Fix to accept mixed input types

[anjalijain22]

closes #75

• Removed the "input" parameter from config.yaml
• Removed rules cramtofastq, fastq_prep and bamtofastq, and replaced with one rule called input_prep which can deal with all input types. Also, removed the shadow parameter from the rule
• Based on the column contents of units.tsv, the crg2/wrappers/samtools/fastq/wrapper.py decides if file type is fastq, BAM or CRAM and performs the necessary conversion
• BAM to Fastq conversion now uses samtools instead of bedtools and generates zipped fastq files
• Testing done on exomes with only fastq/BAM/CRAM input and combination of fastq+bam, bam+cram, fastq+cram
• Testing done on a genome with bam+fastq input

[Madelinehazel]

Looks good to me! A few changes I made:

• formatted wrappers/samtools/fastq/wrapper.py wrappers/samtools/fastq/fastq_prep.py with black
• removed logic in parser_exomes.py parser_genomes.py to specify input type in config.yaml
• removed scripts/fastq_prep.py as it's now at wrappers/samtools/fastq/