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

.gitmodules

@@ -895,3 +895,6 @@
 [submodule "vendor/grammars/Sublime-HTTP"]
 	path = vendor/grammars/Sublime-HTTP
 	url = https://github.com/samsalisbury/Sublime-HTTP
+[submodule "vendor/grammars/atom-language-nextflow"]
+	path = vendor/grammars/atom-language-nextflow
+	url = https://github.com/nextflow-io/atom-language-nextflow

grammars.yml

@@ -195,6 +195,9 @@ vendor/grammars/atom-language-clean:
 vendor/grammars/atom-language-julia:
 - source.julia
 - source.julia.console
+vendor/grammars/atom-language-nextflow:
+- source.nextflow
+- source.nextflow-groovy
 vendor/grammars/atom-language-p4:
 - source.p4
 vendor/grammars/atom-language-perl6:

lib/linguist/languages.yml

@@ -2905,6 +2905,18 @@ NewLisp:
   codemirror_mode: commonlisp
   codemirror_mime_type: text/x-common-lisp
   language_id: 247
+Nextflow:
+  type: programming
+  ace_mode: groovy
+  tm_scope: source.nextflow
+  color: "#3ac486"
+  extensions:
+  - ".nf"
+  filenames:
+  - "nextflow.config"  
+  interpreters:
+  - nextflow
+  language_id: 506780613
 Nginx:
   type: data
   extensions:

samples/Nextflow/blast.nf

@@ -0,0 +1,67 @@
+#!/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/>
+ */
+ 
+/* 
+ * Author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+
+
+params.query = "$HOME/sample.fa"
+params.db = "$HOME/tools/blast-db/pdb/pdb"
+
+process blast {
+    output:
+     file top_hits
+
+    """
+    blastp -query ${params.query} -db ${params.db} -outfmt 6 \
+    | head -n 10 \
+    | cut -f 2 > top_hits
+    """
+}
+
+process extract {
+    input:
+     file top_hits
+    output:
+     file sequences
+
+    """
+    blastdbcmd -db ${params.db} -entry_batch $top_hits > sequences
+    """
+}
+
+process align {
+    input:
+     file sequences
+    echo true
+
+    """
+    t_coffee $sequences 2>&- | tee align_result
+    """
+}

samples/Nextflow/callings.nf

@@ -0,0 +1,496 @@
+#!/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/>
+ */
+  
+  
+/* 
+ * 'CalliNGS-NF' - A Nextflow pipeline for variant calling with NGS data
+ * 
+ * This pipeline that reproduces steps from the GATK best practics of SNP 
+ * calling with RNAseq data procedure:
+ * https://software.broadinstitute.org/gatk/guide/article?id=3891
+ * 
+ * Anna Vlasova 
+ * Emilio Palumbo 
+ * Paolo Di Tommaso
+ * Evan Floden 
+ */
+
+
+/*
+ * Define the default parameters
+ */ 
+
+params.genome     = "$baseDir/data/genome.fa"
+params.variants   = "$baseDir/data/known_variants.vcf.gz"
+params.blacklist  = "$baseDir/data/blacklist.bed" 
+params.reads      = "$baseDir/data/reads/rep1_{1,2}.fq.gz"
+params.results    = "results"
+params.gatk       = '/usr/local/bin/GenomeAnalysisTK.jar'
+params.gatk_launch = "java -jar $params.gatk" 
+
+log.info "C A L L I N G S  -  N F    v 1.0" 
+log.info "================================"
+log.info "genome   : $params.genome"
+log.info "reads    : $params.reads"
+log.info "variants : $params.variants"
+log.info "blacklist: $params.blacklist"
+log.info "results  : $params.results" 
+log.info "gatk     : $params.gatk"
+log.info ""
+
+/*
+ *  Parse the input parameters
+ */
+
+GATK            = params.gatk_launch
+genome_file     = file(params.genome)
+variants_file   = file(params.variants)
+blacklist_file  = file(params.blacklist)
+reads_ch        = Channel.fromFilePairs(params.reads)
+
+
+/**********
+ * PART 1: Data preparation
+ *
+ * Process 1A: Create a FASTA genome index (.fai) with samtools for GATK
+ */
+
+process '1A_prepare_genome_samtools' { 
+  tag "$genome.baseName"
+  
+  input: 
+      file genome from genome_file 
+ 
+  output: 
+      file "${genome}.fai" into genome_index_ch  
+  
+  script:
+  """
+  samtools faidx ${genome}
+  """
+}
+
+
+/*
+ * Process 1B: Create a FASTA genome sequence dictionary with Picard for GATK
+ */
+
+process '1B_prepare_genome_picard' {
+  tag "$genome.baseName"
+
+  input:
+      file genome from genome_file
+  output:
+      file "${genome.baseName}.dict" into genome_dict_ch
+
+  script:
+  """
+  PICARD=`which picard.jar`
+  java -jar \$PICARD CreateSequenceDictionary R= $genome O= ${genome.baseName}.dict
+  """
+}
+
+
+/*
+ * Process 1C: Create STAR genome index file.
+ */
+
+process '1C_prepare_star_genome_index' {
+  tag "$genome.baseName"
+
+  input:
+      file genome from genome_file
+  output:
+      file "genome_dir" into genome_dir_ch
+
+  script:
+  """
+  mkdir genome_dir
+
+  STAR --runMode genomeGenerate \
+       --genomeDir genome_dir \
+       --genomeFastaFiles ${genome} \
+       --runThreadN ${task.cpus}
+  """
+}
+
+
+/*
+ * Process 1D: Create a file containing the filtered and recoded set of variants
+ */
+
+process '1D_prepare_vcf_file' {
+  tag "$variantsFile.baseName"
+
+  input: 
+      file variantsFile from variants_file
+      file blacklisted from blacklist_file
+
+  output:
+      set file("${variantsFile.baseName}.filtered.recode.vcf.gz"), file("${variantsFile.baseName}.filtered.recode.vcf.gz.tbi") into prepared_vcf_ch
+  
+  script:  
+  """
+  vcftools --gzvcf $variantsFile -c \
+           --exclude-bed ${blacklisted} \
+           --recode | bgzip -c \
+           > ${variantsFile.baseName}.filtered.recode.vcf.gz
+
+  tabix ${variantsFile.baseName}.filtered.recode.vcf.gz
+  """
+}
+
+/*
+ *  END OF PART 1
+ *********/
+
+
+
+/**********
+ * PART 2: STAR RNA-Seq Mapping
+ *
+ * Process 2: Align RNA-Seq reads to the genome with STAR
+ */
+
+process '2_rnaseq_mapping_star' {
+  tag "$replicateId"
+
+  input: 
+      file genome from genome_file 
+      file genomeDir from genome_dir_ch
+      set replicateId, file(reads) from reads_ch 
+
+  output: 
+      set replicateId, file('Aligned.sortedByCoord.out.bam'), file('Aligned.sortedByCoord.out.bam.bai') into aligned_bam_ch
+
+  script:    
+  """
+  # ngs-nf-dev Align reads to genome
+  STAR --genomeDir $genomeDir \
+       --readFilesIn $reads \
+       --runThreadN ${task.cpus} \
+       --readFilesCommand zcat \
+       --outFilterType BySJout \
+       --alignSJoverhangMin 8 \
+       --alignSJDBoverhangMin 1 \
+       --outFilterMismatchNmax 999
+    
+  # 2nd pass (improve alignmets using table of splice junctions and create a new index)  
+  mkdir genomeDir  
+  STAR --runMode genomeGenerate \
+       --genomeDir genomeDir \
+       --genomeFastaFiles $genome \
+       --sjdbFileChrStartEnd SJ.out.tab \
+       --sjdbOverhang 75 \
+       --runThreadN ${task.cpus}  
+    
+  # Final read alignments  
+  STAR --genomeDir genomeDir \
+       --readFilesIn $reads \
+       --runThreadN ${task.cpus} \
+       --readFilesCommand zcat \
+       --outFilterType BySJout \
+       --alignSJoverhangMin 8 \
+       --alignSJDBoverhangMin 1 \
+       --outFilterMismatchNmax 999 \
+       --outSAMtype BAM SortedByCoordinate \
+       --outSAMattrRGline ID:$replicateId LB:library PL:illumina PU:machine SM:GM12878
+
+  # Index the BAM file
+  samtools index Aligned.sortedByCoord.out.bam
+  """
+}
+
+/*
+ *  END OF PART 2
+ ******/
+
+
+/**********
+ * PART 3: GATK Prepare Mapped Reads
+ *
+ * Process 3: Split reads that contain Ns in their CIGAR string.
+ *            Creates k+1 new reads (where k is the number of N cigar elements) 
+ *            that correspond to the segments of the original read beside/between 
+ *            the splicing events represented by the Ns in the original CIGAR.
+ */
+
+process '3_rnaseq_gatk_splitNcigar' {
+  tag "$replicateId"
+  
+  input: 
+      file genome from genome_file 
+      file index from genome_index_ch
+      file genome_dict from genome_dict_ch
+      set replicateId, file(bam), file(index) from aligned_bam_ch
+
+  output:
+      set replicateId, file('split.bam'), file('split.bai') into splitted_bam_ch
+  
+  script:
+  """
+  # SplitNCigarReads and reassign mapping qualities
+  $GATK -T SplitNCigarReads \
+          -R $genome -I $bam \
+          -o split.bam \
+          -rf ReassignOneMappingQuality \
+          -RMQF 255 -RMQT 60 \
+          -U ALLOW_N_CIGAR_READS \
+          --fix_misencoded_quality_scores
+  """
+}
+
+/*
+ *  END OF PART 3
+ ******/
+
+
+/***********
+ * PART 4: GATK Base Quality Score Recalibration Workflow
+ *
+ * Process 4: Base recalibrate to detect systematic errors in base quality scores, 
+ *            select unique alignments and index
+ *             
+ */
+
+process '4_rnaseq_gatk_recalibrate' {
+  tag "$replicateId"
+    
+  input: 
+      file genome from genome_file 
+      file index from genome_index_ch
+      file dict from genome_dict_ch
+      set replicateId, file(bam), file(index) from splitted_bam_ch
+      set file(variants_file), file(variants_file_index) from prepared_vcf_ch
+
+  output:
+      set sampleId, file("${replicateId}.final.uniq.bam"), file("${replicateId}.final.uniq.bam.bai") into (final_output_ch, bam_for_ASE_ch)
+  
+  script: 
+  sampleId = replicateId.replaceAll(/[12]$/,'')
+  """
+  # Indel Realignment and Base Recalibration
+  $GATK -T BaseRecalibrator \
+          --default_platform illumina \
+          -cov ReadGroupCovariate \
+          -cov QualityScoreCovariate \
+          -cov CycleCovariate \
+          -knownSites ${variants_file} \
+          -cov ContextCovariate \
+          -R ${genome} -I ${bam} \
+          --downsampling_type NONE \
+          -nct ${task.cpus} \
+          -o final.rnaseq.grp 
+
+  $GATK -T PrintReads \
+          -R ${genome} -I ${bam} \
+          -BQSR final.rnaseq.grp \
+          -nct ${task.cpus} \
+          -o final.bam
+
+  # Select only unique alignments, no multimaps
+  (samtools view -H final.bam; samtools view final.bam| grep -w 'NH:i:1') \
+  |samtools view -Sb -  > ${replicateId}.final.uniq.bam
+
+  # Index BAM files
+  samtools index ${replicateId}.final.uniq.bam
+  """
+}
+
+/*
+ *  END OF PART 4
+ ******/
+
+
+
+/***********
+ * PART 5: GATK Variant Calling
+ *
+ * Process 5: Call variants with GATK HaplotypeCaller.
+ *            Calls SNPs and indels simultaneously via local de-novo assembly of 
+ *            haplotypes in an active region.
+ *            Filter called variants with GATK VariantFiltration.    
+ */
+
+
+process '5_rnaseq_call_variants' {
+  tag "$sampleId"
+
+  input:
+      file genome from genome_file
+      file index from genome_index_ch
+      file dict from genome_dict_ch
+      set sampleId, file(bam), file(bai) from final_output_ch.groupTuple()
+  
+  output: 
+      set sampleId, file('final.vcf') into vcf_files
+
+  script:
+  """
+  # fix absolute path in dict file
+  sed -i 's@UR:file:.*${genome}@UR:file:${genome}@g' $dict
+  echo "${bam.join('\n')}" > bam.list
+  
+  # Variant calling
+  $GATK -T HaplotypeCaller \
+          -R $genome -I bam.list \
+          -dontUseSoftClippedBases \
+          -stand_call_conf 20.0 \
+          -o output.gatk.vcf.gz
+
+  # Variant filtering
+  $GATK -T VariantFiltration \
+          -R $genome -V output.gatk.vcf.gz \
+          -window 35 -cluster 3 \
+          -filterName FS -filter "FS > 30.0" \
+          -filterName QD -filter "QD < 2.0" \
+          -o final.vcf
+  """
+}
+
+/*
+ *  END OF PART 5
+ ******/
+
+
+/***********
+ * PART 6: Post-process variants file and prepare for Allele-Specific Expression and RNA Editing Analysis
+ *
+ * Process 6A: Post-process the VCF result  
+ */
+
+process '6A_post_process_vcf' {
+  tag "$sampleId"
+  publishDir "$params.results/$sampleId" 
+  
+  input:
+      set sampleId, file('final.vcf') from vcf_files
+      set file('filtered.recode.vcf.gz'), file('filtered.recode.vcf.gz.tbi') from prepared_vcf_ch 
+  output: 
+      set sampleId, file('final.vcf'), file('commonSNPs.diff.sites_in_files') into vcf_and_snps_ch
+  
+  script:
+  '''
+  grep -v '#' final.vcf | awk '$7~/PASS/' |perl -ne 'chomp($_); ($dp)=$_=~/DP\\=(\\d+)\\;/; if($dp>=8){print $_."\\n"};' > result.DP8.vcf
+  
+  vcftools --vcf result.DP8.vcf --gzdiff filtered.recode.vcf.gz  --diff-site --out commonSNPs
+  '''
+}
+
+/* 
+ * Process 6B: Prepare variants file for allele specific expression (ASE) analysis
+ */
+
+process '6B_prepare_vcf_for_ase' {
+  tag "$sampleId"
+  publishDir "$params.results/$sampleId" 
+  
+  input: 
+      set sampleId, file('final.vcf'), file('commonSNPs.diff.sites_in_files') from vcf_and_snps_ch
+  output: 
+      set sampleId, file('known_snps.vcf') into vcf_for_ASE
+      file('AF.histogram.pdf') into gghist_pdfs
+
+  script:
+  '''
+  awk 'BEGIN{OFS="\t"} $4~/B/{print $1,$2,$3}' commonSNPs.diff.sites_in_files  > test.bed
+    
+  vcftools --vcf final.vcf --bed test.bed --recode --keep-INFO-all --stdout > known_snps.vcf
+
+  grep -v '#'  known_snps.vcf | awk -F '\\t' '{print $10}' \
+               |awk -F ':' '{print $2}'|perl -ne 'chomp($_); \
+               @v=split(/\\,/,$_); if($v[0]!=0 ||$v[1] !=0)\
+               {print  $v[1]/($v[1]+$v[0])."\\n"; }' |awk '$1!=1' \
+               >AF.4R
+
+  gghist.R -i AF.4R -o AF.histogram.pdf
+  '''
+}
+
+
+/* 
+ * Group data for allele-specific expression.
+ * 
+ * The `bam_for_ASE_ch` emites tuples having the following structure, holding the final BAM/BAI files:
+ *  
+ *   ( sample_id, file_bam, file_bai )
+ * 
+ * The `vcf_for_ASE` channel emits tuples having the following structure, holding the VCF file:
+ *  
+ *   ( sample_id, output.vcf ) 
+ * 
+ * The BAMs are grouped together and merged with VCFs having the same sample id. Finally 
+ * it creates a channel named `grouped_vcf_bam_bai_ch` emitting the following tuples: 
+ *  
+ *   ( sample_id, file_vcf, List[file_bam], List[file_bai] )
+ */
+
+bam_for_ASE_ch
+    .groupTuple()
+    .phase(vcf_for_ASE)
+    .map{ left, right -> 
+      def sampleId = left[0]
+      def bam = left[1]
+      def bai = left[2]
+      def vcf = right[1]
+      tuple(sampleId, vcf, bam, bai)  
+    }
+    .set { grouped_vcf_bam_bai_ch }
+
+
+/* 
+ * Process 6C: Allele-Specific Expression analysis with GATK ASEReadCounter.
+ *             Calculates allele counts at a set of positions after applying 
+ *             filters that are tuned for enabling allele-specific expression 
+ *             (ASE) analysis
+ */
+
+process '6C_ASE_knownSNPs' {
+  tag "$sampleId"
+  publishDir "$params.results/$sampleId" 
+  
+  input:
+      file genome from genome_file 
+      file index from genome_index_ch
+      file dict from genome_dict_ch
+      set sampleId, file(vcf),  file(bam), file(bai) from grouped_vcf_bam_bai_ch
+  
+  output:
+      file "ASE.tsv"
+  
+  script:
+  """
+  echo "${bam.join('\n')}" > bam.list
+    
+  $GATK -R ${genome} \
+          -T ASEReadCounter \
+          -o ASE.tsv \
+          -I bam.list \
+          -sites ${vcf}
+  """
+}

samples/Nextflow/filenames/nextflow.config

@@ -0,0 +1,50 @@
+aws {
+   region = 'eu-west-1'
+}
+
+cloud {
+   autoscale {
+      enabled = true
+      minInstances = 3
+      starvingTimeout = '2 min'
+      terminateWhenIdle = true
+   }
+   imageId = 'ami-78ds78d'
+   instanceProfile = 'MyRole'
+   instanceType = 'r4.large'
+   sharedStorageId = 'fs-76ds76s'
+   spotPrice = 0.06
+   subnetId = 'subnet-8d98d7s'
+}
+
+env {
+   BAR = 'world'
+   FOO = 'hola'
+}
+
+mail {
+   from = 'paolo.ditommaso@gmail.com'
+   smtp {
+      auth = true
+      host = 'email-smtp.us-east-1.amazonaws.com'
+      password = 'my-secret'
+      port = 587
+      starttls {
+         enable = true
+         required = true
+      }
+      user = 'my-name'
+   }
+}
+
+process {
+   executor = 'slurm'
+   queue = 'cn-el7'
+   memory = '16GB'
+   cpus = 8
+   container = 'user/rnaseq-nf:latest'
+}
+
+trace {
+   fields = 'task_id,name,status,attempt,exit,queue'
+}

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" )
+}

vendor/README.md

@@ -239,6 +239,7 @@ This is a list of grammars that Linguist selects to provide syntax highlighting
 - **NetLinx+ERB:** [amclain/sublime-netlinx](https://github.com/amclain/sublime-netlinx)
 - **NetLogo:** [textmate/lisp.tmbundle](https://github.com/textmate/lisp.tmbundle)
 - **NewLisp:** [textmate/lisp.tmbundle](https://github.com/textmate/lisp.tmbundle)
+- **Nextflow:** [nextflow-io/atom-language-nextflow](https://github.com/nextflow-io/atom-language-nextflow)
 - **Nginx:** [brandonwamboldt/sublime-nginx](https://github.com/brandonwamboldt/sublime-nginx)
 - **Nim:** [Varriount/NimLime](https://github.com/Varriount/NimLime)
 - **Ninja:** [khyo/language-ninja](https://github.com/khyo/language-ninja)

vendor/licenses/grammar/atom-language-nextflow.txt

@@ -0,0 +1,25 @@
+---
+type: grammar
+name: atom-language-nextflow
+license: mit
+---
+Copyright (c) 2018 Paolo Di Tommaso
+Copyright (c) 2014-2017 Jakehp https://github.com/Jakehp/language-groovy
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+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 OR COPYRIGHT HOLDERS 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.