[Do not merge!] Pseudo PR for first release #155
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Improve tests in dog genome
change output directory
* Template update for nf-core/tools version 3.0.0 * Template update for nf-core/tools version 3.0.1 * Update template_version_comment.yml * Update template_version_comment.yml * Add title to usage files * Remove old way igenomes config * Update main.nf and utils nf-core sbwf * Update schema json * Fix linting * Update validation snap --------- Co-authored-by: nf-core-bot <core@nf-co.re>
* Template update for nf-core/tools version 3.0.0 * Template update for nf-core/tools version 3.0.1 * Template update for nf-core/tools version 3.0.2 * Update sha --------- Co-authored-by: Louis Le Nezet <louislenezet@gmail.com>
* New dev * Rename function * Fix function * Update workflow name * Update tests * Update function usage * Update tests snapshot * Update changelog * Change phased to phase * Update documentation * Update snapshot * Update publishing panel * Update test * Update docs/usage.md Co-authored-by: Anabella Trigila <18577080+atrigila@users.noreply.github.com> --------- Co-authored-by: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
* Update workflow metro map * Update metro map * Update metro map and add animation * Improve timing svg * Update README.md --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com>
* Remove phase autodetect * Aggregate glimpse1 bams, merge vcf * Aggregate glimpse and quilt bams * Add to conf * Add fasta to quilt and keep vcf merged * Add modules list_to_file * Order called sample * Take out GL computation from swf glimpse1 * Add bamlist to quilt and glimpse2 * Put stitch parameters preparation in stitch sbwf * Add batch_size and group samples in main workflow * Update config * Update config * Add validation of batch size and tools compatibility * Update test workflow * Add batch to metamap * Update conf * Fix bam regions map * Use dot as separator * Update test and Changelog * Update docs * Improve documentation * Patch modified modules * Order samples names in snaphot * Update changelog * Improve pipeline * Order files before grouping and split output vcf * Add validation to snapshot * Update schema description * Fix tags * Add splitting by samples for each output * Split validation truth set by sample * Fix split * Put in samples folder --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com>
* Update bcftools annotate * Update bcftools concat * Update bcftools convert * Update bcftools index * Update bcftools merge * Update bcftools mpileup * Update bcftools norm * Update bcftools pluginsplit * Update bcftools stats * Update bcftools view * Update bedtools makewindows * Remove dumpsoftware * Update gawk * Update glimpse * Update glimpse2 * Update gunzip * Update quilt * Update samtools * Update shapeit5 * Update shapeit5 * Update stitch * Update tabix * Update vcflib * Fix linting * Update pluginsplit
* typo fixes in readme * remove some to-dos * remove todos, add bibliography * add conditional detection of tools * add missing tools to citations * add conditional params * add release name and date * bump versions * add contributors and reviewers * Update README.md * Update README.md * Update README.md --------- Co-authored-by: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com>
Fix checkchr
* Remove conda from PR test * Add seed for stitch and quilt * Bump version in nf-core yml * Update changelog
* updates in the README and usage files * updated README file * documents after prettier * lastest update in usage file * Conda check removed and seed parameters added for QUILT (#146) * Remove conda from PR test * Add seed for stitch and quilt * Bump version in nf-core yml * Update changelog * updates in the README and usage files * Fix linting * CHANGELOG prettier * alteration added to the Changed section --------- Co-authored-by: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com>
Replacing "./" from usage file.
* Fix workflow dispatch * Remove TODO
Improve config and reduce fulltest
Update metromap and logo
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Do not merge! This is a PR of
devcompared to theTEMPLATEbranch for whole-pipeline reviewing purposes. Changes should be made todevand this PR should not be merged into first-commit-for-pseudo-pr!