Update 04-snippy's lablog

[victor5lm]

A few adjustments should be made to the lablog file from 04-snippy:

1. In line 8, you should add the command that allows the inclusion of external genomes, with their corresponding .FASTA files, to the generation of input.tab. This line should be commented, since it will only be useful when .FASTA files are included in the analysis.
   

   buisciii-tools/bu_isciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/04-snippy/lablog

   Lines 6 to 8 in 86556c4

   	cat ../samples_id.txt | while read in; do echo -e "${in}\t${scratch_dir}/../02-preprocessing/${in}/${in}_R1_filtered.fastq.gz\t${scratch_dir}/../02-preprocessing/${in}/${in}_R2_filtered.fastq.gz"; done >> input.tab

2. You should change this block, so that it is easier to understand. More importantly, you should include the command that allows for the removal of low coverage reads, since right now the only command that appears in this file is the one relative to the removal of complex variants.
   

   buisciii-tools/bu_isciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/04-snippy/lablog

   Lines 16 to 20 in 86556c4

   	# Execute core genome SNIPPY
   	# CODE CONTEXT: this block was used in the service: AZORHIZOBIOUMOUTBREAK01 on november 2022
   	# Comment las line from _00_snippy.sh
   	# echo "grep \"complex\" ./*/snps.vcf | cut -f 1,2,4,5 | cut -d \":\" -f 2 | sort -u | awk '{pos1=\$2; len_ref=length(\$3); printf \"%s\t%s\t%s\n\", \$1, pos1-1, pos1+len_ref+1}' | grep -v \"^#\" > mask_complex_variants.bed" > _01_snippy_core.sh
   	# ls ${scratch_dir}/../../../REFERENCES | xargs -I %% echo "snippy-core --debug --mask ./mask_complex_variants.bed --mask-char 'N' --ref '../../../REFERENCES/%%' $(cat ../samples_id.txt | xargs)" >> _01_snippy_core.sh

3. Say what this is for:
   

   buisciii-tools/bu_isciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/04-snippy/lablog

   Line 24 in 86556c4

   # awk 'BEGIN{FS="[> ]"} /^>/{val=$2;next} {print val,length($0)}' phylo.aln

4. Make sure this is still correct:
   

   buisciii-tools/bu_isciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/04-snippy/lablog

   Lines 26 to 27 in 86556c4

   	#code to compare samples inpairs
   	# awk '$4 != $5 || $4 != $6 || $5 != $6' core.tab > differences.txt