Updating bisulfite pipeline to accept bams and fastqs

[chrisamiller]

Also bumps the biscuit version - dependent on merging genome/docker-biscuit#4 first for the docker container

[chrisamiller]

docker image is live - this is ready for review

[tmooney]

This generally looks good from a CWL perspective. I'm kind of wondering if there might be a way to avoid having the subworkflow adapter layer (both here and for bwa mem sequence alignment) along the lines of

analysis-workflows/definitions/tools/sequence_to_bam.cwl

Lines 31 to 33 in 4aba7c6

	- { valueFrom: "$(inputs.sequence.sequence.hasOwnProperty('bam')? inputs.sequence.sequence.bam : null)", prefix: 'bam', position: -1 }
	- { valueFrom: "$(inputs.sequence.sequence.hasOwnProperty('fastq1')? inputs.sequence.sequence.fastq1 : null)", prefix: '--FASTQ' }
	- { valueFrom: "$(inputs.sequence.sequence.hasOwnProperty('fastq2')? inputs.sequence.sequence.fastq2 : null)", prefix: '--FASTQ2' }

, but we could worry about that later.

[tmooney]

Do the various uses of biscuit align after a pipe in this script need the -p option?

       -p            smart pairing (ignoring in2.fq)

as seen here, for example:

analysis-workflows/definitions/tools/sequence_align_and_tag.cwl

Line 68 in 87faba2

| /usr/local/bin/bwa mem -K 100000000 -t "$NTHREADS" -Y -p -R "$READGROUP" "$REFERENCE" /dev/stdin | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin