update examples add nextflow

case_studies/Covid_RNA-Seq/Nextflow/README.md

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+
+## Integrating pyrpipe scripts within a workflow management system (Nextflow)
+This example shows usage of pyrpipe with Nextflow workflow management system. The example is identical to the [Snakemake example](https://github.com/urmi-21/pyrpipe/tree/master/case_studies/Covid_RNA-Seq).
+This example downloads COVID-19 infected human RNA-Seq data from [Rother et. al.](https://www.medrxiv.org/content/10.1101/2020.06.08.20122143v1) published under accession [SRP287810](https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP287810).
+
+Uses salmon to quantify the RNA-Seq samples and compile The transcripts TPMs for exploratory analysis with [MetaOmGraph](https://github.com/urmi-21/MetaOmGraph)
+The final output file of this workflow, `results_TPM.tsv`, can be directly imported in MetaOmGraph together with the metadata file.
+
+
+
+## Running this example
+
+### Build the conda environment (optional)
+* Please have conda installed
+* Run `conda env create -f env.yaml`
+* Activate the environment: `conda activate pyrpipe_human`
+
+### Prepare reference data
+To install the reference data and build Salmon index, run [this file]() as 
+
+`bash prepare_data.sh`
+
+### Execute using Nextflow
+
+`nextflow run run_quant.nf`

case_studies/Covid_RNA-Seq/Nextflow/run_quant.nf

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+#!/usr/bin/env nextflow
+
+params.outdir = 'myout'
+params.infile='runids.txt'
+projectdir = projectDir
+
+srrids= new File("runids.txt").collect {it}
+//create a list of outfile paths
+def qflist = []
+srrids.each { val -> qflist.add("$projectdir/$params.outdir/$val/salmon_out/quant.sf")}
+qflist.each { println it }
+
+process rnaseq {
+
+    publishDir "$projectdir/$params.outdir"
+
+    input:
+    val srr from srrids
+    output:
+    file "${srr}*" into result
+
+    script:
+    """
+    #!/usr/bin/env python3
+    from pyrpipe import sra,mapping,quant
+    salmon=quant.Salmon(index="$projectdir/human_data/salmon_index")
+    thisid='${srr}'
+    print('Processing:',thisid)
+    sra.SRA(thisid).quant(salmon)
+    """
+}
+
+process merge {
+    input:
+    file("*") from result.collect()
+    output:
+    stdout res
+
+    """
+    echo ${qflist}
+    python ${projectdir}/scripts/merge.py ${qflist.join(",")} ${projectdir}/${params.outdir}
+    """
+}
+
+res.subscribe { println it }