mirror of
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95dfa7bc8d
* 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 * Generalized intersect and genomecov * Finished subtract and tests for intersect and genomecov * Finished up meta YAMLs * Replaced functions.nf in subtract * do not add "." in prefix when suffix is set (#550) when using the suffix option in the fastqc module it gets added with a "." to the ${meta.id}, this leads to sample name clashing when passing the fastqc output of raw and processed files suffixed with "trim" or "clean" to multiqc. I suggest to remove the "." this would also be more consistent with the prefix def in most of the other nf-core modules. ##' Ref: https://nfcore.slack.com/archives/CJRH30T6V/p1625129138043900 * Modules TLC (#551) * Modules TLC * Fix all the tests * Fix linting failures (#552) * Modules TLC * Fix all the tests * Fix linting failures * Soft-link build files to bypass lint error * Update software/rseqc/junctionannotation/main.nf * Fix rsem (#555) * bump bcftools filter * fix bcftools * rsem/preparereference * added calculateexpression * meta.yml and pytest_software * paired end * add test.yml * fix rseqc/junctionsaturation (#553) * bump bcftools filter * junctionsaturation meta.yml and test * pytest config entry * bump bcftools version down again * fix test * fix bcftools * Adapt linting action (#556) * bump bcftools filter * fix bcftools * adapt module linting * Update software/bedtools/genomecov/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/bedtools/genomecov/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/bedtools/genomecov/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/bedtools/genomecov/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/bedtools/genomecov/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/bedtools/genomecov/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/bedtools/genomecov/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/bedtools/genomecov/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/bedtools/genomecov/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/bedtools/intersect/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/bedtools/genomecov/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/bedtools/genomecov/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/bedtools/intersect/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/bedtools/intersect/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/bedtools/intersect/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/bedtools/intersect/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/bedtools/intersect/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/bedtools/intersect/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/bedtools/intersect/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/bedtools/intersect/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/bedtools/subtract/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/bedtools/subtract/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/bedtools/subtract/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/bedtools/subtract/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/bedtools/genomecov/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/bedtools/genomecov/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/bedtools/intersect/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/bedtools/intersect/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Fixed variable names in intersect and genomecov Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk> Co-authored-by: riederd <dietmar.rieder@i-med.ac.at> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Kevin Menden <kevin.menden@t-online.de> |
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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 | ||
| damageprofiler | ||
| deeptools | ||
| delly/call | ||
| dshbio | ||
| ensemblvep | ||
| fastp | ||
| fastqc | ||
| fasttree | ||
| fgbio | ||
| flash | ||
| gatk4 | ||
| genmap | ||
| gffread | ||
| graphmap2 | ||
| gubbins | ||
| gunzip | ||
| hisat2 | ||
| hmmer/hmmalign | ||
| homer/annotatepeaks | ||
| iqtree | ||
| ivar | ||
| kallisto/index | ||
| kallistobustools | ||
| kraken2/kraken2 | ||
| last | ||
| lib | ||
| lofreq | ||
| macs2/callpeak | ||
| mash/sketch | ||
| metaphlan3 | ||
| methyldackel | ||
| minia | ||
| minimap2 | ||
| mosdepth | ||
| msisensor | ||
| multiqc | ||
| muscle | ||
| 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 | ||
| snpeff | ||
| snpsites | ||
| sortmerna | ||
| spades | ||
| star | ||
| strelka/germline | ||
| stringtie | ||
| subread/featurecounts | ||
| tabix | ||
| tiddit/sv | ||
| trimgalore | ||
| ucsc | ||
| umitools | ||
| unicycler | ||
| untar | ||
| vcftools | ||
| yara | ||