Next release v3.0.0#222

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abhi18av wants to merge 98 commits intomasterfrom

Commits on May 15, 2025

Update convert_ismapper_to_vcf.py

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Update convert_ismapper_to_vcf.py

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Update convert_ismapper_to_vcf.py

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Update merge__delly.nf

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Update convert_ismapper_to_vcf.py

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Update merge__delly.nf

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Update convert_ismapper_to_vcf.py

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Update merge__delly.nf

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Update convert_ismapper_to_vcf.py

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Update convert_ismapper_to_vcf.py

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Update convert_ismapper_to_vcf.py

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Update convert_ismapper_to_vcf.py

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Update convert_ismapper_to_vcf.py

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Update convert_ismapper_to_vcf.py

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Update convert_ismapper_to_vcf.py

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Update convert_ismapper_to_vcf.py

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Update convert_ismapper_to_vcf.py

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Update convert_ismapper_to_vcf.py

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Update convert_ismapper_to_vcf.py

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Update convert_ismapper_to_vcf.py

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Update convert_ismapper_to_vcf.py

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Update convert_ismapper_to_vcf.py

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Update convert_ismapper_to_vcf.py

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Update merge__delly.nf

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Update merge__delly.nf

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Update merge__delly.nf

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Update merge__delly.nf

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Update merge__delly.nf

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Update merge__delly.nf

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Update merge__delly.nf

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Update merge__delly.nf

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initial docs website template [ci skip]
abhi18av
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update the website config [ci skip
abhi18av
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add the baseline script from wilma [ci skip]
abhi18av
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refactor wilma's script to a standard structure [ci skip]
abhi18av
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reenable ismapper related code [ci skip]
abhi18av
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convert the bash script to a python one for better experience [ci skip]
abhi18av
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iterim commit [ci skip]
abhi18av
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update the samplesheet validation script to use functions
abhi18av
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add the sanitization logic [ci skip]
abhi18av
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refine the sample name extraction
abhi18av
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fix the escape characters
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fix escapes
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temp disable some analysis
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reenable the analysis
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isolate the bash script to a proper bin/script
abhi18av
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rename file for the script template
abhi18av
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update the process
abhi18av
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updated the python and bash scripts for eventual merge
abhi18av
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update the shell script as per Tim's comment
abhi18av
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prepend study name
abhi18av
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make the colname explicit
abhi18av
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temp
abhi18av
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remove -W since we are using an older version of bcftools
abhi18av
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push the updated merge script, bcftools native gzip
abhi18av
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iterate on patching structural variants [ci skip]
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dev iteration [ci skip]
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dev iteration [ci skip]
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dev iteration
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dev iteration
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dev iteration
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transition to python script
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tweak the filenames for interim output
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dev iteration [ci skip]
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update container defs
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update container
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update the parameters of python script
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dev iteration
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update the container
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rely upon updated tbprofiler containers for patch script
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temp
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finalize the patch script
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dev iteration [ci skip]
abhi18av
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update the patching script
abhi18av
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revert the changes to magma-env-1
abhi18av
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initial docs website template [ci skip]
abhi18av
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update the website config [ci skip
abhi18av
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handle type-casting of fractional values into boolean one [ci skip]
abhi18av
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add a license header for all source files
abhi18av
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add licenseheaders for all config files as well
abhi18av
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handle type-casting of fractional values into boolean one [ci skip]
abhi18av
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Update IS_Queries_Mtb.multi.fasta

mdediegofuertes
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abhi18av
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fix indentation
abhi18av
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fix commented code
abhi18av
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move from delly bcf to vcf
abhi18av
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forward the patched json output from structural variants
abhi18av
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add explicit svmethod for ismapper
abhi18av
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disable the extra view command
abhi18av
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Update patch_tbprofiler_sv_output.py

mdediegofuertes
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abhi18av
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Update patch_tbprofiler_sv_output.py

mdediegofuertes
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abhi18av
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Update patch_tbprofiler_sv_output.py

mdediegofuertes
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abhi18av
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Update patch_tbprofiler_sv_output.py

mdediegofuertes
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abhi18av
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Update patch_tbprofiler_sv_output.py

mdediegofuertes
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abhi18av
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Update patch_tbprofiler_sv_output.py

mdediegofuertes
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abhi18av
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update changelog for v2.0.0
abhi18av
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Commits on Jun 21, 2025

Commits on Sep 4, 2025

Update sample_stats.py (#236)
vrennie
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