Add Nextflow language support (#3870)

* Added nextflow language * Added main.nf to list of filenames * Fixed duplicate groovy scope * Removed hello-world example * Update grammar submodule * Removed main.nf from filenames * Added nextflow.config example
2025-10-29 17:50:22 +00:00 · 2018-01-09 12:47:59 +01:00
parent 5fbe9c0902
commit bee7e55618
10 changed files with 793 additions and 0 deletions
--- a/samples/Nextflow/rnaseq.nf
+++ b/samples/Nextflow/rnaseq.nf
@@ -0,0 +1,135 @@
+#!/usr/bin/env nextflow
+/*
+ * This is free and unencumbered software released into the public domain.
+ * 
+ * Anyone is free to copy, modify, publish, use, compile, sell, or
+ * distribute this software, either in source code form or as a compiled
+ * binary, for any purpose, commercial or non-commercial, and by any
+ * means.
+ * 
+ * In jurisdictions that recognize copyright laws, the author or authors
+ * of this software dedicate any and all copyright interest in the
+ * software to the public domain. We make this dedication for the benefit
+ * of the public at large and to the detriment of our heirs and
+ * successors. We intend this dedication to be an overt act of
+ * relinquishment in perpetuity of all present and future rights to this
+ * software under copyright law.
+ * 
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ * IN NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR
+ * OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
+ * ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ * 
+ * For more information, please refer to <http://unlicense.org/>
+ */
+ 
+  
+/* 
+ * Proof of concept of a RNAseq pipeline implemented with Nextflow
+ * 
+ * Authors:
+ * - Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ * - Emilio Palumbo <emiliopalumbo@gmail.com> 
+ * - Evan Floden <evanfloden@gmail.com> 
+ */ 
+
+ 
+params.reads = "$baseDir/data/ggal/*_{1,2}.fq"
+params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
+params.outdir = "."
+params.multiqc = "$baseDir/multiqc"
+
+log.info """\
+         R N A S E Q - N F   P I P E L I N E    
+         ===================================
+         transcriptome: ${params.transcriptome}
+         reads        : ${params.reads}
+         outdir       : ${params.outdir}
+         """
+         .stripIndent()
+
+
+transcriptome_file = file(params.transcriptome)
+multiqc_file = file(params.multiqc)
+ 
+
+Channel
+    .fromFilePairs( params.reads )
+    .ifEmpty { error "Cannot find any reads matching: ${params.reads}" }
+    .into { read_pairs_ch; read_pairs2_ch } 
+ 
+
+process index {
+    tag "$transcriptome_file.simpleName"
+    
+    input:
+    file transcriptome from transcriptome_file
+     
+    output:
+    file 'index' into index_ch
+
+    script:       
+    """
+    salmon index --threads $task.cpus -t $transcriptome -i index
+    """
+}
+ 
+ 
+process quant {
+    tag "$pair_id"
+     
+    input:
+    file index from index_ch
+    set pair_id, file(reads) from read_pairs_ch
+ 
+    output:
+    file(pair_id) into quant_ch
+ 
+    script:
+    """
+    salmon quant --threads $task.cpus --libType=U -i index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
+    """
+}
+  
+process fastqc {
+    tag "FASTQC on $sample_id"
+
+    input:
+    set sample_id, file(reads) from read_pairs2_ch
+
+    output:
+    file("fastqc_${sample_id}_logs") into fastqc_ch
+
+
+    script:
+    """
+    mkdir fastqc_${sample_id}_logs
+    fastqc -o fastqc_${sample_id}_logs -f fastq -q ${reads}
+    """  
+}  
+  
+  
+process multiqc {
+    publishDir params.outdir, mode:'copy'
+       
+    input:
+    file('*') from quant_ch.mix(fastqc_ch).collect()
+    file(config) from multiqc_file
+    
+    output:
+    file('multiqc_report.html')  
+     
+    script:
+    """
+    cp $config/* .
+    echo "custom_logo: \$PWD/logo.png" >> multiqc_config.yaml
+    multiqc . 
+    """
+}
+ 
+workflow.onComplete { 
+	println ( workflow.success ? "\nDone! Open the following report in your browser --> $params.outdir/multiqc_report.html\n" : "Oops .. something went wrong" )
+}