Commit b1ea057c authored by Joanna Fourquet's avatar Joanna Fourquet
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Update usage.md

parent c54b0fc4
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### 1. General mandatory files
Launching metagWGS involves the use of mandatory files:
* The **metagenomic whole genome shotgun data** you want to analyze: `.fastq` or `.fastq.gz` R1 and R2 files (Illumina HiSeq3000 or NovaSeq sequencing, 2*150bp). For a cleaner MultiQC html report at the end of the pipeline, raw data with extension `_R1` and `_R2` are preferred to those with extensions `_1` and `_2`.
* The **metagenomic whole genome shotgun data** you want to analyze: `.fastq` or `.fastq.gz` R1 and R2 files (Illumina HiSeq3000 or NovaSeq sequencing, 2*150bp). 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`.
* The **metagWGS.sif** and **eggnog_mapper.sif** Singularity images (into `metagwgs/dev` folder).
### 2. Mandatory files for certain steps
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### 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`.
`--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`.
### 2. `--step`
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