Rename processes (#4)

* Many changes, streamlining and renaming

* Remove unused scripts

* Update help, README

* Update README, help

* Remove unnecessary change

* Remove unused config, adjust alignment

.gitignore

@@ -3,3 +3,5 @@ nextflow
 results
 *.sif
 work
+test_output
+test_input

README.md

@@ -5,16 +5,39 @@ A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (h
 
 #### Introduction
 
-------------
 This pipeline is based on the [BCCDC-PHL/ncov2019-artic-nf](https://github.com/BCCDC-PHL/ncov2019-artic-nf) pipeline, which is a fork of the [connor-lab/ncov2019-artic-nf](https://github.com/connor-lab/ncov2019-artic-nf) pipeline. It has been modified to support analysis of monkeypox virus.
-
+
+```mermaid
+flowchart TD
+  ref[ref.fa]
+  composite_ref[composite_ref.fa]
+  primers[primer.bed]
+  fastq[fastq_dir]
+  fastq --> performHostFilter(performHostFilter)
+  composite_ref --> performHostFilter
+  performHostFilter(performHostFilter) --> normalizeDepth(normalizeDepth)
+  readTrimming(readTrimming) --> filterResidualAdapters(filterResidualAdapters) 
+  normalizeDepth(normalizeDepth) --> readTrimming(readTrimming)
+  filterResidualAdapters --> readMapping(readMapping)
+  ref --> readMapping(readMapping)
+  readMapping(readMapping) --> trimPrimerSequences(trimPrimerSequences)
+  primers --> trimPrimerSequences(trimPrimerSequences)
+  trimPrimerSequences(trimPrimerSequences) --> callConsensusFreebayes(callConsensusFreebayes)
+  callConsensusFreebayes(callConsensusFreebayes) --> alignConsensusToReference(alignConsensusToReference)
+  ref --> alignConsensusToReference
+  trimPrimerSequences --> makeQCCSV(makeQCCSV)
+  callConsensusFreebayes --> makeQCCSV
+  callConsensusFreebayes --> consensus[consensus.fa]
+  callConsensusFreebayes --> variants[variants.vcf]
+  ref --> makeQCCSV
+  makeQCCSV --> qcCSV(qc.csv)
+```
 
 #### Quick-start
-##### Illumina
 
 ```
 nextflow run BCCDC-PHL/mpxv-artic-nf -profile conda \
-  --illumina --prefix "output_file_prefix" \
+  --prefix "output_file_prefix" \
   --bed /path/to/primers.bed \
   --ref /path/to/ref.fa \
   --primer_pairs_tsv /path/to/primer_pairs_tsv \
@@ -33,33 +56,23 @@ The repo contains a environment.yml files which automatically build the correct
 
 --cache /some/dir can be specified to have a fixed, shared location to store the conda build for use by multiple runs of the workflow.
 
-#### Executors
-By default, the pipeline just runs on the local machine. You can specify `-profile slurm` to use a SLURM cluster, or `-profile lsf` to use an LSF cluster. In either case you may need to also use one of the COG-UK institutional config profiles (phw or sanger), or provide queue names to use in your own config file.
-
-#### Profiles
-You can use multiple profiles at once, separating them with a comma. This is described in the Nextflow [documentation](https://www.nextflow.io/docs/latest/config.html#config-profiles) 
-
 #### Config
-Common configuration options are set in `conf/base.config`. Workflow specific configuration options are set in `conf/illumina.config` They are described and set to sensible defaults (as suggested in the [nCoV-2019 novel coronavirus bioinformatics protocol](https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html "nCoV-2019 novel coronavirus bioinformatics protocol"))
 
 Important config options are:
 
 | Option                           | Default  | Description                                                                                                         |
 |:---------------------------------|---------:|--------------------------------------------------------------------------------------------------------------------:|
-| `allowNoprimer`                  | `true`   | Allow reads that don't have primer sequence? Ligation prep = `false`, nextera = `true`                              |
-| `illuminaKeepLen`                | `50`     | Length of illumina reads to keep after primer trimming                                                              |
-| `illuminaQualThreshold`          | `20`     | Sliding window quality threshold for keeping reads after primer trimming (illumina)                                 |
-| `mpileupDepth`                   | `100000` | Mpileup depth for ivar                                                                                              |
-| `varFreqThreshold`               | `0.75`   | ivar/freebayes frequency threshold for consensus variant                                                            |
-| `varMinFreqThreshold             | `0.25`   | ivar/freebayes frequency threshold for ambiguous variant                                                            |
+| `normalizationTargetDepth`       | `200`    | Target depth of coverage to normalize to prior to alignment                                                         |
+| `normalizationMinDepth`          | `5`      | Minimum depth of coverage to normalize to prior to alignment                                                        |
+| `keepLen`                        | `50`     | Length of reads to keep after primer trimming                                                                       |
+| `qualThreshold`                  | `20`     | Sliding window quality threshold for keeping reads after primer trimming                                            |
+| `varMinFreqThreshold`            | `0.25`   | Allele frequency threshold for ambiguous variant                                                                    |
+| `varFreqThreshold`               | `0.75`   | Allele frequency threshold for unambiguous variant                                                                  |
 | `varMinDepth`                    | `10`     | Minimum coverage depth to call variant                                                                              |
-| `ivarMinVariantQuality`          | `20`     | ivear minimum mapping quality to call variant                                                                       |
-| `downsampleMappingQuality`       | `20`     | Exclude reads below this mapping quality while downsampling                                                         |
-| `downsampleAmpliconSubdivisions` | `3`      | Number of times amplicons are subdivided to determine locations of checkpoints to test for depth while downsampling |
 
 
 #### QC
 A script to do some basic QC is provided in `bin/qc.py`. This currently tests if >50% of reference bases are covered by >10 reads (Illumina) or >20 reads (Nanopore), OR if there is a stretch of more than 10 Kb of sequence without N - setting qc_pass in `<outdir>/<prefix>.qc.csv` to TRUE. `bin/qc.py` can be extended to incorporate any QC test, as long as the script outputs a csv file a "qc_pass" last column, with samples TRUE or FALSE.
 
 #### Output
-A subdirectory for each process in the workflow is created in `--outdir`. A `nml_upload` subdirectory containing files important for [CanCOGeN](https://www.genomecanada.ca/en/cancogen) is created. 
+A subdirectory for each process in the workflow is created in `--outdir`. A `nml_upload` subdirectory containing dehosted fastq files and consensus sequences is included.