Import demultiplexed data (with bclfastq) to qiime2

Hi there,

I’m trying to import import demultiplexed data (with bclfastq) to qiime2 with the command:

qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path fastq_files --output-path demux-paired-end.qza --source-format PairedEndFastqManifestPhred33
and get this output:
Usage: qiime tools import [OPTIONS]
Try “qiime tools import --help” for help.

Error: no such option: --source-format

In the fastq_files directory, my files are named:
2_S2_R1_001.fastq.gz
2_S2_R2_001.fastq.gz
3_S3_R1_001.fastq.gz
3_S3_R2_001.fastq.gz
4_S4_R1_001.fastq.gz

I’m using qiime2-2019.1
Many thanks for your feedback
Isa

You appear to be referencing outdated documentation — please see the latest importing guide:

https://docs.qiime2.org/2019.1/tutorials/importing/

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