Answers to challenge activities and CLI/cluster warmup

1. Win scp, filezilla or secure copy (scp)
2. samples = ["A", "B", "C"] https://snakemake.readthedocs.io/en/stable/project_info/faq.html#how-do-i-remove-all-files-created-by-snakemake-i-e-like-make-clean OR rm -rf calls/ mapped/ plots/

3. shell:
       "module load samtools; "
       "module load bcftools; "
   

4. rule vcf_tsv:
   input:
       "calls/all.vcf"
   output:
       "calls/vcf.tsv"
   shell:
       "sed '/##/d' {input} > {output}" 
   

rule all:
    input:
        "calls/all.vcf",
        "plots/quals.svg",
        "calls/vcf.tsv"

OR

   "sed '1,28d' {input} > {output}"

1. temp() on the sort rule output like bwa rule.