Merge branch '21-software_versions' into 'master'
Resolve "Output software versions and methods and references" Closes #21 See merge request !23
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- .gitlab-ci.yml 4 additions, 0 deletions.gitlab-ci.yml
- docs/references.md 49 additions, 0 deletionsdocs/references.md
- workflow/conf/biohpc.config 5 additions, 2 deletionsworkflow/conf/biohpc.config
- workflow/conf/multiqc_config.yaml 36 additions, 0 deletionsworkflow/conf/multiqc_config.yaml
- workflow/main.nf 52 additions, 5 deletionsworkflow/main.nf
- workflow/scripts/annotate_peaks.R 5 additions, 0 deletionsworkflow/scripts/annotate_peaks.R
- workflow/scripts/call_peaks_macs.py 34 additions, 10 deletionsworkflow/scripts/call_peaks_macs.py
- workflow/scripts/convert_reads.py 18 additions, 0 deletionsworkflow/scripts/convert_reads.py
- workflow/scripts/diff_peaks.R 5 additions, 0 deletionsworkflow/scripts/diff_peaks.R
- workflow/scripts/experiment_qc.py 9 additions, 1 deletionworkflow/scripts/experiment_qc.py
- workflow/scripts/generate_references.py 67 additions, 0 deletionsworkflow/scripts/generate_references.py
- workflow/scripts/generate_versions.py 138 additions, 0 deletionsworkflow/scripts/generate_versions.py
- workflow/scripts/map_qc.py 30 additions, 1 deletionworkflow/scripts/map_qc.py
- workflow/scripts/map_reads.py 21 additions, 0 deletionsworkflow/scripts/map_reads.py
- workflow/scripts/motif_search.py 22 additions, 3 deletionsworkflow/scripts/motif_search.py
- workflow/scripts/overlap_peaks.py 13 additions, 0 deletionsworkflow/scripts/overlap_peaks.py
- workflow/scripts/pool_and_psuedoreplicate.py 0 additions, 2 deletionsworkflow/scripts/pool_and_psuedoreplicate.py
- workflow/scripts/trim_reads.py 18 additions, 0 deletionsworkflow/scripts/trim_reads.py
- workflow/scripts/xcor.py 26 additions, 3 deletionsworkflow/scripts/xcor.py
- workflow/tests/test_generate_software_references.py 36 additions, 0 deletionsworkflow/tests/test_generate_software_references.py
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