Raise an error if too few reads are left after trimming with cutadapt

[kelly-sovacool]

Changes

At end of cutadapt rules, thrown an error if the trimmed fastq files have fewer than a certain number of reads (default 100). This is set in config['bin'][pfamily]['tool_parameters']['CUTADAPT_MIN_READS'].

Issues

resolves #118

Testing

RENEE_DIR=/data/CCBR_Pipeliner/Pipelines/RENEE/renee-dev-sovacool
module load ccbrpipeliner/7

${RENEE_DIR}/bin/renee run \
    --input ${RENEE_DIR}/.tests/*.R?.fastq.gz \
    --output /data/$USER/renee_test_paired \
    --genome hg38_45 \
    --mode slurm \
    --sif-cache /data/CCBR_Pipeliner/SIFs

${RENEE_DIR}/bin/renee run \
    --input ${RENEE_DIR}/.tests/*.R1.fastq.gz \
    --output /data/$USER/renee_test_single \
    --genome hg38_45 \
    --mode slurm \
    --sif-cache /data/CCBR_Pipeliner/SIFs

${RENEE_DIR}/bin/renee run \
    --input ${RENEE_DIR}/.tests/*.R1.fastq.gz \
    --output /data/$USER/renee_test_small \
    --genome hg38_45 \
    --mode slurm \
    --sif-cache /data/CCBR_Pipeliner/SIFs \
    --small-rna

PR Checklist

(Strikethrough any points that are not applicable.)

• This comment contains a description of changes with justifications, with any relevant issues linked.
• [ ] Update docs if there are any API changes.
• Update CHANGELOG.md with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/

[kelly-sovacool]

tested reads that fail:

${RENEE_DIR}/bin/renee run \
    --input ${RENEE_DIR}/tests/data/fastq/*.fastq.gz \
    --output /data/$USER/renee_test_trunc \
    --genome hg38_45 \
    --mode slurm \
    --sif-cache /data/CCBR_Pipeliner/SIFs

logfiles/slurmfiles/42116317.42116467.trim_pe.name=WT_S1.trunc.out

number of reads passing filters: 5
ERROR: too few reads are left after trimming.