +00:00
qualimap/bamqc	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
quast	update tests for new config (#384)	2021-04-01 20:22:06 +01:00
salmon	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
samtools	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
seacr/callpeak	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
seqkit/split2	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
sequenzautils	PR for sequenzautils/bam2seqz (#395)	2021-04-01 07:08:27 +02:00
seqwish/induce	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
shovill	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
snpsites	New Snpsites module (#416)	2021-04-09 08:00:33 +01:00
spades	Version bumps and minor module updates (#406)	2021-04-06 13:38:41 +01:00
star	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
strelka/germline	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
stringtie	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
subread/featurecounts	Add tests for subread #106 (#393)	2021-04-01 20:02:36 +01:00
tabix	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
tiddit/sv	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
trimgalore	Fix a bunch of failing tests after switching to test config (#378)	2021-03-24 18:28:54 +00:00
ucsc	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00
unicycler	update tests for new config (#384)	2021-04-01 20:22:06 +01:00
untar	Fix some module tests after switching to config data (#386)	2021-03-24 18:28:07 +00:00
vcftools	Fixing vcftools and bismark tests (#383)	2021-03-25 09:12:08 +00:00
yara	Lint modules ci (#389)	2021-04-08 09:10:52 +01:00