Fix genome size

conf/modules.config

@@ -22,7 +22,7 @@ process {
 
     // Files to be uploaded to the TreeVal JBrowse2 instance
     // .genome, .gz.{tbi|csi}, .bigBed, .bigWig, .paf
-    withName: 'GENERATE_GENOME_FILE|TABIX_BGZIPTABIX|UCSC_BEDTOBIGBED|UCSC_BEDGRAPHTOBIGWIG|.*:.*:SYNTENY:MINIMAP2_ALIGN|.*:.*:GENERATE_GENOME:CUSTOM_GETCHROMSIZES' {
+    withName: 'GENERATE_GENOME_FILE|TABIX_BGZIPTABIX|UCSC_BEDTOBIGBED|UCSC_BEDGRAPHTOBIGWIG|.*:.*:SYNTENY:MINIMAP2_ALIGN|.*:.*:GENERATE_GENOME:GNU_SORT' {
         publishDir = [
             path: { "${params.outdir}/treeval_upload" },
             mode: params.publish_dir_mode,

docs/usage.md

@@ -93,10 +93,31 @@ samtools index {prefix}.cram
 
 Find information on this here: [PacBio Data Prep](pacbio.md)
 
+#### PreText Accessory ingestion
+
+Note: This will require you to install bigwigToBedGraph from the ucsc package. Instructions on downloading this can be found at [EXAMPLE #3](https://genome.ucsc.edu/goldenPath/help/bigWig.html#:~:text=Alternatively%2C%20bigWig%20files%20can%20be,to%20the%20Genome%20Browser%20server.)
+
+The PreText files generated by the pipeline are not automatically ingested into the pretext files. For this you must use the following code:
+
+```bash
+cd {outdir}/hic_files
+
+bigWigToBedGraph {coverage.bigWig} /dev/stdout | PretextGraph -i { your.pretext } -n "coverage"
+
+bigWigToBedGraph {repeat_density.bigWig} /dev/stdout | PretextGraph -i { your.pretext } -n "repeat_density"
+
+cat {telomere.bedgraph} | awk -v OFS="\t" '{$4 = 1000; print}'|PretextGraph -i { your.pretext } -n "telomere"
+
+cat {gap.bedgraph} | awk -v OFS="\t" '{$4= 1000; print}'| PretextGraph -i  { your.pretext } -n "gap"
+```
+
 ## Full samplesheet
 
-The samplesheet for this pipeline is as shown below. This yaml is parsed by the pipeline and converted into the relevant channels.
-A real production version of this YAML can be found here: [nxOscDF5033.yaml](../assets/local_testing/nxOscDF5033.yaml)
+YAML is "Yet Another Markdown Language", it is a human-readable format that we use to tell TreeVal a number of things. This includes assembly location, telomere motif, pacbio data files (in fasta.gz format) and HiC cram files. The full Yaml is detailed below.
+
+### YAML contents
+
+The following is an example YAML file we have used during production: [nxOscDF5033.yaml](../assets/local_testing/nxOscDF5033.yaml) and is shown below. This contains some annotations we believe to be helpful, information on the alignment, synteny, pacbio and hic are explained here: [pacbio](pacbio.md), [genealignment and synteny](genealignmentsynteny.md). [nxOscDF5033.yaml](../assets/local_testing/nxOscDF5033.yaml)
 
 - `assembly`
   - `sample_id`: ToLID of the sample.
@@ -286,3 +307,12 @@ We recommend adding the following line to your environment to limit this (typica
 ```console
 NXF_OPTS='-Xms1g -Xmx4g'
 ```
+
+## Nextflow memory requirements
+
+In some cases, the Nextflow Java virtual machines can start to request a large amount of memory.
+We recommend adding the following line to your environment to limit this (typically in `~/.bashrc` or `~./bash_profile`):
+
+```console
+NXF_OPTS='-Xms1g -Xmx4g'
+```