Updating bisulfite pipeline to accept bams and fastqs #996
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…flows into bisulfite_seq
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docker image is live - this is ready for review |
tmooney
reviewed
Jan 28, 2021
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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
| /usr/bin/biscuit align -t "$NTHREADS" -M -R "$READGROUP" "$REFERENCE" "$FASTQ1" "$FASTQ2" | /usr/bin/sambamba view -S -f bam -l 0 /dev/stdin | /usr/bin/sambamba sort -t "$SORT_THREADS" -m 8G -o "$OUTDIR/aligned.bam" /dev/stdin | ||
| else | ||
| /opt/flexbar/flexbar --adapters "$TRIMMING_ADAPTERS" --reads "$FASTQ1" --reads2 "$FASTQ2" --adapter-trim-end LTAIL --adapter-min-overlap "$TRIMMING_ADAPTER_MIN_OVERLAP" --adapter-error-rate 0.1 --max-uncalled 300 --stdout-reads \ | ||
| | /usr/bin/biscuit align -t "$NTHREADS" -M -R "$READGROUP" "$REFERENCE" /dev/stdin | /usr/bin/sambamba view -S -f bam -l 0 /dev/stdin | /usr/bin/sambamba sort -t "$SORT_THREADS" -m 8G -o "$OUTDIR/aligned.bam" /dev/stdin |
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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:
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Also bumps the biscuit version - dependent on merging genome/docker-biscuit#4 first for the docker container