... | ... | @@ -23,7 +23,7 @@ You also need to make sure you define the output directory with the `-w` argumen |
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For example, if the directory structure is like:
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```sh
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📦MYPROJECT # main output folder
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📦MYPROJECT # main output folder specified with '-w' argument
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┣ 📂NTS-XXX # project folder (column 4 in samplesheet)
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┃ ┣ 📂FASTQ # temporary folder for fastq files
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┃ ┣ 📂FASTQC # FastQC results
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... | ... | @@ -50,6 +50,19 @@ snakemake -nrp --config conf="config.json" |
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```
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If everything is fine, the pipeline **SHOULD NOT** run the `split_fastq` rule as it should find the already created `XXX.fastq.gz` in the `CUTADAPT` directory of your previously analyzed data. If this is not the case, have a look at the reasons why snakemake wants to create these files again by looking at the output of the dry run.
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#### Re-analyzing with sample splitting into multiple projects
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If you want to split the samples into multiple projects, you will have to create as many different project folders as specified in the samplesheet used.
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Lets say half of the samples belong to project "NTS-XXX_1" and the other half to project "NTS-XXX_2". You will have to create those two folders and move the already created fastq files in the "CUTADAPT" folders in their corresponding project:
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```sh
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📦MYPROJECT # main output folder specified with '-w' argument
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┣ 📂NTS-XXX_1 # project folder (column 4 in samplesheet)
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┃ ┣ 📂CUTADAPT # fastq files after cutadapt belonging to project 'NTS-XXX_1'
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┣ 📂NTS-XXX_2 # project folder (column 4 in samplesheet)
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┃ ┣ 📂CUTADAPT # fastq files after cutadapt belonging to project 'NTS-XXX_2'
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```
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