mirror of
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01dc6a289d
* hifiasm copied from fastqc * hifiasm tests init from fastqc * meta.yml init; test.yml and main.nf for printing version * Add hifiasm version printing * Removed spaced on an empty line * Reverted hifiasm from main * hifiasm copied from fastqc * hifiasm tests init from fastqc * meta.yml init; test.yml and main.nf for printing version * Add hifiasm version printing * Removed spaced on an empty line * Reverted hifiasm from main * Added seqtk/subseq and checking for seed in seqtk/sample * Separate authors in software/seqtk/sample/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Align commans in output channesl software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Define prefix in software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Use prefix in output file name software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Define suffix in options in tests/software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Change output file name in tests/software/seqtk/subseq/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Remove a to-do point from tests/software/seqtk/subseq/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Added --no-name into gzip commands * Update samtools from 1.10 to 1.12 (#530) * feat: remove social preview image to use GitHub OpenGraph * feat: update samtools from 1.10 to 1.12 * fix: CI tests * fix: add meta.yml file for samtools/merge * Update software/samtools/merge/meta.yml Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update software/samtools/merge/meta.yml Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * hifiasm copied from fastqc * hifiasm tests init from fastqc * meta.yml init; test.yml and main.nf for printing version * Add hifiasm version printing * Removed spaced on an empty line * Reverted hifiasm from main * Added seqtk/subseq and checking for seed in seqtk/sample * hifiasm copied from fastqc * hifiasm tests init from fastqc * meta.yml init; test.yml and main.nf for printing version * Add hifiasm version printing * Removed spaced on an empty line * Reverted hifiasm from main * Separate authors in software/seqtk/sample/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Align commans in output channesl software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Define prefix in software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Use prefix in output file name software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Define suffix in options in tests/software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Change output file name in tests/software/seqtk/subseq/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Remove a to-do point from tests/software/seqtk/subseq/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Added --no-name into gzip commands * Replaced functions.nf in seqtk/subseq * Refreshed tests for sample and subseq * Corrected paired-end test and YAML description for sample Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> |
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| .. | ||
| abacas | ||
| adapterremoval | ||
| allelecounter | ||
| artic | ||
| bandage/image | ||
| bbmap/bbduk | ||
| bcftools | ||
| bedtools | ||
| bismark | ||
| blast | ||
| bowtie | ||
| bowtie2 | ||
| bwa | ||
| bwamem2 | ||
| bwameth | ||
| cat/fastq | ||
| cnvkit | ||
| cooler | ||
| cutadapt | ||
| deeptools | ||
| dshbio | ||
| fastp | ||
| fastqc | ||
| fasttree | ||
| fgbio | ||
| flash | ||
| gatk4 | ||
| genmap | ||
| gffread | ||
| graphmap2 | ||
| gubbins | ||
| gunzip | ||
| hisat2 | ||
| hmmer/hmmalign | ||
| homer/annotatepeaks | ||
| iqtree | ||
| ivar | ||
| kallisto/index | ||
| kallistobustools | ||
| kraken2/run | ||
| last | ||
| lib | ||
| macs2/callpeak | ||
| mash/sketch | ||
| methyldackel | ||
| minia | ||
| minimap2 | ||
| mosdepth | ||
| msisensor | ||
| multiqc | ||
| nanolyse | ||
| nanoplot | ||
| nextclade | ||
| optitype | ||
| pairix | ||
| pairtools | ||
| pangolin | ||
| phantompeakqualtools | ||
| picard | ||
| plasmidid | ||
| preseq/lcextrap | ||
| prodigal | ||
| prokka | ||
| pycoqc | ||
| qcat | ||
| qualimap | ||
| quast | ||
| rapidnj | ||
| rasusa | ||
| raxmlng | ||
| rsem | ||
| rseqc | ||
| salmon | ||
| samtools | ||
| seacr/callpeak | ||
| seqkit/split2 | ||
| seqtk | ||
| sequenzautils | ||
| seqwish/induce | ||
| shovill | ||
| snpsites | ||
| sortmerna | ||
| spades | ||
| star | ||
| strelka/germline | ||
| stringtie | ||
| subread/featurecounts | ||
| tabix | ||
| tiddit/sv | ||
| trimgalore | ||
| ucsc | ||
| umitools | ||
| unicycler | ||
| untar | ||
| vcftools | ||
| yara | ||