Merge branch 'configure-tronflow' into 'master'

Configure tronflow

See merge request tron/covigator-ngs-pipeline!4

README.md

@@ -85,3 +85,25 @@ Output:
 - Wilm, A., Aw, P. P. K., Bertrand, D., Yeo, G. H. T., Ong, S. H., Wong, C. H., Khor, C. C., Petric, R., Hibberd, M. L., & Nagarajan, N. (2012). LoFreq: A sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Research, 40(22), 11189–11201. https://doi.org/10.1093/nar/gks918
 - Grubaugh, N. D., Gangavarapu, K., Quick, J., Matteson, N. L., De Jesus, J. G., Main, B. J., Tan, A. L., Paul, L. M., Brackney, D. E., Grewal, S., Gurfield, N., Van Rompay, K. K. A., Isern, S., Michael, S. F., Coffey, L. L., Loman, N. J., & Andersen, K. G. (2019). An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar. Genome Biology, 20(1), 8. https://doi.org/10.1186/s13059-018-1618-7
 - Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu; fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, 1 September 2018, Pages i884–i890, https://doi.org/10.1093/bioinformatics/bty560
+
+
+## Known issues
+
+The variant normalization workflow may appear as corrupt when calling to it concurrently. 
+A workaround to this situation is to clone the tronflow dependencies and let covigator pipeline know of the location of the `main.nf` files.
+
+For instance:
+```
+cd /covigator/dependencies
+git clone --branch v1.4.0 https://github.com/TRON-Bioinformatics/tronflow-bwa.git
+git clone --branch v1.5.0 https://github.com/TRON-Bioinformatics/tronflow-bam-preprocessing.git
+git clone --branch v1.1.0 https://github.com/TRON-Bioinformatics/tronflow-variant-normalization.git
+```
+
+And then use the following parameters:
+```
+nextflow run tron-bioinformatics/covigator-ngs-pipeline -profile conda \ 
+--tronflow_bwa /covigator/dependencies/tronflow-bwa/main.nf \
+--tronflow_bam_preprocessing /covigator/dependencies/tronflow-bam-preprocessing/main.nf \
+--tronflow_variant_normalization /covigator/dependencies/tronflow-variant-normalization/main.nf ...
+```