diff --git a/episodes/09-Simple_Rna-Seq_pipeline.md b/episodes/09-Simple_Rna-Seq_pipeline.md index a499766a..e5f69743 100644 --- a/episodes/09-Simple_Rna-Seq_pipeline.md +++ b/episodes/09-Simple_Rna-Seq_pipeline.md @@ -565,7 +565,7 @@ The working directory should be considered a temporary storage space and any dat **Note:** by default the `publishDir` directive creates a symbolic link to the files in the working this behaviour can be changed using the `mode` parameter. -> ## Add a publishDir directive +## Add a publishDir directive Add a `publishDir` directive to the quantification process of `script4.nf` to store the process results into folder specified by the `params.outdir` Nextflow variable. Include the `publishDir` `mode` option to copy the output. @@ -642,37 +642,31 @@ $ nextflow run script5.nf -resume The `FASTQC` process will not run as the process has not been declared in the workflow scope. -> ## Add FASTQC process -> -> Add the `FASTQC` process to the `workflow scope` of `script5.nf` adding the `read_pairs_ch` channel as an input. -> Run the nextflow script using the `-resume` option. -> -> ```bash -> $ nextflow run script5.nf -resume -> ``` -> -> > ## Solution -> > -> > ``` -> > workflow { -> > read_pairs_ch = Channel.fromFilePairs( params.reads, checkIfExists:true ) -> > transcriptome_ch = Channel.fromPath( params.transcriptome, checkIfExists:true ) -> > -> > index_ch = INDEX( transcriptome_ch ) -> > quant_ch=QUANT(index_ch,read_pairs_ch) -> > fastqc_ch=FASTQC(read_pairs_ch) -> > ``` - -} - ::::::::::::::::::::::::::::::::::::::: challenge -::::::::::::::: solution +## Add FASTQC process + +Add the `FASTQC` process to the `workflow scope` of `script5.nf` adding the `read_pairs_ch` channel as an input. +Run the nextflow script using the `-resume` option. +```bash +$ nextflow run script5.nf -resume ``` -{: .language-groovy } +::::::::::::::: solution +## Solution + +```groovy +workflow { +read_pairs_ch = Channel.fromFilePairs( params.reads, checkIfExists:true ) +transcriptome_ch = Channel.fromPath( params.transcriptome, checkIfExists:true ) + +index_ch = INDEX( transcriptome_ch ) +quant_ch=QUANT(index_ch,read_pairs_ch) +fastqc_ch=FASTQC(read_pairs_ch) ``` +} + ::::::::::::::::::::::::: ::::::::::::::::::::::::::::::::::::::::::::::::::