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Commit 44df7c75 authored by cbedet's avatar cbedet
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modification in script.sh to include both kallisto and bowtie2

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doc/pipeline_building_cec.md
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...@@ -341,11 +341,11 @@ cd .. ...@@ -341,11 +341,11 @@ cd ..
It is better to writ a script as a.sh file to lauch nextflow : Here is the RNAseq_script for Kallisto: It is better to writ a script as a.sh file to lauch nextflow : Here is the RNAseq_script for Kallisto:
```sh ```sh
./nextflow run src/RNAseq_cec_transcripts.nf \ ./nextflow run src/RNAseq_cec.nf \
-profile psmn \ -profile psmn \
--fastq "data/*.fastq" \ --fastq "data/*.fastq" \
--fasta "data/c_elegans.PRJNA13758.WS278.all_transcripts.fa" \ --cds_fasta "data/c_elegans.PRJNA13758.WS278.all_transcripts.fa" \
--mapping_fastq_out "quantif/" --genomic_fasta "data/c_elegans.PRJNA13758.WS278.genomic.fa"
``` ```
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