From 686a58f88170cc0d073450c15dd2f630cd1da448 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 3 Jul 2018 16:35:16 +0200
Subject: [PATCH] HISAT2:2.0.0: add docker files
---
src/Rnaseq.config | 121 -----------------
src/Rnaseq.nf | 122 ------------------
.../HISAT2/2.0.0/docker_init.sh | 0
src/fasta_sampler.nf | 18 ---
4 files changed, 261 deletions(-)
delete mode 100644 src/Rnaseq.config
delete mode 100644 src/Rnaseq.nf
mode change 100644 => 100755 src/docker_modules/HISAT2/2.0.0/docker_init.sh
delete mode 100644 src/fasta_sampler.nf
diff --git a/src/Rnaseq.config b/src/Rnaseq.config
deleted file mode 100644
index 1170cb83..00000000
--- a/src/Rnaseq.config
+++ /dev/null
@@ -1,121 +0,0 @@
-profiles {
- docker {
- docker.temp = 'auto'
- docker.enabled = true
- process {
- $adaptor_removal {
- container = "cutadapt:1.14"
- }
- }
- }
- sge {
- process{
- $adaptor_removal {
- beforeScript = "module purge; module load cutadapt/1.14"
- executor = "sge"
- cpus = 1
- memory = "5GB"
- time = "6h"
- queueSize = 1000
- pollInterval = '60sec'
- queue = 'h6-E5-2667v4deb128'
- penv = 'openmp8'
- }
- }
- }
-}
-
-profiles {
- docker {
- docker.temp = 'auto'
- docker.enabled = true
- process {
- $trimming {
- container = "urqt:d62c1f8"
- }
- }
- }
- sge {
- process{
- $trimming {
- beforeScript = "module purge; module load UrQt/d62c1f8"
- executor = "sge"
- cpus = 4
- memory = "5GB"
- time = "6h"
- queueSize = 1000
- pollInterval = '60sec'
- queue = 'h6-E5-2667v4deb128'
- penv = 'openmp8'
- }
- }
- }
-}
-profiles {
- docker {
- docker.temp = 'auto'
- docker.enabled = true
- process {
- $fasta_from_bed {
- container = "bedtools:2.25.0"
- }
- }
- }
- sge {
- process{
- $fasta_from_bed {
- beforeScript = "module purge; module load BEDtools/2.25.0"
- executor = "sge"
- cpus = 1
- memory = "5GB"
- time = "6h"
- queueSize = 1000
- pollInterval = '60sec'
- queue = 'h6-E5-2667v4deb128'
- penv = 'openmp8'
- }
- }
- }
-}
-
-profiles {
- docker {
- docker.temp = 'auto'
- docker.enabled = true
- process {
- $index_fasta {
- container = "kallisto:0.43.1"
- }
- $mapping_fastq {
- container = "kallisto:0.43.1"
- }
- }
- }
- sge {
- process{
- $index_fasta {
- beforeScript = "module purge; module load Kallisto/0.43.1"
- executor = "sge"
- cpus = 1
- memory = "5GB"
- time = "6h"
- queueSize = 1000
- pollInterval = '60sec'
- queue = 'h6-E5-2667v4deb128'
- penv = 'openmp8'
- }
- $mapping_fastq {
- beforeScript = "module purge; module load Kallisto/0.43.1"
- executor = "sge"
- cpus = 4
- memory = "5GB"
- time = "6h"
- queueSize = 1000
- pollInterval = '60sec'
- queue = 'h6-E5-2667v4deb128'
- penv = 'openmp8'
- }
- }
- }
-}
-
diff --git a/src/Rnaseq.nf b/src/Rnaseq.nf
deleted file mode 100644
index 1b59e883..00000000
--- a/src/Rnaseq.nf
+++ /dev/null
@@ -1,122 +0,0 @@
-params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
-params.fasta = "$baseDir/data/fasta/*.fasta"
-params.bed = "$baseDir/data/annot/*.bed"
-
-log.info "fasta file : ${params.fasta}"
-log.info "bed file : ${params.bed}"
-log.info "fastq files : ${params.fastq}"
-
-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 }
-
-Channel
- .fromFilePairs( params.fastq )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
- .set { fastq_files }
-
-process adaptor_removal {
- tag "$pair_id"
- publishDir "results/fastq/adaptor_removal/", mode: 'copy'
-
- input:
- set pair_id, file(reads) from fastq_files
-
- output:
- file "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
-
- script:
- """
- cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT -A AGATCGGAAGAG -G CTCTTCCGATCT \
- -o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \
- ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
- """
-}
-
-process trimming {
- tag "${reads}"
- cpus 4
- publishDir "results/fastq/trimming/", mode: 'copy'
-
- input:
- file reads from fastq_files_cut
-
- output:
- file "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
-
- script:
-"""
-UrQt --t 20 --m ${task.cpus} --gz \
---in ${reads[0]} --inpair ${reads[1]} \
---out ${reads[0].baseName}_trim_R1.fastq.gz --outpair ${reads[1].baseName}_trim_R2.fastq.gz \
-> ${reads[0].baseName}_trimming_report.txt
-"""
-}
-
-process fasta_from_bed {
- tag "${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 ${bed.baseName}_extracted.fasta
-"""
-}
-
-process index_fasta {
- tag "$fasta.baseName"
- publishDir "results/mapping/index/", mode: 'copy'
-
- input:
- file fasta from fasta_files_extracted
-
- output:
- file "*.index*" into index_files
-
- script:
-"""
-kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \
-> ${fasta.baseName}_kallisto_report.txt
-"""
-}
-
-
-process mapping_fastq {
- tag "$reads"
- cpus 4
- publishDir "results/mapping/quantification/", mode: 'copy'
-
- input:
- file reads from fastq_files_trim
- file index from index_files
-
- output:
- file "*" into counts_files
-
- script:
-"""
-mkdir ${reads[0].baseName}
-kallisto quant -i ${index} -t ${task.cpus} \
---bias --bootstrap-samples 100 -o ${reads[0].baseName} \
-${reads[0]} ${reads[1]} &> ${reads[0].baseName}_kallisto_report.txt
-"""
-}
-
-
-
-
diff --git a/src/docker_modules/HISAT2/2.0.0/docker_init.sh b/src/docker_modules/HISAT2/2.0.0/docker_init.sh
old mode 100644
new mode 100755
diff --git a/src/fasta_sampler.nf b/src/fasta_sampler.nf
deleted file mode 100644
index d1200ed4..00000000
--- a/src/fasta_sampler.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-Channel
- .fromPath( "data/tiny_dataset/fasta/*.fasta" )
- .set { fasta_file }
-
-process sample_fasta {
- publishDir "results/sampling/", mode: 'copy'
-
- input:
-file fasta from fasta_file
-
- output:
-file "*_sample.fasta" into fasta_sample
-
- script:
-"""
-head ${fasta} > ${fasta.baseName}_sample.fasta
-"""
-}
--
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