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* update the parameter name to use_ref_gvcf * add the v2 reference GVCF and remove the old one * tweak the default for phylogeny and clustering param
* initial removal of bundled who-magma database for tb-profiler * fix dangling reference for exit_rif gvcf * fix dangling reference again * fix typo * fix more typos
Compute FASTQ stats from the input samplesheet
Enable the ITOL annotations in the tb-profiler command
VQSR should not be skipped by default
…iles Add clarification for bqsr recaliberated files
* Add the ismapper module [ci skip] * add files from @vrennie * add CLI interface to the script * accommodate docker container and the gbk ref * fix input * quickfix * fix * fix * fix * fix * fix * fix * interim commit for python script * iteration to accommodate ismapper * Update the IS sequence * NOTE: Hard code the element name for testing * refactor to use query file instead of te * patch-work to accommodate a single IS element * tweak globing pattern * fix type in python script * fix imports * iterate upon the ismapper output * Update magma-env-1.yml * tweak the var name * add default publishDir * change the module name to align with the actual subworkflow * fix the import file location * enable the publication of ismapper vcf indexes * enable view for some channels * view ismapper channel contents * merge delly and ismapper vcf files * fix channel concatenation * update channel view tag * collect concatenated results * add view onto the channels * add distince * replace distinct -> unique * update views * unique channel contents * update bcftools merge * separate bcftools merge for delly and lofreq * get structural variants * dev iteration * iter * dev iteration * fix * iter * update the main conversion script * update the baseline magma-container-1 for overall setup * update the relevant containers and environments * tweak the config file comments * enable dump on structural variants channels * add publish Dir defaults * prune comments * tweak comments * Delete resources/regions/IS_Queries_Mtb.multi.fasta Replace fasta with original file used by authors (https://doi.org/10.1016/S2666-5247(24)00053-3) for IS6110 detection. * Add files via upload * Rename IS_queries_Mtb.multi.fasta to IS_Queries_Mtb.multi.fasta Fix typo * Update IS_Queries_Mtb.multi.fasta Fix header in fasta --------- Co-authored-by: vrennie <113892099+vrennie@users.noreply.github.com> Co-authored-by: Miguel de Diego Fuertes <118442908+mdediegofuertes@users.noreply.github.com>
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Principal additions introduced by this PR are enumerated below
#192
#199
#203
#210
#205
#197
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#203
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#213