Commit 80cbb24a authored by Joanna Fourquet's avatar Joanna Fourquet
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Update usage.md

parent b1ea057c
......@@ -136,7 +136,7 @@ The next parameters can be used when you run metagWGS.
### 1. Mandatory parameter: `--reads`
`--reads "SAMPLE_NAME.fastq.gz"`: indicate location of `.fastq` or `.fastq.gz` input files. For example, `--reads PATH/*_{R1,R2}.fastq.gz` run the pipeline with all the `R1.fastq.gz` and `R2.fastq.gz` files available in the indicated `PATH`. For a cleaner MultiQC html report at the end of the pipeline, raw data with extensions `_R1` and `_R2` are preferred to those with extensions `_1` and `_2`.
`--reads "PATH/*_{R1,R2}.fastq.gz"`: indicate location of `.fastq` or `.fastq.gz` input files. For example, `--reads "PATH/*_{R1,R2}.fastq.gz"` run the pipeline with all the `R1.fastq.gz` and `R2.fastq.gz` files available in the indicated `PATH`. For a cleaner MultiQC html report at the end of the pipeline, raw data with extensions `_R1` and `_R2` are preferred to those with extensions `_1` and `_2`.
### 2. `--step`
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