Merge branch 'dev'

CHANGELOG

+# Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.1.0] - 2018-08-22
+
+### Added
+- This fine changelog
+
+### Changed
+- the structure of `src/nf_modules`: the `tests` folder was removed
+
+### Removed
+- nothings
+

src/docker_modules/HTSeq/0.8.0/Dockerfile

@@ -14,4 +14,5 @@ RUN apt-get update && \
     apt-get clean
 
 RUN pip3 install numpy==1.14.3
+RUN pip3 install pysam==0.15.0
 RUN pip3 install HTSeq==${HTSEQ_VERSION}

src/docker_modules/RSEM/1.3.0/Dockerfile

@@ -4,7 +4,7 @@ MAINTAINER Laurent Modolo
 ENV RSEM_VERSION=1.3.0
 ENV BOWTIE2_VERSION=2.3.4.1
 ENV SAMTOOLS_VERSION=1.7
-ENV PACKAGES git=1:2.17.0* \
+ENV PACKAGES git=1:2.17* \
    build-essential=12.4* \
    ca-certificates=20180409 \
    zlib1g-dev=1:1.2.11* \

src/nf_modules/BEDtools/tests/tests.sh → src/nf_modules/BEDtools/tests.sh

-nextflow src/nf_modules/BEDtools/tests/fasta_from_bed.nf \
-  -c src/nf_modules/BEDtools/bedtools.config \
+nextflow src/nf_modules/BEDtools/fasta_from_bed.nf \
+  -c src/nf_modules/BEDtools/fasta_from_bed.config \
   -profile docker \
   --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
   --bed "data/tiny_dataset/annot/tiny.bed" \

src/nf_modules/BEDtools/tests/fasta_from_bed.nf

-params.fastq = "$baseDir/data/fasta/*.fasta"
-params.bed = "$baseDir/data/annot/*.bed"
-
-log.info "fasta file : ${params.fasta}"
-log.info "bed file : ${params.bed}"
-
-Channel
-  .fromPath( params.fasta )
-  .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
-  .set { fasta_files }
-Channel
-  .fromPath( params.bed )
-  .ifEmpty { error "Cannot find any bed files matching: ${params.bed}" }
-  .set { bed_files }
-
-process fasta_from_bed {
-  tag "${bed.baseName}"
-  cpus 4
-  publishDir "results/fasta/", mode: 'copy'
-
-  input:
-  file fasta from fasta_files
-  file bed from bed_files
-
-  output:
-  file "*_extracted.fasta" into fasta_files_extracted
-
-  script:
-"""
-bedtools getfasta -name \
--fi ${fasta} -bed ${bed} -fo ${bed.baseName}_extracted.fasta
-"""
-}

src/nf_modules/Bowtie/bowtie.nf

-/*
-* Bowtie :
-* Imputs : fastq files
-* Imputs : fasta files
-* Output : bam files
-*/
-
-/*                      fasta indexing                                     */
-params.fasta = "$baseDir/data/bam/*.fasta"
-
-log.info "fasta files : ${params.fasta}"
-
-Channel
-  .fromPath( params.fasta )
-  .ifEmpty { error "Cannot find any bam files matching: ${params.fasta}" }
-  .set { fasta_file }
-
-process index_fasta {
-  tag "$fasta.baseName"
-  cpus 4
-  publishDir "results/mapping/index/", mode: 'copy'
-
-  input:
-    file fasta from fasta_file
-
-  output:
-    file "*.index*" into index_files
-    file "*_report.txt" into indexing_report
-
-  script:
-"""
-bowtie-build --threads ${task.cpus} -f ${fasta} ${fasta.baseName}.index &> ${fasta.baseName}_bowtie_report.txt
-
-if grep -q "Error" ${fasta.baseName}_bowtie_report.txt; then
-  exit 1
-fi
-"""
-}
-
-
-
-/*
-* for paired-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
-params.index = "$baseDir/data/index/*.index.*"
-
-log.info "fastq files : ${params.fastq}"
-log.info "index files : ${params.index}"
-
-Channel
-  .fromFilePairs( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .set { fastq_files }
-Channel
-  .fromPath( params.index )
-  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
-  .set { index_files }
-
-process mapping_fastq {
-  tag "$pair_id"
-  cpus 4
-  publishDir "results/mapping/bams/", mode: 'copy'
-
-  input:
-  set pair_id, file(reads) from fastq_files
-  file index from index_files.collect()
-
-  output:
-  file "*.bam" into bam_files
-  file "*_report.txt" into mapping_report
-
-  script:
-  index_id = index[0]
-  for (index_file in index) {
-  if (index_file =~ /.*\.1\.ebwt/ && !(index_file =~ /.*\.rev\.1\.ebwt/)) {
-        index_id = ( index_file =~ /(.*)\.1\.ebwt/)[0][1]
-    }
-  }
-"""
-# -v specify the max number of missmatch, -k the number of match reported per
-# reads
-bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
--1 ${reads[0]} -2 ${reads[1]} 2> \
-${pair_id}_bowtie_report.txt | \
-samtools view -Sb - > ${pair_id}.bam
-
-if grep -q "Error" ${pair_id}_bowtie_report.txt; then
-  exit 1
-fi
-"""
-}
-
-
-/*
-* for single-end data
-*/
-params.mean = 200
-params.sd = 100
-
-log.info "fastq files : ${params.fastq}"
-log.info "index files : ${params.index}"
-log.info "mean read size: ${params.mean}"
-log.info "sd read size: ${params.sd}"
-
-Channel
-  .fromPath( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
-  .set { fastq_files }
-Channel
-  .fromPath( params.index )
-  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
-  .set { index_files }
-
-process mapping_fastq {
-  tag "$file_id"
-  cpus 4
-  publishDir "results/mapping/quantification/", mode: 'copy'
-
-  input:
-  set file_id, file(reads) from fastq_files
-  file index from index_files.collect()
-
-  output:
-  file "*" into count_files
-
-  script:
-"""
-mkdir ${file_id}
-kallisto quant -i ${index} -t ${task.cpus} --single \
---bias --bootstrap-samples 100 -o ${file_id} \
--l ${params.mean} -s ${params.sd} \
-${reads} > ${file_id}_kallisto_report.txt
-"""
-}
-

src/nf_modules/Bowtie/indexing.config

+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      $index_fasta {
+        container = "bowtie:1.2.2"
+      }
+    }
+  }
+  sge {
+    process{
+      $index_fasta {
+        beforeScript = "module purge; module load Bowtie/1.2.2"
+      }
+    }
+  }
+}

src/nf_modules/Bowtie/tests/index.nf → src/nf_modules/Bowtie/indexing.nf

+/*                      fasta indexing                                     */
+
 params.fasta = "$baseDir/data/bam/*.fasta"
 
 log.info "fasta files : ${params.fasta}"

src/nf_modules/Bowtie/bowtie.config → src/nf_modules/Bowtie/mapping_paired.config

@@ -3,9 +3,6 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $index_fasta {
-        container = "bowtie:1.2.2"
-      }
       $mapping_fastq {
         container = "bowtie:1.2.2"
       }
@@ -13,9 +10,6 @@ profiles {
   }
   sge {
     process{
-      $index_fasta {
-        beforeScript = "module purge; module load Bowtie/1.2.2"
-      }
       $mapping_fastq {
         beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie/1.2.2"
       }

src/nf_modules/Bowtie/tests/mapping_paired.nf → src/nf_modules/Bowtie/mapping_paired.nf

+/*
+* mapping paired fastq
+*/
+
 params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
 params.index = "$baseDir/data/index/*.index.*"
 

src/nf_modules/Bowtie/mapping_single.config

+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      $mapping_fastq {
+        container = "bowtie:1.2.2"
+      }
+    }
+  }
+  sge {
+    process{
+      $mapping_fastq {
+        beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie/1.2.2"
+      }
+    }
+  }
+}

src/nf_modules/Bowtie/tests/mapping_single.nf → src/nf_modules/Bowtie/mapping_single.nf

+/*
+* mapping single end fastq
+*/
+
 params.fastq = "$baseDir/data/fastq/*.fastq"
 
 log.info "fastq files : ${params.fastq}"

src/nf_modules/Bowtie/tests/tests.sh → src/nf_modules/Bowtie/tests.sh

-./nextflow src/nf_modules/Bowtie/tests/index.nf \
-  -c src/nf_modules/Bowtie/bowtie.config \
+./nextflow src/nf_modules/Bowtie/indexing.nf \
+  -c src/nf_modules/Bowtie/indexing.config \
   -profile docker \
   --fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
 
-./nextflow src/nf_modules/Bowtie/tests/mapping_single.nf \
-  -c src/nf_modules/Bowtie/bowtie.config \
+./nextflow src/nf_modules/Bowtie/mapping_single.nf \
+  -c src/nf_modules/Bowtie/mapping_single.config \
   -profile docker \
   --index "results/mapping/index/*.ebwt" \
   --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
 
-./nextflow src/nf_modules/Bowtie/tests/mapping_paired.nf \
-  -c src/nf_modules/Bowtie/bowtie.config \
+./nextflow src/nf_modules/Bowtie/mapping_paired.nf \
+  -c src/nf_modules/Bowtie/mapping_paired.config \
   -profile docker \
   --index "results/mapping/index/*.ebwt" \
   --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"

src/nf_modules/Bowtie2/bowtie2.nf

-/*
-* Bowtie2 :
-* Imputs : fastq files
-* Imputs : fasta files
-* Output : bam files
-*/
-
-/*                      fasta indexing                                     */
-params.fasta = "$baseDir/data/bam/*.fasta"
-
-log.info "fasta files : ${params.fasta}"
-
-Channel
-  .fromPath( params.fasta )
-  .ifEmpty { error "Cannot find any bam files matching: ${params.fasta}" }
-  .set { fasta_file }
-
-process index_fasta {
-  tag "$fasta.baseName"
-  cpus 4
-  publishDir "results/mapping/index/", mode: 'copy'
-
-  input:
-    file fasta from fasta_file
-
-  output:
-    file "*.index*" into index_files
-    file "*_report.txt" into indexing_report
-
-  script:
-"""
-bowtie2-build --threads ${task.cpus} ${fasta} ${fasta.baseName}.index &> ${fasta.baseName}_bowtie2_report.txt
-
-if grep -q "Error" ${fasta.baseName}_bowtie2_report.txt; then
-  exit 1
-fi
-"""
-}
-
-
-/*
-* for paired-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
-params.index = "$baseDir/data/index/*.index.*"
-
-log.info "fastq files : ${params.fastq}"
-log.info "index files : ${params.index}"
-
-Channel
-  .fromFilePairs( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .set { fastq_files }
-Channel
-  .fromPath( params.index )
-  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
-  .set { index_files }
-
-process mapping_fastq {
-  tag "$pair_id"
-  cpus 4
-  publishDir "results/mapping/bams/", mode: 'copy'
-
-  input:
-  set pair_id, file(reads) from fastq_files
-  file index from index_files.collect()
-
-  output:
-  set pair_id, "*.bam" into bam_files
-  file "*_report.txt" into mapping_report
-
-  script:
-  index_id = index[0]
-  for (index_file in index) {
-    if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
-        index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
-    }
-  }
-"""
-bowtie2 --very-sensitive -p ${task.cpus} -x ${index_id} \
--1 ${reads[0]} -2 ${reads[1]} 2> \
-${pair_id}_bowtie2_report.txt | \
-samtools view -Sb - > ${pair_id}.bam
-
-if grep -q "Error" ${pair_id}_bowtie2_report.txt; then
-  exit 1
-fi
-"""
-}
-
-/*
-* for single-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*.fastq"
-
-log.info "fastq files : ${params.fastq}"
-log.info "index files : ${params.index}"
-
-Channel
-  .fromPath( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
-  .set { fastq_files }
-Channel
-  .fromPath( params.index )
-  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
-  .set { index_files }
-
-process mapping_fastq {
-  tag "$file_id"
-  cpus 4
-  publishDir "results/mapping/bams/", mode: 'copy'
-
-  input:
-  set file_id, file(reads) from fastq_files
-  file index from index_files.collect()
-
-  output:
-  set file_id, "*.bam" into bam_files
-  file "*_report.txt" into mapping_report
-
-  script:
-  index_id = index[0]
-  for (index_file in index) {
-    if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
-        index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
-    }
-  }
-"""
-bowtie2 --very-sensitive -p ${task.cpus} -x ${index_id} \
--U ${reads} 2> \
-${file_id}_bowtie2_report.txt | \
-samtools view -Sb - > ${file_id}.bam
-
-if grep -q "Error" ${file_id}_bowtie2_report.txt; then
-  exit 1
-fi
-"""
-}

src/nf_modules/Bowtie2/indexing.config

+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      $index_fasta {
+        container = "bowtie2:2.3.4.1"
+      }
+    }
+  }
+  sge {
+    process{
+      $index_fasta {
+        beforeScript = "module purge; module load Bowtie2/2.3.4.1"
+      }
+    }
+  }
+}

src/nf_modules/Bowtie2/bowtie2.config → src/nf_modules/Bowtie2/mapping_paired.config

@@ -3,9 +3,6 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $index_fasta {
-        container = "bowtie2:2.3.4.1"
-      }
       $mapping_fastq {
         container = "bowtie2:2.3.4.1"
       }
@@ -13,9 +10,6 @@ profiles {
   }
   sge {
     process{
-      $index_fasta {
-        beforeScript = "module purge; module load Bowtie2/2.3.4.1"
-      }
       $mapping_fastq {
         beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
       }