No mem_mb allocation for phase_chrY

[alextidd]

Hi Joe,
Got the develop version up and running, thanks for the conda env! I have encountered a small issue towards the end of the run. I get this error:

RuleException in rule phase_chrY in file "/nfs/casm/team268im/at31/bin/repos/SCAN2/snakemake/snakefile.phasing_shared", line 151:
AttributeError: 'ResourceList' object has no attribute 'mem_mb', when formatting the following:
bsub -J {rule} -q basement -n {threads} -M {resources.mem_mb} -R 'select[mem>{resources.mem_mb}] rusage[mem={resources.mem_mb}] span[hosts=1]' -W 336:00 -o cluster-logs/%J_{rule}.out -e cluster-logs/%J_{rule}.err

This is due to there being no mem_mb allocation in the phase_chrY rule in snakefile.phasing_shared. I fixed this by adding one here:

# Handling for haploid chromosomes
rule phase_chrY:
    input:
        # eagle uses .vcf.gz, shapeit2 does not compress the vcf
        vcf=config["phaser"] + "/" + config['chrY'] + "/final_for_phasing.analyzable_sites.mmq60.vcf" + (".gz" if config["phaser"] == "eagle" else "")
    output:
        vcf=temp(config["phaser"] + "/" + config['chrY'] + "/phased.vcf")
    log:
        config["phaser"] + "/" + config['chrY'] + "/phaser.log"
    benchmark:
        config["phaser"] + "/" + config['chrY'] + "/benchmark_phaser.tsv"
    resources:
        mem_mb=250

Thanks so much again for the help with running the dev version!
Alex