... | ... | @@ -82,7 +82,71 @@ python SCRIPTS/make_srp_config.py -s <my_samplesheet> -r <path_to_reference_fold |
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In every case, check the generated configuration file to see if everything seems ok.
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```
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more config.json
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$ cat config.json
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{
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"maindir": "/path/to/RESULTS",
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"fastq_folder": "FASTQ",
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"cutadapt_folder": "CUTADAPT",
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"fastqc_folder": "FASTQC",
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"multiqc_folder": "MULTIQC",
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"align_folder": "ALIGNMENT",
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"expression_folder": "EXPRESSION",
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"de_folder": "DE",
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"report_folder": "REPORT",
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"ref_folder": "/path/to/TESTDATA/REFERENCES",
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"samples": [
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{
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"well": "D09",
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"name": "sample1",
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"index": "AGACCT",
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"project": "TestProject",
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"condition": "cond1",
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"species": "hg19"
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},
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{
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"well": "E08",
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"name": "sample2",
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"index": "ACGGGG",
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"project": "TestProject",
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"condition": "cond2",
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"species": "hg19"
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},
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...
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],
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"comparisons": {
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"TestProject": {
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"species": "hg19",
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"minRep": 2,
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"minGenes": 0,
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"minReads": 0,
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"minLogFC": 0.58,
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"performComps": true,
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"comps": [
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{
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"condition1": "cond1",
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"condition2": "cond2"
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},
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{
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"condition1": "cond1",
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"condition2": "cond3"
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},
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{
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"condition1": "cond2",
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"condition2": "cond3"
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}
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]
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}
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},
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"fastq_pairs": [
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{
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"read1": "TESTDATA/split.aa_R1.fastq.gz",
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"read2": "TESTDATA/split.aa_R2.fastq.gz"
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},
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{
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"read1": "TESTDATA/split.ab_R1.fastq.gz",
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"read2": "TESTDATA/split.ab_R2.fastq.gz"
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},
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...
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```
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## Launch the snakemake pipeline.
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... | ... | @@ -91,6 +155,12 @@ Test the launch with a dry run: |
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```
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snakemake -nrp --config conf="config.json"
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```
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where:
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- `--config` inject the configuration file in the snakefile
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- `-n` dry run
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- `-r` print reason to run the rules
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- `-p` print shell commands
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If you see the rules and commands that will be run, everything's fine.
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Launch the run on a personal computer:
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