mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
8a2a9f7e81
* Normal bam file added * Normal bam.bai file added * Tumour bam bai files added * human dir added * annotation dir added * cnvkit dir added * cnvkit dir added * Update software/cnvkit/main.nf Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se> * Update software/cnvkit/main.nf Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se> * Update software/cnvkit/main.nf Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se> * changed input filenames * edited main.nf * edited main.nf * edited meta.nf * edited test.yml * filters.yml * edited main * edited main * edited meta * edited meta * edited main * removed unwanted lines * edited the path to the main.nf * removed function.nf * added functions.nf * deleted 2 workflows and craeted a common workflow * deleted paths for 2 workflows and created paths for a common workflow * Deleted annotation dir * deleted params.modules * Edited meta.with_normal * deleted normal_280_sub_chr21.bam * deleted normal_280_sub_chr21.bam.bai * deleted tumour_278_sub_chr21.bam * deleted tumour_278_sub_chr21.bam.bai * Edited input and script parts * Edited input part * Added * Edited args * Edited script * Edited input * Changed annotation to annotationfile * Changed description of the tool * edited singularuty container * edited input * line 44 removed trailing whitespace * Edited addParams * Deleted pdf output * Deleted pdf output * edited the path to main.nf * edited path to the main.nf * Added docker image version * Removed extra ../ * added md5sums * added md5sums * Update software/cnvkit/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/cnvkit/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Edited the script * Edited the input * Edited main.nf * Edited main.nf * edited md5sum for reference.cnn * removed human fasta * removed human fasta.fai * added GRCh38 fasta * added GRCh38 fasta.fai * added hg19 fasta.fai * added hg19 fasta * Edited fasta file name * Edited bed file names and md5sums * Edited md5sums * edited the input and script section * edited input section * added targetfile * changed the files * changed the output files * added bam files * added bam files * remove files * added md5sums * replace file * added files * edited tests/software/cnvkit files * edited tests/software/cnvkit files * edited authors list * removed files * added files * added files * added files * added files * added file * added file * added file * added file * edited files * edited files * edited files * edited files * edited files * edited files * added new module * added new module * edited files * edited file * edited file * edited file * removed files Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com> Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> |
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| .. | ||
| adapterremoval | ||
| bandage/image | ||
| bcftools | ||
| bedtools | ||
| bismark | ||
| blast | ||
| bowtie | ||
| bowtie2 | ||
| bwa | ||
| bwamem2 | ||
| bwameth | ||
| cat/fastq | ||
| cnvkit | ||
| cutadapt | ||
| deeptools | ||
| dsh | ||
| fastp | ||
| fastqc | ||
| gatk4 | ||
| gffread | ||
| gunzip | ||
| hisat2 | ||
| homer/annotatepeaks | ||
| ivar | ||
| kraken2/run | ||
| lib | ||
| macs2/callpeak | ||
| methyldackel | ||
| minia | ||
| minimap2/align | ||
| mosdepth | ||
| multiqc | ||
| pangolin | ||
| phantompeakqualtools | ||
| picard | ||
| preseq/lcextrap | ||
| qualimap | ||
| quast | ||
| rsem | ||
| rseqc | ||
| salmon | ||
| samtools | ||
| seacr/callpeak | ||
| seqkit/split2 | ||
| seqwish/induce | ||
| sortmerna | ||
| spades | ||
| star | ||
| stringtie | ||
| subread/featurecounts | ||
| tabix | ||
| tiddit/sv | ||
| trimgalore | ||
| ucsc/bedgraphtobigwig | ||
| umitools | ||
| unicycler | ||
| untar | ||