Initializing gh-pages branch

.gitignore

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+.DS_Store
+*.log
+tmp/
+
+data/mock_data/
+data/test_data/
+
+resources/exit_rif/
+
+containers/magma-container-1/resistance_db_who
+
+*/**/*fastq.gz
+*/**/*fasta
+*/**/*gbk
+*/**/*dot
+*/**/*svg
+*/**/*mp4
+
+.idea
+work/
+data/full_data
+results*
+*.nextflow*
+
+conda_envs/magma-env*
+containers/**/*yml
+
+samplesheet.csv
+magma.sh
+.Rproj.user

CHANGELOG.md

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+# CHANGELOG FOR THE MAGMA PIPELINE VERSIONS
+
+## v2.0.0
+
+1. Update `tb-profiler` to `v6.2.1` along with the `WHO mutations catalog v2` with the database version `30f8bc37df15affa378ebbfbd3e1eb4c5903056e`
+
+2. Addition of `ntm-profiler` with the database FIXME
+
+3. Two new `conda-envs` and containers have been added to the pipeline, relying directly on upstream biocontainers for both `ntm-profiler` and `tb-profiler`
+
+4. Changes to the directory structure
+
+5. Addition of mixed-infections resistance summary script
+
+6. Addition of `low_memory` profile to accommodate lower end infrastructure
+
+7. Updates to the names of parameters for triggering partial/optional workflows
+
+
+## v1.1.1
+
+Created a parallel workflow for mapping without using the strict seed lenght for use in the structural variant workflow.
+
+Updated TBProfiler to version 5.0.0 and recreated the resistance database to work with the the new version
+
+Updated the summarize resistance script to include the structural variants in the excel output
+
+
+## v1.0.0
+
+Initial release of the pipeline

Makefile

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+# https://makefiletutorial.com/
+
+run_dev:
+	nextflow run main.nf -profile conda,dev -entry TEST  -resume -with-tower
+
+run_devslurm:
+	nextflow run main.nf -profile conda,dev_slurm -entry TEST  -resume
+
+run_test:
+	nextflow run main.nf -params-file params/standard.yml -entry test -resume
+
+sync:
+	bash _resources/sync.sh
+
+sync_devslurm:
+	bash _resources/sync_slurmhpc.sh