touch up example workflow

example/example_workflow.sh

@@ -1,6 +1,10 @@
 #!/bin/sh
 
-## Download some genomes
+# This file serves as an example workflow illustrating how and when to use msyd.
+# It is a part of the msyd CI, and should pass so long as your system 
+
+
+## Download three publicly available, high quality A. thaliana genomes
 
 # download the Col-CC assembly
 curl -OJX GET "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/GCA_028009825.1/download?include_annotation_type=GENOME_FASTA&filename=GCA_028009825.1.zip" -H "Accept: application/zip"
@@ -15,14 +19,15 @@ curl -OJX GET "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/GC
 unzip "./*.zip"
 mv ncbi_dataset/data/*/*.fna ./
 
-## Prepare them for running msyd
+### Prepare them for running msyd
 
-# rename them to shorter names
+## rename them to shorter names
 mv GCA_001651475.1_Ler_Assembly_genomic.fna ler.fna
 mv GCA_028009825.1_Col-CC_genomic.fna col.fna
 mv GCA_902460295.1_Arabidopsis_thaliana_Sha_genomic.fna sha.fna
 mv GCA_024498555.1_ASM2449855v1_genomic.fna swe.fna
 
+## filter out small scaffolds
 grep -n -P ">" ./*.fna
 # col and swe do not require truncating,
 # for ler the small scaffolds start at line 1442097
@@ -33,45 +38,50 @@ head -n 1480076 sha.fna > sha.filtered.fna
 mv sha.filtered.fna sha.fna
 
 
-## Generate inputs for msyd
+### Generate inputs for msyd
 
-# generate alignments to col-CC
+## generate alignments to col-CC
 mv col.fna ref.fna
-minimap2 -cx asm5 --eqx ref.fna ler.fna > ler.paf
-minimap2 -cx asm5 --eqx ref.fna sha.fna > sha.paf
-minimap2 -cx asm5 --eqx ref.fna swe.fna > swe.paf
+minimap2 -cx asm10 --eqx ref.fna ler.fna > ler.paf
+minimap2 -cx asm10 --eqx ref.fna sha.fna > sha.paf
+minimap2 -cx asm10 --eqx ref.fna swe.fna > swe.paf
 
-# run syri on the alignments
+## run syri on the alignments
+# make sure to pass --cigar and specify appropriate prefixes, so the msyd output is more easily interpretable
 syri --nc 5 -F P --cigar --prefix ler -c ler.paf -r ref.fna -q ler.fna --lf ler.syri.log --samplename ler
 syri --nc 5 -F P --cigar --prefix sha -c sha.paf -r ref.fna -q sha.fna --lf sha.syri.log --samplename sha
 syri --nc 5 -F P --cigar --prefix swe -c swe.paf -r ref.fna -q swe.fna --lf swe.syri.log --samplename swe
 
 ## construct genomes.tsv file
+# as msyd needs many input files, the paths are stored in a samplesheet
 echo "#name\taln\tsyri\tvcf\tseq" > genomes.tsv
 for f in *syri.out
 do
 	bs=$(basename $f syri.out)
 	echo "$bs\t$bs.paf\t${bs}syri.out\t${bs}syri.vcf\t${bs}.fna" >> genomes.tsv
 done
 
-# run msyd to call pansynteny
-msyd call -i genomes.tsv -o athalianas.pff -m athalianas.vcf -r ref.fna
+### run msyd to call multisynteny
+msyd call -c 5 -i genomes.tsv -o athalianas.psf -m athalianas.vcf -r ref.fna
+
+### work with the output
 
-## work with the output
+## export multisynteny on Chr3 for use in visualization/other software
 
-# CP116282 is the id corresponding to chromosome 3 in Col-CC
-msyd view -e "on CP116283.1" -i athalianas.pff -o athalianas-chr3.pff
+# CP116283 is the id corresponding to chromosome 3 in Col-CC
+# filter for multisynteny on this chromosome
+msyd view -e "on CP116283.1" -i athalianas.psf -o athalianas-chr3.psf
 
-# convert to VCF for use in visualization/other software
-msyd view -i athalianas-chr3.pff -o athalianas-chr3-syn.vcf
+# export to VCF; this could also be done in the command above
+msyd view -i athalianas-chr3.psf -o athalianas-chr3-syn.vcf
 
-## download 1001 genome project VCF, filter for vars in pansyntenic regions
+## download 1001 genome project VCF, filter for small variants structurally conserved regions
 
 curl https://ftp.ebi.ac.uk/ensemblgenomes/pub/release-56/plants/variation/vcf/arabidopsis_thaliana/arabidopsis_thaliana.vcf.gz -o ensembl_athaliana.vcf.gz
 gunzip ensembl_athaliana.vcf.gz
 
 # change from ids to chr numbers, to match vcf nomenclature
-sed -e s/CP116280.1/1/ -e s/CP116281.1/2/ -e s/CP116282.1/3/ -e s/CP116283.1/4/ -e s/CP116284.1/5/ athalianas.pff > athalianas-chrnames.pff
+sed -e s/CP116280\.1/Chr1/ -e s/CP116281\.1/Chr2/ -e s/CP116282\.1/Chr3/ -e s/CP116283\.1/Chr4/ -e s/CP116284\.1/Chr5/ athalianas.psf > athalianas-chrnames.psf
 
-# filter for variants in pansyntenic regions!
-msyd view -i athalianas-chrnames.pff -e "deg >= 3" -o pansynt-vars.vcf --intersect ensembl_athaliana.vcf
+# filter for variants in coresyntenic regions!
+msyd view -i athalianas-chrnames.psf -e "deg >= 3" -o coresynt-snvs.vcf --intersect ensembl_athaliana.vcf