TMP_FASTQ, TMP_FASTQ2

[thedam]

hey, I've noticed some inconsistency in Fred's metabarcoding pipeline

    # Discard sequences containing Ns, add expected error rates
    "${VSEARCH}" \
        --quiet \
        --fastq_filter "${TMP_FASTQ}" \
        --fastq_maxns 0 \
        --relabel_sha1 \
        --eeout \
        --fastqout "${TMP_FASTQ2}" 2>> "${LOG}"

    # Discard sequences containing Ns, convert to fasta
    "${VSEARCH}" \
        --quiet \
        --fastq_filter "${TMP_FASTQ}" \
        --fastq_maxns 0 \
        --fastaout "${TMP_FASTA}" 2>> "${LOG}"

in the second command, shouldn't we use --fastq_filter "${TMP_FASTQ2}" ?

cheers Damian