mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
e526eae472
* initial commit hisat2/build * initial commit hisat2/build * changed names for hisat2 * fixed directory structure and args * added splice site test data * added splice site inputs * replaced list with individual args * fixed removed commas * added test yml file * updated hisat2 conda version * added meta.yml * added meta.yml description * added meta.yml inputs * added meta.yml outputs * update conda version for hisat2 * removed trailing whitespace meta.yml * fixed version number for containers * added test data to test config * updated for new test logic * fix pytest issue? * fix pytest issue * fixed wrong tool in meta.yaml * updated tets.yaml name * handle build bug for testing * handle build bug for testing in yaml * moved test folder to fix build bug * use old hisat2 version to avoid conda giving inconsistent md5sum * initial commit * removed temp file * added meta yaml * add to pytest * added tests * added test yml * add align meta yaml * add hisat2 align to pytest * remove need for splice data by calling process * add hisat2 align se test * add hisat2 align pe test * update names hisat2 align * update software pytest for using mutiple modules * remove splice site test data since using module instead * remove splice site from config since using module instead * fixed extra brace * added hisat2 align test.yml * removed md5sum for bam files * updated build md5sums * Apply suggestions from code review Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> |
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| .. | ||
| adapterremoval | ||
| allelecounter | ||
| bandage/image | ||
| bcftools | ||
| bedtools | ||
| bismark | ||
| blast | ||
| bowtie | ||
| bowtie2 | ||
| bwa | ||
| bwamem2 | ||
| bwameth | ||
| cat/fastq | ||
| cnvkit | ||
| cutadapt | ||
| dsh | ||
| fastp | ||
| fastqc | ||
| flash | ||
| gatk4 | ||
| gffread | ||
| gunzip | ||
| hisat2 | ||
| homer/annotatepeaks | ||
| ivar | ||
| kallisto/index | ||
| kraken2/run | ||
| methyldackel | ||
| minia | ||
| minimap2/align | ||
| mosdepth | ||
| msisensor | ||
| multiqc | ||
| optitype | ||
| pangolin | ||
| picard | ||
| preseq/lcextrap | ||
| prodigal | ||
| prokka | ||
| qualimap/bamqc | ||
| quast | ||
| salmon | ||
| samtools | ||
| seacr/callpeak | ||
| seqkit/split2 | ||
| sequenzautils/gcwiggle | ||
| seqwish/induce | ||
| shovill | ||
| spades | ||
| star | ||
| strelka/germline | ||
| stringtie | ||
| tabix | ||
| tiddit/sv | ||
| trimgalore | ||
| ucsc | ||
| unicycler | ||
| untar | ||
| vcftools | ||
| yara | ||