Summary of changes (more details in individual commits):
Added module load statement to all rules using perl (unless they already load it))
Updated target bed file input in vardict_tumoronly.rl to match vardict.rl (in my testing, vardict_tumoronly.rl was running even before exome_targets.bed was created, prob cuz it was using the 'ancient' snakemake directive)
Fixed starfusion.rl to load default perl module; it was throwing an error about mismatched Perl binaries, module loading perl after loading star fusion seems to fix it
Fixed "missing FREECFASTA" error for mm10 by changing if statements in "freec_exome_somatic_pass1.rl", "freec_exome_somatic_pass2.rl", and "sequenza.rl"; now will only run Freec/sequenza if genome is "hg19" or "hg38"
Fixed all-exomeseq-somatic.rl, missing comma after "QC/decoy" in input rules for mm10;
Fixed fusioninsp_starfus.rl; fusion inspector exits gracefully without output if there are no fusions in the input file, which causes Snakemake to fail; now a dummy file will be created if no fusions in the input file
--- NOTE the fusion_summary rule does not run; I haven't fixed that yet; but fusion Pipeline "finishes" without error
Bumped up memory for fusion inspector
Replaced 'reformat_bed.pl' with an equivalent python script 'reformat_bed.py'; FREEC throws an error if two regions in the bed have the same chr/start position, so this script skips these occurrences
--- Updated 'make_target_files.rl' to call python script instead of perl script
Tested for tumor-normal and tumor-only using hg19, hg38, and mm10.
Summary of changes (more details in individual commits):
Tested for tumor-normal and tumor-only using hg19, hg38, and mm10.