From cc2d49f6d0ec1e4a95b4acf6d91f231d03494aae Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 4 Jun 2021 09:24:00 +0200
Subject: [PATCH] switcth to nextflow DSL2
---
src/nf_modules/bedtools/fasta_from_bed.config | 55 ---------
src/nf_modules/bedtools/fasta_from_bed.nf | 41 -------
src/nf_modules/bowtie/indexing.config | 56 ----------
src/nf_modules/bowtie/indexing.nf | 33 ------
src/nf_modules/bowtie/mapping_paired.config | 56 ----------
src/nf_modules/bowtie/mapping_paired.nf | 55 ---------
src/nf_modules/bowtie/mapping_single.config | 56 ----------
src/nf_modules/bowtie/mapping_single.nf | 51 ---------
src/nf_modules/bowtie2/indexing.config | 56 ----------
src/nf_modules/bowtie2/indexing.nf | 32 ------
src/nf_modules/bowtie2/mapping_paired.config | 56 ----------
src/nf_modules/bowtie2/mapping_paired.nf | 48 --------
src/nf_modules/bowtie2/mapping_single.config | 56 ----------
src/nf_modules/bowtie2/mapping_single.nf | 47 --------
src/nf_modules/bwa/indexing.config | 56 ----------
src/nf_modules/bwa/indexing.nf | 28 -----
src/nf_modules/bwa/mapping_paired.config | 56 ----------
src/nf_modules/bwa/mapping_paired.nf | 37 -------
.../cutadapt/adaptor_removal_paired.config | 55 ---------
.../cutadapt/adaptor_removal_paired.nf | 25 -----
.../cutadapt/adaptor_removal_single.config | 55 ---------
.../cutadapt/adaptor_removal_single.nf | 26 -----
.../cutadapt/trimming_paired.config | 55 ---------
src/nf_modules/cutadapt/trimming_paired.nf | 25 -----
.../cutadapt/trimming_single.config | 55 ---------
src/nf_modules/cutadapt/trimming_single.nf | 26 -----
src/nf_modules/deeptools/bam_to_bigwig.config | 76 -------------
src/nf_modules/deeptools/bam_to_bigwig.nf | 49 ---------
.../deeptools/compute_matrix.config | 57 ----------
src/nf_modules/deeptools/compute_matrix.nf | 38 -------
src/nf_modules/deeptools/plot_profile.config | 57 ----------
src/nf_modules/deeptools/plot_profile.nf | 36 ------
src/nf_modules/fastp/fastp_paired.config | 56 ----------
src/nf_modules/fastp/fastp_paired.nf | 34 ------
src/nf_modules/fastp/fastp_single.config | 56 ----------
src/nf_modules/fastp/fastp_single.nf | 32 ------
src/nf_modules/fastqc/fastqc_paired.config | 56 ----------
src/nf_modules/fastqc/fastqc_paired.nf | 26 -----
src/nf_modules/fastqc/fastqc_single.config | 56 ----------
src/nf_modules/fastqc/fastqc_single.nf | 26 -----
src/nf_modules/hisat2/indexing.config | 57 ----------
src/nf_modules/hisat2/indexing.nf | 32 ------
src/nf_modules/hisat2/mapping_paired.config | 55 ---------
src/nf_modules/hisat2/mapping_paired.nf | 48 --------
src/nf_modules/hisat2/mapping_single.config | 55 ---------
src/nf_modules/hisat2/mapping_single.nf | 53 ---------
src/nf_modules/htseq/htseq.config | 75 -------------
src/nf_modules/htseq/htseq.nf | 52 ---------
src/nf_modules/kallisto/indexing.config | 57 ----------
src/nf_modules/kallisto/indexing.nf | 28 -----
src/nf_modules/kallisto/mapping_paired.config | 59 ----------
src/nf_modules/kallisto/mapping_paired.nf | 36 ------
src/nf_modules/kallisto/mapping_single.config | 59 ----------
src/nf_modules/kallisto/mapping_single.nf | 42 -------
src/nf_modules/macs2/peak_calling.config | 57 ----------
src/nf_modules/macs2/peak_calling.nf | 52 ---------
src/nf_modules/multiqc/multiqc_paired.config | 84 --------------
src/nf_modules/multiqc/multiqc_paired.nf | 43 --------
src/nf_modules/multiqc/multiqc_single.config | 82 --------------
src/nf_modules/multiqc/multiqc_single.nf | 44 --------
.../music/peak_calling_single.config | 94 ----------------
src/nf_modules/music/peak_calling_single.nf | 104 ------------------
src/nf_modules/rsem/indexing.config | 57 ----------
src/nf_modules/rsem/indexing.nf | 39 -------
.../rsem/quantification_paired.config | 57 ----------
src/nf_modules/rsem/quantification_paired.nf | 48 --------
.../rsem/quantification_single.config | 57 ----------
src/nf_modules/rsem/quantification_single.nf | 53 ---------
src/nf_modules/sambamba/index_bams.config | 57 ----------
src/nf_modules/sambamba/index_bams.nf | 25 -----
src/nf_modules/sambamba/sort_bams.config | 58 ----------
src/nf_modules/sambamba/sort_bams.nf | 26 -----
src/nf_modules/sambamba/split_bams.config | 57 ----------
src/nf_modules/sambamba/split_bams.nf | 27 -----
src/nf_modules/samblaster/dedup_sams.config | 57 ----------
src/nf_modules/samblaster/dedup_sams.nf | 27 -----
src/nf_modules/samtools/filter_bams.config | 57 ----------
src/nf_modules/samtools/filter_bams.nf | 32 ------
src/nf_modules/samtools/index_bams.config | 56 ----------
src/nf_modules/samtools/index_bams.nf | 25 -----
src/nf_modules/samtools/sort_bams.config | 57 ----------
src/nf_modules/samtools/sort_bams.nf | 25 -----
src/nf_modules/samtools/split_bams.config | 56 ----------
src/nf_modules/samtools/split_bams.nf | 26 -----
src/nf_modules/sratoolkit/fastqdump.config | 56 ----------
src/nf_modules/sratoolkit/fastqdump.nf | 48 --------
src/nf_modules/star/indexing.config | 56 ----------
src/nf_modules/star/indexing.nf | 36 ------
src/nf_modules/star/mapping_paired.config | 56 ----------
src/nf_modules/star/mapping_paired.nf | 40 -------
src/nf_modules/star/mapping_single.config | 56 ----------
src/nf_modules/star/mapping_single.nf | 39 -------
src/nf_modules/subread/subread.config | 75 -------------
src/nf_modules/subread/subread.nf | 52 ---------
src/nf_modules/urqt/trimming_paired.config | 58 ----------
src/nf_modules/urqt/trimming_paired.nf | 27 -----
src/nf_modules/urqt/trimming_single.config | 58 ----------
src/nf_modules/urqt/trimming_single.nf | 30 -----
98 files changed, 4786 deletions(-)
delete mode 100644 src/nf_modules/bedtools/fasta_from_bed.config
delete mode 100644 src/nf_modules/bedtools/fasta_from_bed.nf
delete mode 100644 src/nf_modules/bowtie/indexing.config
delete mode 100644 src/nf_modules/bowtie/indexing.nf
delete mode 100644 src/nf_modules/bowtie/mapping_paired.config
delete mode 100644 src/nf_modules/bowtie/mapping_paired.nf
delete mode 100644 src/nf_modules/bowtie/mapping_single.config
delete mode 100644 src/nf_modules/bowtie/mapping_single.nf
delete mode 100644 src/nf_modules/bowtie2/indexing.config
delete mode 100644 src/nf_modules/bowtie2/indexing.nf
delete mode 100644 src/nf_modules/bowtie2/mapping_paired.config
delete mode 100644 src/nf_modules/bowtie2/mapping_paired.nf
delete mode 100644 src/nf_modules/bowtie2/mapping_single.config
delete mode 100644 src/nf_modules/bowtie2/mapping_single.nf
delete mode 100644 src/nf_modules/bwa/indexing.config
delete mode 100644 src/nf_modules/bwa/indexing.nf
delete mode 100644 src/nf_modules/bwa/mapping_paired.config
delete mode 100644 src/nf_modules/bwa/mapping_paired.nf
delete mode 100644 src/nf_modules/cutadapt/adaptor_removal_paired.config
delete mode 100644 src/nf_modules/cutadapt/adaptor_removal_paired.nf
delete mode 100644 src/nf_modules/cutadapt/adaptor_removal_single.config
delete mode 100644 src/nf_modules/cutadapt/adaptor_removal_single.nf
delete mode 100644 src/nf_modules/cutadapt/trimming_paired.config
delete mode 100644 src/nf_modules/cutadapt/trimming_paired.nf
delete mode 100644 src/nf_modules/cutadapt/trimming_single.config
delete mode 100644 src/nf_modules/cutadapt/trimming_single.nf
delete mode 100644 src/nf_modules/deeptools/bam_to_bigwig.config
delete mode 100644 src/nf_modules/deeptools/bam_to_bigwig.nf
delete mode 100644 src/nf_modules/deeptools/compute_matrix.config
delete mode 100644 src/nf_modules/deeptools/compute_matrix.nf
delete mode 100644 src/nf_modules/deeptools/plot_profile.config
delete mode 100644 src/nf_modules/deeptools/plot_profile.nf
delete mode 100644 src/nf_modules/fastp/fastp_paired.config
delete mode 100644 src/nf_modules/fastp/fastp_paired.nf
delete mode 100644 src/nf_modules/fastp/fastp_single.config
delete mode 100644 src/nf_modules/fastp/fastp_single.nf
delete mode 100644 src/nf_modules/fastqc/fastqc_paired.config
delete mode 100644 src/nf_modules/fastqc/fastqc_paired.nf
delete mode 100644 src/nf_modules/fastqc/fastqc_single.config
delete mode 100644 src/nf_modules/fastqc/fastqc_single.nf
delete mode 100644 src/nf_modules/hisat2/indexing.config
delete mode 100644 src/nf_modules/hisat2/indexing.nf
delete mode 100644 src/nf_modules/hisat2/mapping_paired.config
delete mode 100644 src/nf_modules/hisat2/mapping_paired.nf
delete mode 100644 src/nf_modules/hisat2/mapping_single.config
delete mode 100644 src/nf_modules/hisat2/mapping_single.nf
delete mode 100644 src/nf_modules/htseq/htseq.config
delete mode 100644 src/nf_modules/htseq/htseq.nf
delete mode 100644 src/nf_modules/kallisto/indexing.config
delete mode 100644 src/nf_modules/kallisto/indexing.nf
delete mode 100644 src/nf_modules/kallisto/mapping_paired.config
delete mode 100644 src/nf_modules/kallisto/mapping_paired.nf
delete mode 100644 src/nf_modules/kallisto/mapping_single.config
delete mode 100644 src/nf_modules/kallisto/mapping_single.nf
delete mode 100644 src/nf_modules/macs2/peak_calling.config
delete mode 100644 src/nf_modules/macs2/peak_calling.nf
delete mode 100644 src/nf_modules/multiqc/multiqc_paired.config
delete mode 100644 src/nf_modules/multiqc/multiqc_paired.nf
delete mode 100644 src/nf_modules/multiqc/multiqc_single.config
delete mode 100644 src/nf_modules/multiqc/multiqc_single.nf
delete mode 100644 src/nf_modules/music/peak_calling_single.config
delete mode 100644 src/nf_modules/music/peak_calling_single.nf
delete mode 100644 src/nf_modules/rsem/indexing.config
delete mode 100644 src/nf_modules/rsem/indexing.nf
delete mode 100644 src/nf_modules/rsem/quantification_paired.config
delete mode 100644 src/nf_modules/rsem/quantification_paired.nf
delete mode 100644 src/nf_modules/rsem/quantification_single.config
delete mode 100644 src/nf_modules/rsem/quantification_single.nf
delete mode 100644 src/nf_modules/sambamba/index_bams.config
delete mode 100644 src/nf_modules/sambamba/index_bams.nf
delete mode 100644 src/nf_modules/sambamba/sort_bams.config
delete mode 100644 src/nf_modules/sambamba/sort_bams.nf
delete mode 100644 src/nf_modules/sambamba/split_bams.config
delete mode 100644 src/nf_modules/sambamba/split_bams.nf
delete mode 100644 src/nf_modules/samblaster/dedup_sams.config
delete mode 100644 src/nf_modules/samblaster/dedup_sams.nf
delete mode 100644 src/nf_modules/samtools/filter_bams.config
delete mode 100644 src/nf_modules/samtools/filter_bams.nf
delete mode 100644 src/nf_modules/samtools/index_bams.config
delete mode 100644 src/nf_modules/samtools/index_bams.nf
delete mode 100644 src/nf_modules/samtools/sort_bams.config
delete mode 100644 src/nf_modules/samtools/sort_bams.nf
delete mode 100644 src/nf_modules/samtools/split_bams.config
delete mode 100644 src/nf_modules/samtools/split_bams.nf
delete mode 100644 src/nf_modules/sratoolkit/fastqdump.config
delete mode 100644 src/nf_modules/sratoolkit/fastqdump.nf
delete mode 100644 src/nf_modules/star/indexing.config
delete mode 100644 src/nf_modules/star/indexing.nf
delete mode 100644 src/nf_modules/star/mapping_paired.config
delete mode 100644 src/nf_modules/star/mapping_paired.nf
delete mode 100644 src/nf_modules/star/mapping_single.config
delete mode 100644 src/nf_modules/star/mapping_single.nf
delete mode 100644 src/nf_modules/subread/subread.config
delete mode 100644 src/nf_modules/subread/subread.nf
delete mode 100644 src/nf_modules/urqt/trimming_paired.config
delete mode 100644 src/nf_modules/urqt/trimming_paired.nf
delete mode 100644 src/nf_modules/urqt/trimming_single.config
delete mode 100644 src/nf_modules/urqt/trimming_single.nf
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
deleted file mode 100644
index 077270d7..00000000
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ /dev/null
@@ -1,55 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withLabel: bedtools {
- container = "lbmc/bedtools:2.25.0"
- cpus = 1
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withLabel: bedtools {
- container = "lbmc/bedtools:2.25.0"
- cpus = 1
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withLabel: bedtools {
- container = "lbmc/bedtools:2.25.0"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "20GB"
- time = "12h"
- queue = "monointeldeb128"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withLabel: bedtools {
- container = "lbmc/bedtools:2.25.0"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/bedtools/fasta_from_bed.nf b/src/nf_modules/bedtools/fasta_from_bed.nf
deleted file mode 100644
index 85dce555..00000000
--- a/src/nf_modules/bedtools/fasta_from_bed.nf
+++ /dev/null
@@ -1,41 +0,0 @@
-/*
-* bedtools :
-* Imputs : fasta files
-* Imputs : bed files
-* Output : fasta files
-*/
-/* fasta extraction */
-
-params.fasta = "$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}"
- publishDir "results/fasta/", mode: 'copy'
- label "bedtools"
-
- 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 ${bed.baseName}_extracted.fasta
-"""
-}
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
deleted file mode 100644
index 50dff965..00000000
--- a/src/nf_modules/bowtie/indexing.config
+++ /dev/null
@@ -1,56 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withLabel: bowtie {
- cpus = 4
- container = "lbmc/bowtie:1.2.2"
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withLabel: bowtie {
- cpus = 4
- container = "lbmc/bowtie:1.2.2"
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withLabel: bowtie {
- container = "lbmc/bowtie:1.2.2"
- executor = "sge"
- clusterOptions = "-cwd -V"
- memory = "20GB"
- cpus = 32
- time = "12h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withLabel: bowtie {
- container = "lbmc/bowtie:1.2.2"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/bowtie/indexing.nf b/src/nf_modules/bowtie/indexing.nf
deleted file mode 100644
index d09a5de8..00000000
--- a/src/nf_modules/bowtie/indexing.nf
+++ /dev/null
@@ -1,33 +0,0 @@
-/* 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"
- publishDir "results/mapping/index/", mode: 'copy'
- label "bowtie"
-
- 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" ${fasta.baseName}_bowtie_report.txt; then
- exit 1
-fi
-"""
-}
-
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
deleted file mode 100644
index 1d924e9b..00000000
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ /dev/null
@@ -1,56 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withLabel: bowtie {
- container = "lbmc/bowtie:1.2.2"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withLabel: bowtie {
- cpus = 4
- container = "lbmc/bowtie:1.2.2"
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withLabel: bowtie {
- container = "lbmc/bowtie:1.2.2"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withLabel: bowtie {
- container = "lbmc/bowtie:1.2.2"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/bowtie/mapping_paired.nf b/src/nf_modules/bowtie/mapping_paired.nf
deleted file mode 100644
index 6357a8b6..00000000
--- a/src/nf_modules/bowtie/mapping_paired.nf
+++ /dev/null
@@ -1,55 +0,0 @@
-/*
-* mapping paired fastq
-*/
-
-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"
- publishDir "results/mapping/bams/", mode: 'copy'
- label "bowtie"
-
- 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_tmp.txt | \
-samtools view -Sb - > ${pair_id}.bam
-
-if grep -q "Error" ${pair_id}_bowtie_report_tmp.txt; then
- exit 1
-fi
-tail -n 19 ${pair_id}_bowtie_report_tmp.txt > ${pair_id}_bowtie_report.txt
-"""
-}
-
-
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
deleted file mode 100644
index 1d924e9b..00000000
--- a/src/nf_modules/bowtie/mapping_single.config
+++ /dev/null
@@ -1,56 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withLabel: bowtie {
- container = "lbmc/bowtie:1.2.2"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withLabel: bowtie {
- cpus = 4
- container = "lbmc/bowtie:1.2.2"
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withLabel: bowtie {
- container = "lbmc/bowtie:1.2.2"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withLabel: bowtie {
- container = "lbmc/bowtie:1.2.2"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/bowtie/mapping_single.nf b/src/nf_modules/bowtie/mapping_single.nf
deleted file mode 100644
index ac287193..00000000
--- a/src/nf_modules/bowtie/mapping_single.nf
+++ /dev/null
@@ -1,51 +0,0 @@
-/*
-* mapping single end fastq
-*/
-
-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"
- publishDir "results/mapping/bams/", mode: 'copy'
- label "bowtie"
-
- 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\.ebwt/ && !(index_file =~ /.*\.rev\.1\.ebwt/)) {
- index_id = ( index_file =~ /(.*)\.1\.ebwt/)[0][1]
- }
-}
-"""
-bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
--q ${reads} 2> \
-${file_id}_bowtie_report_tmp.txt | \
-samtools view -Sb - > ${file_id}.bam
-
-if grep -q "Error" ${file_id}_bowtie_report_tmp.txt; then
- exit 1
-fi
-tail -n 19 ${file_id}_bowtie_report_tmp.txt > ${file_id}_bowtie_report.txt
-"""
-}
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
deleted file mode 100644
index 5a487f8e..00000000
--- a/src/nf_modules/bowtie2/indexing.config
+++ /dev/null
@@ -1,56 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withLabel: bowtie2 {
- container = "lbmc/bowtie2:2.3.4.1"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withLabel: bowtie2 {
- container = "lbmc/bowtie2:2.3.4.1"
- cpus = 4
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withLabel: bowtie2 {
- container = "lbmc/bowtie2:2.3.4.1"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "20GB"
- time = "12h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withLabel: bowtie2 {
- container = "lbmc/bowtie2:2.3.4.1"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/bowtie2/indexing.nf b/src/nf_modules/bowtie2/indexing.nf
deleted file mode 100644
index e1ec9ae9..00000000
--- a/src/nf_modules/bowtie2/indexing.nf
+++ /dev/null
@@ -1,32 +0,0 @@
-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"
- publishDir "results/mapping/index/", mode: 'copy'
- label "bowtie2"
-
- 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" ${fasta.baseName}_bowtie2_report.txt; then
- exit 1
-fi
-"""
-}
-
-
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
deleted file mode 100644
index addc6b2e..00000000
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ /dev/null
@@ -1,56 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withLabel: bowtie2 {
- container = "lbmc/bowtie2:2.3.4.1"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withLabel: bowtie2 {
- container = "lbmc/bowtie2:2.3.4.1"
- cpus = 4
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withLabel: bowtie2 {
- container = "lbmc/bowtie2:2.3.4.1"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withLabel: bowtie2 {
- container = "lbmc/bowtie2:2.3.4.1"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/bowtie2/mapping_paired.nf b/src/nf_modules/bowtie2/mapping_paired.nf
deleted file mode 100644
index 96c209fd..00000000
--- a/src/nf_modules/bowtie2/mapping_paired.nf
+++ /dev/null
@@ -1,48 +0,0 @@
-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"
- publishDir "results/mapping/bams/", mode: 'copy'
- label "bowtie2"
-
- 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_tmp.txt | \
-samtools view -Sb - > ${pair_id}.bam
-
-if grep -q "Error" ${pair_id}_bowtie2_report_tmp.txt; then
- exit 1
-fi
-tail -n 19 ${pair_id}_bowtie2_report_tmp.txt > ${pair_id}_bowtie2_report.txt
-"""
-}
-
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
deleted file mode 100644
index addc6b2e..00000000
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ /dev/null
@@ -1,56 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withLabel: bowtie2 {
- container = "lbmc/bowtie2:2.3.4.1"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withLabel: bowtie2 {
- container = "lbmc/bowtie2:2.3.4.1"
- cpus = 4
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withLabel: bowtie2 {
- container = "lbmc/bowtie2:2.3.4.1"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withLabel: bowtie2 {
- container = "lbmc/bowtie2:2.3.4.1"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/bowtie2/mapping_single.nf b/src/nf_modules/bowtie2/mapping_single.nf
deleted file mode 100644
index 69db77e2..00000000
--- a/src/nf_modules/bowtie2/mapping_single.nf
+++ /dev/null
@@ -1,47 +0,0 @@
-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"
- publishDir "results/mapping/bams/", mode: 'copy'
- label "bowtie2"
-
- 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_tmp.txt | \
-samtools view -Sb - > ${file_id}.bam
-
-if grep -q "Error" ${file_id}_bowtie2_report_tmp.txt; then
- exit 1
-fi
-tail -n 19 ${file_id}_bowtie2_report_tmp.txt > ${file_id}_bowtie2_report.txt
-"""
-}
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
deleted file mode 100644
index b3b90059..00000000
--- a/src/nf_modules/bwa/indexing.config
+++ /dev/null
@@ -1,56 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: index_fasta {
- container = "lbmc/bwa:0.7.17"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: index_fasta {
- container = "lbmc/bwa:0.7.17"
- cpus = 4
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: index_fasta {
- container = "lbmc/bwa:0.7.17"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: index_fasta {
- container = "lbmc/bwa:0.7.17"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/bwa/indexing.nf b/src/nf_modules/bwa/indexing.nf
deleted file mode 100644
index 09096eea..00000000
--- a/src/nf_modules/bwa/indexing.nf
+++ /dev/null
@@ -1,28 +0,0 @@
-params.fasta = "$baseDir/data/bam/*.fasta"
-
-log.info "fasta files : ${params.fasta}"
-
-Channel
- .fromPath( params.fasta )
- .ifEmpty { error "Cannot find any bam files matching: ${params.fasta}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
- .set { fasta_file }
-
-process index_fasta {
- tag "$fasta_id"
- publishDir "results/mapping/index/", mode: 'copy'
-
- input:
- set fasta_id, file(fasta) from fasta_file
-
- output:
- set fasta_id, "${fasta.baseName}.*" into index_files
- file "*_bwa_report.txt" into index_files_report
-
- script:
-"""
-bwa index -p ${fasta.baseName} ${fasta} \
-&> ${fasta.baseName}_bwa_report.txt
-"""
-}
-
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
deleted file mode 100644
index b28e5b9c..00000000
--- a/src/nf_modules/bwa/mapping_paired.config
+++ /dev/null
@@ -1,56 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: mapping_fastq {
- container = "lbmc/bwa:0.7.17"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: mapping_fastq {
- container = "lbmc/bwa:0.7.17"
- cpus = 4
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: mapping_fastq {
- container = "lbmc/bwa:0.7.17"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: mapping_fastq {
- container = "lbmc/bwa:0.7.17"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/bwa/mapping_paired.nf b/src/nf_modules/bwa/mapping_paired.nf
deleted file mode 100644
index 7309c605..00000000
--- a/src/nf_modules/bwa/mapping_paired.nf
+++ /dev/null
@@ -1,37 +0,0 @@
-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: ${params.index}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
- .groupTuple()
- .set { index_files }
-
-process mapping_fastq {
- tag "$reads"
- publishDir "results/mapping/sam/", mode: 'copy'
-
- input:
- set pair_id, file(reads) from fastq_files
- set index_id, file(index) from index_files.collect()
-
- output:
- file "${pair_id}.sam" into sam_files
- file "${pair_id}_bwa_report.txt" into mapping_repport_files
-
- script:
-"""
-bwa mem -t ${task.cpus} \
-${index_id} ${reads[0]} ${reads[1]} \
--o ${pair_id}.sam &> ${pair_id}_bwa_report.txt
-"""
-}
-
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
deleted file mode 100644
index 33b2179f..00000000
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ /dev/null
@@ -1,55 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withLabel: cutadapt {
- container = "lbmc/cutadapt:2.1"
- cpus = 1
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withLabel: cutadapt {
- container = "lbmc/cutadapt:2.1"
- cpus = 1
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withLabel: cutadapt {
- container = "lbmc/cutadapt:2.1"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "20GB"
- time = "12h"
- queue = "monointeldeb128"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withLabel: cutadapt {
- container = "lbmc/cutadapt:2.1"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.nf b/src/nf_modules/cutadapt/adaptor_removal_paired.nf
deleted file mode 100644
index 0d203733..00000000
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.nf
+++ /dev/null
@@ -1,25 +0,0 @@
-log.info "fastq files : ${params.fastq}"
-
-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'
- label "cutadapt"
-
- input:
- set pair_id, file(reads) from fastq_files
-
- output:
- set pair_id, "*_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]} > ${pair_id}_report.txt
- """
-}
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
deleted file mode 100644
index 33b2179f..00000000
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ /dev/null
@@ -1,55 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withLabel: cutadapt {
- container = "lbmc/cutadapt:2.1"
- cpus = 1
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withLabel: cutadapt {
- container = "lbmc/cutadapt:2.1"
- cpus = 1
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withLabel: cutadapt {
- container = "lbmc/cutadapt:2.1"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "20GB"
- time = "12h"
- queue = "monointeldeb128"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withLabel: cutadapt {
- container = "lbmc/cutadapt:2.1"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.nf b/src/nf_modules/cutadapt/adaptor_removal_single.nf
deleted file mode 100644
index ac2b631e..00000000
--- a/src/nf_modules/cutadapt/adaptor_removal_single.nf
+++ /dev/null
@@ -1,26 +0,0 @@
-log.info "fastq files : ${params.fastq}"
-
-Channel
- .fromPath( params.fastq )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
- .set { fastq_files }
-
-process adaptor_removal {
- tag "$file_id"
- label "cutadapt"
-
- input:
- set file_id, file(reads) from fastq_files
-
- output:
- set file_id, "*_cut.fastq.gz" into fastq_files_cut
-
- script:
- """
- cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT\
- -o ${file_id}_cut.fastq.gz \
- ${reads} > ${file_id}_report.txt
- """
-}
-
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
deleted file mode 100644
index 33b2179f..00000000
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ /dev/null
@@ -1,55 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withLabel: cutadapt {
- container = "lbmc/cutadapt:2.1"
- cpus = 1
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withLabel: cutadapt {
- container = "lbmc/cutadapt:2.1"
- cpus = 1
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withLabel: cutadapt {
- container = "lbmc/cutadapt:2.1"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "20GB"
- time = "12h"
- queue = "monointeldeb128"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withLabel: cutadapt {
- container = "lbmc/cutadapt:2.1"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/cutadapt/trimming_paired.nf b/src/nf_modules/cutadapt/trimming_paired.nf
deleted file mode 100644
index 9fb317ff..00000000
--- a/src/nf_modules/cutadapt/trimming_paired.nf
+++ /dev/null
@@ -1,25 +0,0 @@
-log.info "fastq files : ${params.fastq}"
-
-Channel
- .fromFilePairs( params.fastq )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
- .set { fastq_files }
-
-process trimming {
- tag "$pair_id"
- publishDir "results/fastq/trimming/", mode: 'copy'
- label "cutadapt"
-
- input:
- set pair_id, file(reads) from fastq_files
-
- output:
- set pair_id, "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
-
- script:
- """
- cutadapt -q 20,20 \
- -o ${pair_id}_trim_R1.fastq.gz -p ${pair_id}_trim_R2.fastq.gz \
- ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
- """
-}
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
deleted file mode 100644
index 33b2179f..00000000
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ /dev/null
@@ -1,55 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withLabel: cutadapt {
- container = "lbmc/cutadapt:2.1"
- cpus = 1
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withLabel: cutadapt {
- container = "lbmc/cutadapt:2.1"
- cpus = 1
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withLabel: cutadapt {
- container = "lbmc/cutadapt:2.1"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "20GB"
- time = "12h"
- queue = "monointeldeb128"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withLabel: cutadapt {
- container = "lbmc/cutadapt:2.1"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/cutadapt/trimming_single.nf b/src/nf_modules/cutadapt/trimming_single.nf
deleted file mode 100644
index 0d125e7e..00000000
--- a/src/nf_modules/cutadapt/trimming_single.nf
+++ /dev/null
@@ -1,26 +0,0 @@
-log.info "fastq files : ${params.fastq}"
-
-Channel
- .fromPath( params.fastq )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
- .set { fastq_files }
-
-process trimming {
- tag "$file_id"
- label "cutadapt"
-
- input:
- set file_id, file(reads) from fastq_files
-
- output:
- set file_id, "*_trim.fastq.gz" into fastq_files_cut
-
- script:
- """
- cutadapt -q 20,20 \
- -o ${file_id}_trim.fastq.gz \
- ${reads} > ${file_id}_report.txt
- """
-}
-
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
deleted file mode 100644
index 9dd57e69..00000000
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ /dev/null
@@ -1,76 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: index_bam {
- container = "lbmc/sambamba:0.6.7"
- cpus = 4
- }
- withName: bam_to_bigwig {
- container = "lbmc/deeptools:3.0.2"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: index_bam {
- container = "lbmc/sambamba:0.6.7"
- cpus = 4
- }
- withName: bam_to_bigwig {
- container = "lbmc/deeptools:3.0.2"
- cpus = 4
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: index_bam {
- container = "lbmc/deeptools:3.0.2"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: index_bam {
- container = "lbmc/sambamba:0.6.7"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- withName: bam_to_bigwig {
- container = "lbmc/deeptools:3.0.2"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.nf b/src/nf_modules/deeptools/bam_to_bigwig.nf
deleted file mode 100644
index 4c30ee0e..00000000
--- a/src/nf_modules/deeptools/bam_to_bigwig.nf
+++ /dev/null
@@ -1,49 +0,0 @@
-params.bam = "$baseDir/data/bam/*.bam"
-
-log.info "bams files : ${params.bam}"
-
-Channel
- .fromPath( params.bam )
- .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
- .set { bam_files }
-
-bam_files.into{
- bam_files_index;
- bam_files_bigwig
- }
-
-process index_bam {
- tag "$file_id"
-
- input:
- set file_id, file(bam) from bam_files_index
-
- output:
- set file_id, "*.bam*" into indexed_bam_file
-
- script:
-"""
-sambamba index -t ${task.cpus} ${bam}
-"""
-}
-
-bam_files_indexed = bam_files_bigwig.join(indexed_bam_file, by: 0)
-
-process bam_to_bigwig {
- tag "$file_id"
-
- publishDir "results/mapping/bigwig/", mode: 'copy'
-
- input:
- set file_id, file(bam), file(idx) from bam_files_indexed
-
- output:
- set file_id, "*.bw" into bw_files
-
- script:
-"""
-bamCoverage -p ${task.cpus} --ignoreDuplicates -b ${bam} -o ${file_id}.bw
-"""
-}
-
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
deleted file mode 100644
index 8c9c1b7a..00000000
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ /dev/null
@@ -1,57 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: compute_matrix {
- container = "lbmc/deeptools:3.0.2"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: compute_matrix {
- container = "lbmc/deeptools:3.0.2"
- cpus = 4
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: compute_matrix {
- container = "lbmc/deeptools:3.0.2"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: compute_matrix {
- container = "lbmc/deeptools:3.0.2"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/deeptools/compute_matrix.nf b/src/nf_modules/deeptools/compute_matrix.nf
deleted file mode 100644
index 2b6e0e91..00000000
--- a/src/nf_modules/deeptools/compute_matrix.nf
+++ /dev/null
@@ -1,38 +0,0 @@
-params.bw = "$baseDir/data/bigwig/*.bw"
-params.bed = "$baseDir/data/annot/*.bed"
-
-log.info "bigwig files : ${params.bw}"
-log.info "bed files : ${params.bed}"
-
-Channel
- .fromPath( params.bw )
- .ifEmpty { error "Cannot find any bigwig files matching: ${params.bw}" }
- .set { bw_files }
-
-Channel
- .fromPath( params.bed )
- .ifEmpty { error "Cannot find any bed files matching: ${params.bed}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
- .set { bed_files }
-
-process compute_matrix {
- tag "$bed_file_id"
- publishDir "results/mapping/region_matrix/", mode: 'copy'
-
- input:
- file bw from bw_files.collect()
- set bed_file_id, file(bed) from bed_files.collect()
-
- output:
- set bed_file_id, "*.mat.gz" into region_matrix
-
- script:
-"""
-computeMatrix scale-regions -S ${bw} \
- -p ${task.cpus} \
- -R ${bed} \
- --beforeRegionStartLength 100 \
- --afterRegionStartLength 100 \
- -o ${bed_file_id}.mat.gz
-"""
-}
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
deleted file mode 100644
index 93207846..00000000
--- a/src/nf_modules/deeptools/plot_profile.config
+++ /dev/null
@@ -1,57 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: plot_profile {
- container = "lbmc/deeptools:3.0.2"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: compute_matrix {
- container = "lbmc/deeptools:3.0.2"
- cpus = 4
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: plot_profile {
- container = "lbmc/deeptools:3.0.2"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: plot_profile {
- container = "lbmc/deeptools:3.0.2"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/deeptools/plot_profile.nf b/src/nf_modules/deeptools/plot_profile.nf
deleted file mode 100644
index dfce4e55..00000000
--- a/src/nf_modules/deeptools/plot_profile.nf
+++ /dev/null
@@ -1,36 +0,0 @@
-params.matrix = "$baseDir/data/region_matrix/*.mat.gz"
-params.title = "plot title"
-
-log.info "matrix files : ${params.matrix}"
-log.info "plot title : ${params.title}"
-
-Channel
- .fromPath( params.matrix )
- .ifEmpty { error "Cannot find any matrix files matching: ${params.matrix}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
- .set { matrix_files }
-
-process plot_profile {
- tag "$file_id"
- publishDir "results/mapping/region_matrix/", mode: 'copy'
-
- input:
- set file_id, file(matrix) from matrix_files
-
- output:
- set file_id, "*.pdf" into region_matrix
-
- script:
-/*
-see more option at
-https://deeptools.readthedocs.io/en/develop/content/tools/plotProfile.html
-*/
-"""
-plotProfile -m ${matrix} \
- --plotFileFormat=pdf \
- -out ${file_id}.pdf \
- --plotType=fill \
- --perGroup \
- --plotTitle "${params.title}"
-"""
-}
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
deleted file mode 100644
index dc9bf8cd..00000000
--- a/src/nf_modules/fastp/fastp_paired.config
+++ /dev/null
@@ -1,56 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: fastp_fastq {
- container = "lbmc/fastp:0.19.7"
- cpus = 1
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: fastp_fastq {
- cpus = 1
- container = "lbmc/fastp:0.19.7"
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: fastp_fastq {
- container = "lbmc/fastp:0.19.7"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "20GB"
- time = "12h"
- queue = "monointeldeb128"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: fastp_fastq {
- container = "lbmc/fastp:0.19.7"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/fastp/fastp_paired.nf b/src/nf_modules/fastp/fastp_paired.nf
deleted file mode 100644
index 88d6710b..00000000
--- a/src/nf_modules/fastp/fastp_paired.nf
+++ /dev/null
@@ -1,34 +0,0 @@
-params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
- .fromFilePairs( params.fastq )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
- .set { fastq_files }
-
-process fastp_fastq {
- tag "$pair_id"
- publishDir "results/fastq/fastp/", mode: 'copy'
-
- input:
- set pair_id, file(reads) from fastq_files
-
- output:
- file "*.{zip,html}" into fastp_report
- set pair_id, file "*.fastq.gz" fastq_trim_files
-
- script:
-"""
-fastp --thread ${task.cpus} \
---qualified_quality_phred 20 \
---disable_length_filtering \
---detect_adapter_for_pe \
---in1 ${reads[0]} \
---in2 ${reads[1]} \
---out1 ${pair_id}_R1_trim.fastq.gz \
---out2 ${pair_id}_R2_trim.fastq.gz \
---html ${pair_id}.html \
---report_title ${pair_id}
-"""
-}
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
deleted file mode 100644
index dc9bf8cd..00000000
--- a/src/nf_modules/fastp/fastp_single.config
+++ /dev/null
@@ -1,56 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: fastp_fastq {
- container = "lbmc/fastp:0.19.7"
- cpus = 1
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: fastp_fastq {
- cpus = 1
- container = "lbmc/fastp:0.19.7"
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: fastp_fastq {
- container = "lbmc/fastp:0.19.7"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "20GB"
- time = "12h"
- queue = "monointeldeb128"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: fastp_fastq {
- container = "lbmc/fastp:0.19.7"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/fastp/fastp_single.nf b/src/nf_modules/fastp/fastp_single.nf
deleted file mode 100644
index 31262172..00000000
--- a/src/nf_modules/fastp/fastp_single.nf
+++ /dev/null
@@ -1,32 +0,0 @@
-params.fastq = "$baseDir/data/fastq/*.fastq"
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
- .fromPath( params.fastq )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
- .set { fastq_files }
-
-process fastp_fastq {
- tag "$file_id"
- publishDir "results/fastq/fastp/", mode: 'copy'
-
- input:
- set file_id, file(reads) from fastq_files
-
- output:
- file "*.{zip,html}" into fastp_report
- set file_id, file "*.fastq.gz" fastq_trim_files
-
- script:
-"""
-fastp --thread ${task.cpus} \
---qualified_quality_phred 20 \
---disable_length_filtering \
---in1 ${reads} \
---out1 ${file_id}_R1_trim.fastq.gz \
---html ${file_id}.html \
---report_title ${file_id}
-"""
-}
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
deleted file mode 100644
index 5f12694b..00000000
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ /dev/null
@@ -1,56 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: fastqc_fastq {
- container = "lbmc/fastqc:0.11.5"
- cpus = 1
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: fastqc_fastq {
- cpus = 1
- container = "lbmc/fastqc:0.11.5"
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: fastqc_fastq {
- container = "lbmc/fastqc:0.11.5"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "20GB"
- time = "12h"
- queue = "monointeldeb128"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: fastqc_fastq {
- container = "lbmc/fastqc:0.11.5"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/fastqc/fastqc_paired.nf b/src/nf_modules/fastqc/fastqc_paired.nf
deleted file mode 100644
index 6755edec..00000000
--- a/src/nf_modules/fastqc/fastqc_paired.nf
+++ /dev/null
@@ -1,26 +0,0 @@
-params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
- .fromFilePairs( params.fastq )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
- .set { fastq_files }
-
-process fastqc_fastq {
- tag "$pair_id"
- publishDir "results/fastq/fastqc/", mode: 'copy'
-
- input:
- set pair_id, file(reads) from fastq_files
-
- output:
- file "*.{zip,html}" into fastqc_report
-
- script:
-"""
-fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ \
-${reads[0]} ${reads[1]}
-"""
-}
-
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
deleted file mode 100644
index 5f12694b..00000000
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ /dev/null
@@ -1,56 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: fastqc_fastq {
- container = "lbmc/fastqc:0.11.5"
- cpus = 1
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: fastqc_fastq {
- cpus = 1
- container = "lbmc/fastqc:0.11.5"
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: fastqc_fastq {
- container = "lbmc/fastqc:0.11.5"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "20GB"
- time = "12h"
- queue = "monointeldeb128"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: fastqc_fastq {
- container = "lbmc/fastqc:0.11.5"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/fastqc/fastqc_single.nf b/src/nf_modules/fastqc/fastqc_single.nf
deleted file mode 100644
index ab7e22aa..00000000
--- a/src/nf_modules/fastqc/fastqc_single.nf
+++ /dev/null
@@ -1,26 +0,0 @@
-params.fastq = "$baseDir/data/fastq/*.fastq"
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
- .fromPath( params.fastq )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
- .set { fastq_files }
-
-process fastqc_fastq {
- tag "$file_id"
- publishDir "results/fastq/fastqc/", mode: 'copy'
-
- input:
- set file_id, file(reads) from fastq_files
-
- output:
- file "*.{zip,html}" into fastqc_report
-
- script:
-"""
-fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ ${reads}
-"""
-}
-
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
deleted file mode 100644
index 5d154dd4..00000000
--- a/src/nf_modules/hisat2/indexing.config
+++ /dev/null
@@ -1,57 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: index_fasta {
- container = "lbmc/hisat2:2.1.0"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: index_fasta {
- cpus = 4
- container = "lbmc/hisat2:2.1.0"
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: index_fasta {
- container = "lbmc/hisat2:2.1.0"
- executor = "sge"
- clusterOptions = "-cwd -V"
- memory = "20GB"
- cpus = 32
- time = "12h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: index_fasta {
- container = "lbmc/hisat2:2.1.0"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/hisat2/indexing.nf b/src/nf_modules/hisat2/indexing.nf
deleted file mode 100644
index 1b11b3ef..00000000
--- a/src/nf_modules/hisat2/indexing.nf
+++ /dev/null
@@ -1,32 +0,0 @@
-/*
-* Hisat2 :
-* 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 fasta files matching: ${params.fasta}" }
- .set { fasta_file }
-
-process index_fasta {
- tag "$fasta.baseName"
- publishDir "results/mapping/index/", mode: 'copy'
-
- input:
- file fasta from fasta_file
-
- output:
- file "*.index*" into index_files
-
- script:
-"""
-hisat2-build -p ${task.cpus} ${fasta} ${fasta.baseName}.index
-"""
-}
diff --git a/src/nf_modules/hisat2/mapping_paired.config b/src/nf_modules/hisat2/mapping_paired.config
deleted file mode 100644
index 964db521..00000000
--- a/src/nf_modules/hisat2/mapping_paired.config
+++ /dev/null
@@ -1,55 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: mapping_fastq {
- cpus = 4
- container = "lbmc/hisat2:2.1.0"
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: mapping_fastq {
- cpus = 4
- container = "lbmc/hisat2:2.1.0"
- }
- }
- }
- sge {
- process{
- withName: mapping_fastq {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "hisat2/2.1.0:samtools/1.7"
- executor = "sge"
- clusterOptions = "-cwd -V"
- memory = "20GB"
- cpus = 32
- time = "12h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: mapping_fastq {
- container = "lbmc/hisat2:2.1.0"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/hisat2/mapping_paired.nf b/src/nf_modules/hisat2/mapping_paired.nf
deleted file mode 100644
index 28b37e00..00000000
--- a/src/nf_modules/hisat2/mapping_paired.nf
+++ /dev/null
@@ -1,48 +0,0 @@
-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"
- publishDir "results/mapping/", mode: 'copy'
-
- input:
- set pair_id, file(reads) from fastq_files
- file index from index_files.collect()
-
- output:
- file "*" into counts_files
- 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\.ht2/ && !(index_file =~ /.*\.rev\.1\.ht2/)) {
- index_id = ( index_file =~ /(.*)\.1\.ht2/)[0][1]
- }
- }
-"""
-hisat2 -p ${task.cpus} \
- -x ${index_id} \
- -1 ${reads[0]} \
- -2 ${reads[1]} 2> \
-${pair_id}_hisat2_report.txt | \
-samtools view -Sb - > ${pair_id}.bam
-
-if grep -q "Error" ${pair_id}_hisat2_report.txt; then
- exit 1
-fi
-"""
-}
diff --git a/src/nf_modules/hisat2/mapping_single.config b/src/nf_modules/hisat2/mapping_single.config
deleted file mode 100644
index 964db521..00000000
--- a/src/nf_modules/hisat2/mapping_single.config
+++ /dev/null
@@ -1,55 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: mapping_fastq {
- cpus = 4
- container = "lbmc/hisat2:2.1.0"
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: mapping_fastq {
- cpus = 4
- container = "lbmc/hisat2:2.1.0"
- }
- }
- }
- sge {
- process{
- withName: mapping_fastq {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "hisat2/2.1.0:samtools/1.7"
- executor = "sge"
- clusterOptions = "-cwd -V"
- memory = "20GB"
- cpus = 32
- time = "12h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: mapping_fastq {
- container = "lbmc/hisat2:2.1.0"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/hisat2/mapping_single.nf b/src/nf_modules/hisat2/mapping_single.nf
deleted file mode 100644
index 0fdb729e..00000000
--- a/src/nf_modules/hisat2/mapping_single.nf
+++ /dev/null
@@ -1,53 +0,0 @@
-/*
-* for single-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*.fastq"
-params.index = "$baseDir/data/index/*.index*"
-
-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"
- publishDir "results/mapping/", mode: 'copy'
-
- input:
- set file_id, file(reads) from fastq_files
- file index from index_files.collect()
-
- output:
- file "*" into count_files
- 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\.ht2/ && !(index_file =~ /.*\.rev\.1\.ht2/)) {
- index_id = ( index_file =~ /(.*)\.1\.ht2/)[0][1]
- }
- }
-"""
-hisat2 -p ${task.cpus} \
- -x ${index_id} \
- -U ${reads} 2> \
-${file_id}_hisat2_report.txt | \
-samtools view -Sb - > ${file_id}.bam
-
-if grep -q "Error" ${file_id}_hisat2_report.txt; then
- exit 1
-fi
-
-"""
-}
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
deleted file mode 100644
index 931ca784..00000000
--- a/src/nf_modules/htseq/htseq.config
+++ /dev/null
@@ -1,75 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: sort_bam {
- container = "lbmc/samtools:1.7"
- cpus = 1
- }
- withName: counting {
- container = "lbmc/htseq:0.11.2"
- cpus = 1
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: sort_bam {
- container = "lbmc/samtools:1.7"
- cpus = 1
- }
- withName: counting {
- container = "lbmc/htseq:0.11.2"
- cpus = 1
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: sort_bam {
- container = "lbmc/htseq:0.11.2"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "20GB"
- time = "12h"
- queue = "monointeldeb128"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: sort_bam {
- container = "lbmc/samtools:1.7"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- withName: counting {
- container = "lbmc/htseq:0.11.2"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/htseq/htseq.nf b/src/nf_modules/htseq/htseq.nf
deleted file mode 100644
index 7cade9a5..00000000
--- a/src/nf_modules/htseq/htseq.nf
+++ /dev/null
@@ -1,52 +0,0 @@
-params.bam = "$baseDir/data/bam/*.bam"
-params.gtf = "$baseDir/data/annotation/*.gtf"
-
-log.info "bam files : ${params.bam}"
-log.info "gtf files : ${params.gtf}"
-
-Channel
- .fromPath( params.bam )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.bam}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
- .set { bam_files }
-Channel
- .fromPath( params.gtf )
- .ifEmpty { error "Cannot find any gtf file matching: ${params.gtf}" }
- .set { gtf_file }
-
-process sort_bam {
- tag "$file_id"
- cpus 4
-
- input:
- set file_id, file(bam) from bam_files
-
- output:
- set file_id, "*_sorted.sam" into sorted_bam_files
-
- script:
-"""
-# sort bam by name
-samtools sort -@ ${task.cpus} -n -O SAM -o ${file_id}_sorted.sam ${bam}
-"""
-}
-
-process counting {
- tag "$file_id"
- publishDir "results/quantification/", mode: 'copy'
-
- input:
- set file_id, file(bam) from sorted_bam_files
- file gtf from gtf_file
-
- output:
- file "*.count" into count_files
-
- script:
-"""
-htseq-count ${bam} ${gtf} \
--r pos --mode=intersection-nonempty -a 10 -s no -t exon -i gene_id \
-> ${file_id}.count
-"""
-}
-
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
deleted file mode 100644
index 1f3f39e8..00000000
--- a/src/nf_modules/kallisto/indexing.config
+++ /dev/null
@@ -1,57 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withLabel kallisto {
- container = "lbmc/kallisto:0.44.0"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withLabel: kallisto {
- container = "lbmc/kallisto:0.44.0"
- cpus = 4
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withLabel: kallisto {
- container = "lbmc/kallisto:0.44.0"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withLabel: kallisto {
- container = "lbmc/kallisto:0.44.0"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/kallisto/indexing.nf b/src/nf_modules/kallisto/indexing.nf
deleted file mode 100644
index 5b0fba5e..00000000
--- a/src/nf_modules/kallisto/indexing.nf
+++ /dev/null
@@ -1,28 +0,0 @@
-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"
- publishDir "results/mapping/index/", mode: 'copy'
- label "kallisto"
-
- input:
- file fasta from fasta_file
-
- output:
- file "*.index*" into index_files
- file "*_kallisto_report.txt" into index_files_report
-
- script:
-"""
-kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \
-2> ${fasta.baseName}_kallisto_report.txt
-"""
-}
-
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
deleted file mode 100644
index 962e1fdc..00000000
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ /dev/null
@@ -1,59 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withLabel: kallisto {
- container = "lbmc/kallisto:0.44.0"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withLabel: kallisto {
- container = "lbmc/kallisto:0.44.0"
- cpus = 4
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withLabel: kallisto {
- container = "lbmc/kallisto:0.44.0"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withLabel: kallisto {
- container = "lbmc/kallisto:0.44.0"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
-
-
diff --git a/src/nf_modules/kallisto/mapping_paired.nf b/src/nf_modules/kallisto/mapping_paired.nf
deleted file mode 100644
index 56f13000..00000000
--- a/src/nf_modules/kallisto/mapping_paired.nf
+++ /dev/null
@@ -1,36 +0,0 @@
-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: ${params.index}" }
- .set { index_files }
-
-process mapping_fastq {
- tag "$reads"
- publishDir "results/mapping/quantification/", mode: 'copy'
- label "kallisto"
-
- input:
- set pair_id, file(reads) from fastq_files
- file index from index_files.collect()
-
- output:
- file "*" into counts_files
-
- script:
-"""
-mkdir ${pair_id}
-kallisto quant -i ${index} -t ${task.cpus} \
---bias --bootstrap-samples 100 -o ${pair_id} \
-${reads[0]} ${reads[1]} &> ${pair_id}/kallisto_report.txt
-"""
-}
-
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
deleted file mode 100644
index 962e1fdc..00000000
--- a/src/nf_modules/kallisto/mapping_single.config
+++ /dev/null
@@ -1,59 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withLabel: kallisto {
- container = "lbmc/kallisto:0.44.0"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withLabel: kallisto {
- container = "lbmc/kallisto:0.44.0"
- cpus = 4
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withLabel: kallisto {
- container = "lbmc/kallisto:0.44.0"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withLabel: kallisto {
- container = "lbmc/kallisto:0.44.0"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
-
-
diff --git a/src/nf_modules/kallisto/mapping_single.nf b/src/nf_modules/kallisto/mapping_single.nf
deleted file mode 100644
index 7ae21280..00000000
--- a/src/nf_modules/kallisto/mapping_single.nf
+++ /dev/null
@@ -1,42 +0,0 @@
-params.fastq = "$baseDir/data/fastq/*.fastq"
-params.index = "$baseDir/data/index/*.index*"
-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"
- publishDir "results/mapping/quantification/", mode: 'copy'
- label "kallisto"
-
- 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} &> ${file_id}/kallisto_report.txt
-"""
-}
-
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
deleted file mode 100644
index d3cbbdb9..00000000
--- a/src/nf_modules/macs2/peak_calling.config
+++ /dev/null
@@ -1,57 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: peak_calling {
- container = "lbmc/macs2:2.1.2"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: peak_calling {
- container = "lbmc/macs2:2.1.2"
- cpus = 4
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: peak_calling {
- container = "lbmc/macs2:2.1.2"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: peak_calling {
- container = "lbmc/macs2:2.1.2"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/macs2/peak_calling.nf b/src/nf_modules/macs2/peak_calling.nf
deleted file mode 100644
index 12398f2e..00000000
--- a/src/nf_modules/macs2/peak_calling.nf
+++ /dev/null
@@ -1,52 +0,0 @@
-params.genome_size = "hs"
-params.control_tag = "control"
-log.info "bam files : ${params.bam}"
-log.info "genome size : ${params.genome_size}"
-log.info "control tag : ${params.control_tag}"
-
-Channel
- .fromPath( params.bam )
- .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
- .set { bam_files }
-
-/* split bam Channel into control and ip if "control" keyword is detected*/
-bam_files_control = Channel.create()
-bam_files_ip = Channel.create()
-bam_files.choice(
- bam_files_control,
- bam_files_ip ) { a -> a[0] =~ /.*${params.control_tag}.*/ ? 0 : 1 }
-
-process peak_calling {
- tag "${file_id}"
- publishDir "results/peak_calling/${file_id}", mode: 'copy'
-
- input:
- set file_id, file(file_ip) from bam_files_ip
- set file_id_control, file(file_control) from bam_files_control
- .ifEmpty {
- error "Cannot find any bam files matching: ${params.control_tag}"
- }
- .collect()
-
- output:
- file "*" into peak_output
- file "*_report.txt" into peak_calling_report
-
- script:
-/* remove --nomodel option for real dataset */
-"""
-macs2 callpeak \
- --nomodel \
- --treatment ${file_ip} \
- --control ${file_control} \
- --name ${file_id} \
- --gsize ${params.genome_size} 2> \
-${file_ip}_macs2_report.txt
-
-if grep -q "ERROR" ${file_ip}_macs2_report.txt; then
- echo "MACS2 error"
- exit 1
-fi
-"""
-}
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
deleted file mode 100644
index 2d786124..00000000
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ /dev/null
@@ -1,84 +0,0 @@
-
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: fastqc_fastq {
- container = "lbmc/fastqc:0.11.5"
- cpus = 1
- }
- withName: multiqc {
- container = "lbmc/multiqc:1.7"
- cpus = 1
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: fastqc_fastq {
- container = "lbmc/fastqc:0.11.5"
- cpus = 1
- }
- withName: multiqc {
- container = "lbmc/multiqc:1.7"
- cpus = 1
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: fastqc_fastq {
- container = "lbmc/fastqc:0.11.5"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "5GB"
- time = "6h"
- queue = "monointeldeb128"
- }
- withName: multiqc {
- container = "lbmc/multiqc:1.7"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "5GB"
- time = "6h"
- queue = "monointeldeb128"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: fastq_fastqc {
- container = "lbmc/fastqc:0.11.5"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r"
- cpus = 1
- queue = "huge"
- }
- withName: multiqc {
- container = "lbmc/multiqc:1.7"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r"
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
-
diff --git a/src/nf_modules/multiqc/multiqc_paired.nf b/src/nf_modules/multiqc/multiqc_paired.nf
deleted file mode 100644
index b459a9bb..00000000
--- a/src/nf_modules/multiqc/multiqc_paired.nf
+++ /dev/null
@@ -1,43 +0,0 @@
-params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
- .fromFilePairs( params.fastq )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
- .set { fastq_files }
-
-process fastqc_fastq {
- tag "$pair_id"
- publishDir "results/fastq/fastqc/", mode: 'copy'
-
- input:
- set pair_id, file(reads) from fastq_files
-
- output:
- file "*.{zip,html}" into fastqc_report
-
- script:
-"""
-fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ \
-${reads[0]} ${reads[1]}
-"""
-}
-
-process multiqc {
- tag "$report[0].baseName"
- publishDir "results/fastq/multiqc/", mode: 'copy'
- cpus = 1
-
- input:
- file report from fastqc_report.collect()
-
- output:
- file "*multiqc_*" into multiqc_report
-
- script:
-"""
-multiqc -f .
-"""
-}
-
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
deleted file mode 100644
index 75f2f9aa..00000000
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ /dev/null
@@ -1,82 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: fastqc_fastq {
- container = "lbmc/fastqc:0.11.5"
- cpus = 1
- }
- withName: multiqc {
- container = "lbmc/multiqc:1.7"
- cpus = 1
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: fastqc_fastq {
- container = "lbmc/fastqc:0.11.5"
- cpus = 1
- }
- withName: multiqc {
- container = "lbmc/multiqc:1.7"
- cpus = 1
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: fastqc_fastq {
- container = "lbmc/fastqc:0.11.5"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "5GB"
- time = "6h"
- queue = "monointeldeb128"
- }
- withName: multiqc {
- container = "lbmc/multiqc:1.7"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "5GB"
- time = "6h"
- queue = "monointeldeb128"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: fastq_fastqc {
- container = "lbmc/fastqc:0.11.5"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r"
- cpus = 1
- queue = "huge"
- }
- withName: multiqc {
- container = "lbmc/multiqc:1.7"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r"
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/multiqc/multiqc_single.nf b/src/nf_modules/multiqc/multiqc_single.nf
deleted file mode 100644
index ea1115b5..00000000
--- a/src/nf_modules/multiqc/multiqc_single.nf
+++ /dev/null
@@ -1,44 +0,0 @@
-params.fastq = "$baseDir/data/fastq/*.fastq"
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
- .fromPath( params.fastq )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
- .set { fastq_files }
-
-process fastqc_fastq {
- tag "$file_id"
- publishDir "results/fastq/fastqc/", mode: 'copy'
- cpus = 1
-
- input:
- set file_id, file(reads) from fastq_files
-
- output:
- file "*.{zip,html}" into fastqc_report
-
- script:
-"""
-fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ ${reads}
-"""
-}
-
-process multiqc {
- tag "$report[0].baseName"
- publishDir "results/fastq/multiqc/", mode: 'copy'
- cpus = 1
-
- input:
- file report from fastqc_report.collect()
-
- output:
- file "*multiqc_*" into multiqc_report
-
- script:
-"""
-multiqc -f .
-"""
-}
-
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
deleted file mode 100644
index dea6fa7b..00000000
--- a/src/nf_modules/music/peak_calling_single.config
+++ /dev/null
@@ -1,94 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: compute_mappability {
- container = "lbmc/music:6613c53"
- cpus = 1
- }
- withName: music_preprocessing {
- container = "lbmc/music:6613c53"
- cpus = 1
- }
- withName: music_computation{
- container = "lbmc/music:6613c53"
- cpus = 1
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: compute_mappability {
- container = "lbmc/music:6613c53"
- cpus = 1
- }
- withName: music_preprocessing {
- container = "lbmc/music:6613c53"
- cpus = 1
- }
- withName: music_computation{
- container = "lbmc/music:6613c53"
- cpus = 1
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: compute_mappability {
- container = "lbmc/music:6613c53"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "20GB"
- time = "12h"
- queue = "monointeldeb128"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: compute_mappability {
- container = "lbmc/music:6613c53"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- withName: music_preprocessing {
- container = "lbmc/music:6613c53"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- withName: music_computation{
- container = "lbmc/music:6613c53"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/music/peak_calling_single.nf b/src/nf_modules/music/peak_calling_single.nf
deleted file mode 100644
index be280394..00000000
--- a/src/nf_modules/music/peak_calling_single.nf
+++ /dev/null
@@ -1,104 +0,0 @@
-params.read_size = 100
-params.frag_size = 200
-params.step_l = 50
-params.min_l = 200
-params.max_l = 5000
-log.info "bam files : ${params.bam}"
-log.info "index files : ${params.index}"
-log.info "fasta files : ${params.fasta}"
-
-Channel
- .fromPath( params.fasta )
- .ifEmpty { error "Cannot find any bam files matching: ${params.fasta}" }
- .set { fasta_files }
-Channel
- .fromPath( params.bam )
- .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
- .set { bam_files }
-Channel
- .fromPath( params.index )
- .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
- .set { index_files }
-
-process compute_mappability {
- tag "${fasta.baseName}"
-
- input:
- file index from index_files.collect()
- file fasta from fasta_files
-
- output:
- file "*.bin" into mappability
- file "temp/chr_ids.txt" into chr_ids
-
- script:
-
-"""
-generate_multimappability_signal.csh ${fasta} ${params.read_size} ./
-bash temp_map_reads.csh
-bash temp_process_mapping.csh
-"""
-}
-
-process music_preprocessing {
- tag "${file_id}"
-
- input:
- set file_id, file(bam) from bam_files
- file chr_ids from chr_ids.collect()
-
- output:
- set file_id, "preprocessed/*.tar" into preprocessed_bam_files
-
- script:
-
-"""
-mkdir preprocessed
-samtools view *.bam | \
-MUSIC -preprocess SAM stdin preprocessed/
-mkdir preprocessed/sorted
-MUSIC -sort_reads preprocessed/ preprocessed/sorted/
-mkdir preprocessed/dedup
-MUSIC -remove_duplicates ./preprocessed/sorted 2 preprocessed/dedup/
-cd preprocessed
-tar -c -f ${file_id}.tar *
-"""
-}
-
-preprocessed_bam_files_control = Channel.create()
-preprocessed_bam_files_chip = Channel.create()
-preprocessed_bam_files.choice(
- preprocessed_bam_files_control,
- preprocessed_bam_files_chip ) { a -> a[0] =~ /.*control.*/ ? 0 : 1 }
-
-process music_computation {
- tag "${file_id}"
- publishDir "results/peak_calling/${file_id}", mode: 'copy'
-
- input:
- set file_id, file(control) from preprocessed_bam_files_chip
- set file_id_control, file(chip) from preprocessed_bam_files_control.collect()
- file mapp from mappability.collect()
-
- output:
- file "*" into music_output_forward
- file "*.bed" into peaks_forward
-
- script:
-
-"""
-mkdir mappability control chip
-mv ${mapp} mappability/
-tar -xf ${control} -C control/
-tar -xf ${chip} -C chip/
-
-MUSIC -get_per_win_p_vals_vs_FC -chip chip/ -control control/ \
- -l_win_step ${params.step_l} \
- -l_win_min ${params.min_l} -l_win_max ${params.max_l}
-MUSIC -get_multiscale_punctate_ERs \
- -chip chip/ -control control/ -mapp mappability/ \
- -l_mapp ${params.read_size} -l_frag ${params.frag_size} -q_val 1 -l_p 0
-ls -l
-"""
-}
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
deleted file mode 100644
index 86f57dde..00000000
--- a/src/nf_modules/rsem/indexing.config
+++ /dev/null
@@ -1,57 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: index_fasta {
- container = "lbmc/rsem:1.3.0"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: index_fasta {
- container = "lbmc/rsem:1.3.0"
- cpus = 4
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: index_fasta {
- container = "lbmc/rsem:1.3.0"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: index_fasta {
- container = "lbmc/rsem:1.3.0"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/rsem/indexing.nf b/src/nf_modules/rsem/indexing.nf
deleted file mode 100644
index 4b95622a..00000000
--- a/src/nf_modules/rsem/indexing.nf
+++ /dev/null
@@ -1,39 +0,0 @@
-params.fasta = "$baseDir/data/bam/*.fasta"
-params.annotation = "$baseDir/data/bam/*.gff3"
-
-log.info "fasta files : ${params.fasta}"
-
-Channel
- .fromPath( params.fasta )
- .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
- .set { fasta_file }
-Channel
- .fromPath( params.annotation )
- .ifEmpty { error "Cannot find any annotation files matching: ${params.annotation}" }
- .set { annotation_file }
-
-process index_fasta {
- tag "$fasta.baseName"
- publishDir "results/mapping/index/", mode: 'copy'
-
- input:
- file fasta from fasta_file
- file annotation from annotation_file
-
- output:
- file "*.index*" into index_files
-
- script:
- def cmd_annotation = "--gff3 ${annotation}"
- if(annotation ==~ /.*\.gtf$/){
- cmd_annotation = "--gtf ${annotation}"
- }
-"""
-rsem-prepare-reference -p ${task.cpus} --bowtie2 \
---bowtie2-path \$(which bowtie2 | sed 's/bowtie2\$//g') \
-${cmd_annotation} ${fasta} ${fasta.baseName}.index > \
-${fasta.baseName}_rsem_bowtie2_report.txt
-"""
-}
-
-
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
deleted file mode 100644
index a959b00f..00000000
--- a/src/nf_modules/rsem/quantification_paired.config
+++ /dev/null
@@ -1,57 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: mapping_fastq {
- container = "lbmc/rsem:1.3.0"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: mapping_fastq {
- container = "lbmc/rsem:1.3.0"
- cpus = 4
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: mapping_fastq {
- container = "lbmc/rsem:1.3.0"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: mapping_fastq {
- container = "lbmc/rsem:1.3.0"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/rsem/quantification_paired.nf b/src/nf_modules/rsem/quantification_paired.nf
deleted file mode 100644
index c9e23ac8..00000000
--- a/src/nf_modules/rsem/quantification_paired.nf
+++ /dev/null
@@ -1,48 +0,0 @@
-params.fastq = "$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"
- publishDir "results/mapping/quantification/", mode: 'copy'
-
- input:
- set pair_id, file(reads) from fastq_files
- file index from index_files.toList()
-
- output:
- file "*" into counts_files
-
- 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]
- }
- }
-"""
-rsem-calculate-expression --bowtie2 \
---bowtie2-path \$(which bowtie2 | sed 's/bowtie2\$//g') \
---bowtie2-sensitivity-level "very_sensitive" \
--output-genome-bam -p ${task.cpus} \
---paired-end ${reads[0]} ${reads[1]} ${index_id} ${pair_id} \
-2> ${pair_id}_rsem_bowtie2_report.txt
-
-if grep -q "Error" ${pair_id}_rsem_bowtie2_report.txt; then
- exit 1
-fi
-"""
-}
-
-
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
deleted file mode 100644
index a959b00f..00000000
--- a/src/nf_modules/rsem/quantification_single.config
+++ /dev/null
@@ -1,57 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: mapping_fastq {
- container = "lbmc/rsem:1.3.0"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: mapping_fastq {
- container = "lbmc/rsem:1.3.0"
- cpus = 4
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: mapping_fastq {
- container = "lbmc/rsem:1.3.0"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: mapping_fastq {
- container = "lbmc/rsem:1.3.0"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/rsem/quantification_single.nf b/src/nf_modules/rsem/quantification_single.nf
deleted file mode 100644
index bacba6b3..00000000
--- a/src/nf_modules/rsem/quantification_single.nf
+++ /dev/null
@@ -1,53 +0,0 @@
-params.fastq = "$baseDir/data/fastq/*.fastq"
-params.index = "$baseDir/data/index/*.index*"
-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"
- 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:
- 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]
- }
- }
-"""
-rsem-calculate-expression --bowtie2 \
---bowtie2-path \$(which bowtie2 | sed 's/bowtie2\$//g') \
---bowtie2-sensitivity-level "very_sensitive" \
---fragment-length-mean ${params.mean} --fragment-length-sd ${params.sd} \
---output-genome-bam -p ${task.cpus} \
-${reads} ${index_id} ${file_id} \
-2> ${file_id}_rsem_bowtie2_report.txt
-
-if grep -q "Error" ${file_id}_rsem_bowtie2_report.txt; then
- exit 1
-fi
-"""
-}
-
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
deleted file mode 100644
index da8f84fc..00000000
--- a/src/nf_modules/sambamba/index_bams.config
+++ /dev/null
@@ -1,57 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: index_bam {
- container = "lbmc/sambamba:0.6.9"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: index_bam {
- container = "lbmc/sambamba:0.6.9"
- cpus = 4
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: index_bam {
- container = "lbmc/sambamba:0.6.9"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: index_bam {
- container = "lbmc/sambamba:0.6.9"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/sambamba/index_bams.nf b/src/nf_modules/sambamba/index_bams.nf
deleted file mode 100644
index 3ea36df4..00000000
--- a/src/nf_modules/sambamba/index_bams.nf
+++ /dev/null
@@ -1,25 +0,0 @@
-params.bam = "$baseDir/data/bam/*.bam"
-
-log.info "bams files : ${params.bam}"
-
-Channel
- .fromPath( params.bam )
- .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
- .set { bam_files }
-
-process index_bam {
- tag "$file_id"
-
- input:
- set file_id, file(bam) from bam_files
-
- output:
- set file_id, "*.bam*" into indexed_bam_file
-
- script:
-"""
-sambamba index -t ${task.cpus} ${bam}
-"""
-}
-
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
deleted file mode 100644
index 61057327..00000000
--- a/src/nf_modules/sambamba/sort_bams.config
+++ /dev/null
@@ -1,58 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: sort_bam {
- container = "lbmc/sambamba:0.6.9"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: sort_bam {
- container = "lbmc/sambamba:0.6.9"
- cpus = 4
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: sort_bam {
- container = "lbmc/sambamba:0.6.9"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 4
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: sort_bam {
- container = "lbmc/sambamba:0.6.9"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
-
- }
- }
-}
diff --git a/src/nf_modules/sambamba/sort_bams.nf b/src/nf_modules/sambamba/sort_bams.nf
deleted file mode 100644
index ac610cdc..00000000
--- a/src/nf_modules/sambamba/sort_bams.nf
+++ /dev/null
@@ -1,26 +0,0 @@
-params.bam = "$baseDir/data/bam/*.bam"
-
-log.info "bams files : ${params.bam}"
-
-Channel
- .fromPath( params.bam )
- .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
- .set { bam_files }
-
-process sort_bam {
- tag "$file_id"
- cpus 4
-
- input:
- set file_id, file(bam) from bam_files
-
- output:
- set file_id, "*_sorted.bam" into sorted_bam_files
-
- script:
-"""
-sambamba sort -t ${task.cpus} -o ${file_id}_sorted.bam ${bam}
-"""
-}
-
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
deleted file mode 100644
index e9df7d69..00000000
--- a/src/nf_modules/sambamba/split_bams.config
+++ /dev/null
@@ -1,57 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: split_bam {
- container = "lbmc/sambamba:0.6.9"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: split_bam {
- container = "lbmc/sambamba:0.6.9"
- cpus = 4
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: split_bam {
- container = "lbmc/sambamba:0.6.9"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: split_bam {
- container = "lbmc/sambamba:0.6.9"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/sambamba/split_bams.nf b/src/nf_modules/sambamba/split_bams.nf
deleted file mode 100644
index ba64d2e2..00000000
--- a/src/nf_modules/sambamba/split_bams.nf
+++ /dev/null
@@ -1,27 +0,0 @@
-params.bam = "$baseDir/data/bam/*.bam"
-
-log.info "bams files : ${params.bam}"
-
-Channel
- .fromPath( params.bam )
- .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
- .set { bam_files }
-
-process split_bam {
- tag "$file_id"
- cpus 4
-
- input:
- set file_id, file(bam) from bam_files
-
- output:
- set file_id, "*_forward.bam*" into forward_bam_files
- set file_id, "*_reverse.bam*" into reverse_bam_files
- script:
-"""
-sambamba view -t ${task.cpus} -h -F "strand == '+'" ${bam} > ${file_id}_forward.bam
-sambamba view -t ${task.cpus} -h -F "strand == '-'" ${bam} > ${file_id}_reverse.bam
-"""
-}
-
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
deleted file mode 100644
index e35185c1..00000000
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ /dev/null
@@ -1,57 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: dedup_sam {
- container = "lbmc/samblaster:0.1.24"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: split_bam {
- container = "lbmc/sambamba:0.6.7"
- cpus = 4
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: dedup_sam {
- container = "lbmc/sambamba:0.6.7"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: dedup_sam {
- container = "lbmc/sambamba:0.6.7"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/samblaster/dedup_sams.nf b/src/nf_modules/samblaster/dedup_sams.nf
deleted file mode 100644
index bcfd829c..00000000
--- a/src/nf_modules/samblaster/dedup_sams.nf
+++ /dev/null
@@ -1,27 +0,0 @@
-params.sam = "$baseDir/data/sam/*.bam"
-
-log.info "bam files : ${params.bam}"
-
-Channel
- .fromPath( params.bam )
- .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
- .set { bam_files }
-
-process dedup_sam {
- tag "$file_id"
-
- input:
- set file_id, file(bam) from bam_files
-
- output:
- set file_id, "*_dedup.bam*" into dedup_bam_files
- script:
-"""
-samtools view -h ${bam} | \
-samblaster --addMateTags 2> /dev/null | \
-samtools view -Sb - > ${file_id}_dedup.bam
-"""
-}
-
-
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
deleted file mode 100644
index dfd7f8bf..00000000
--- a/src/nf_modules/samtools/filter_bams.config
+++ /dev/null
@@ -1,57 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: filter_bam {
- container = "lbmc/samtools:1.7"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: filter_bam {
- container = "lbmc/samtools:1.7"
- cpus = 4
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: filter_bam {
- container = "lbmc/samtools:1.7"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: filter_bam {
- container = "lbmc/samtools:1.7"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/samtools/filter_bams.nf b/src/nf_modules/samtools/filter_bams.nf
deleted file mode 100644
index 6e81b758..00000000
--- a/src/nf_modules/samtools/filter_bams.nf
+++ /dev/null
@@ -1,32 +0,0 @@
-params.bam = "$baseDir/data/bam/*.bam"
-params.bed = "$baseDir/data/bam/*.bed"
-
-log.info "bams files : ${params.bam}"
-log.info "bed file : ${params.bed}"
-
-Channel
- .fromPath( params.bam )
- .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
- .set { bam_files }
-Channel
- .fromPath( params.bed )
- .ifEmpty { error "Cannot find any bed file matching: ${params.bed}" }
- .set { bed_files }
-
-process filter_bam {
- tag "$file_id"
-
- input:
- set file_id, file(bam) from bam_files
- file bed from bed_files
-
- output:
- set file_id, "*_filtered.bam*" into filtered_bam_files
- script:
-"""
-samtools view -@ ${task.cpus} -hb ${bam} -L ${bed} > ${file_id}_filtered.bam
-"""
-}
-
-
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
deleted file mode 100644
index 173af8fe..00000000
--- a/src/nf_modules/samtools/index_bams.config
+++ /dev/null
@@ -1,56 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: index_bam {
- container = "lbmc/samtools:1.7"
- cpus = 1
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: index_bam {
- container = "lbmc/samtools:1.7"
- cpus = 1
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: index_bam {
- container = "lbmc/samtools:1.7"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "20GB"
- time = "12h"
- queue = "monointeldeb128"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: index_bam {
- container = "lbmc/samtools:1.7"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/samtools/index_bams.nf b/src/nf_modules/samtools/index_bams.nf
deleted file mode 100644
index 489b0f4f..00000000
--- a/src/nf_modules/samtools/index_bams.nf
+++ /dev/null
@@ -1,25 +0,0 @@
-params.bam = "$baseDir/data/bam/*.bam"
-
-log.info "bams files : ${params.bam}"
-
-Channel
- .fromPath( params.bam )
- .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
- .set { bam_files }
-
-process index_bam {
- tag "$file_id"
-
- input:
- set file_id, file(bam) from bam_files
-
- output:
- set file_id, "*.bam*" into indexed_bam_file
-
- script:
-"""
-samtools index ${bam}
-"""
-}
-
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
deleted file mode 100644
index 48f18580..00000000
--- a/src/nf_modules/samtools/sort_bams.config
+++ /dev/null
@@ -1,57 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: sort_bam {
- container = "lbmc/samtools:1.7"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: sort_bam {
- container = "lbmc/samtools:1.7"
- cpus = 4
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: sort_bam {
- container = "lbmc/samtools:1.7"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: sort_bam {
- container = "lbmc/samtools:1.7"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/samtools/sort_bams.nf b/src/nf_modules/samtools/sort_bams.nf
deleted file mode 100644
index db1b30d1..00000000
--- a/src/nf_modules/samtools/sort_bams.nf
+++ /dev/null
@@ -1,25 +0,0 @@
-params.bam = "$baseDir/data/bam/*.bam"
-
-log.info "bams files : ${params.bam}"
-
-Channel
- .fromPath( params.bam )
- .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
- .set { bam_files }
-
-process sort_bam {
- tag "$file_id"
-
- input:
- set file_id, file(bam) from bam_files
-
- output:
- set file_id, "*_sorted.bam" into sorted_bam_files
-
- script:
-"""
-samtools sort -@ ${task.cpus} -O BAM -o ${file_id}_sorted.bam ${bam}
-"""
-}
-
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
deleted file mode 100644
index 757a946a..00000000
--- a/src/nf_modules/samtools/split_bams.config
+++ /dev/null
@@ -1,56 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: split_bam {
- container = "lbmc/samtools:1.7"
- cpus = 2
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: split_bam {
- container = "lbmc/samtools:1.7"
- cpus = 2
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: split_bam {
- container = "lbmc/samtools:1.7"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "20GB"
- time = "12h"
- queue = "monointeldeb128"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: split_bam {
- container = "lbmc/samtools:1.7"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/samtools/split_bams.nf b/src/nf_modules/samtools/split_bams.nf
deleted file mode 100644
index 0d02a5d1..00000000
--- a/src/nf_modules/samtools/split_bams.nf
+++ /dev/null
@@ -1,26 +0,0 @@
-params.bam = "$baseDir/data/bam/*.bam"
-
-log.info "bams files : ${params.bam}"
-
-Channel
- .fromPath( params.bam )
- .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
- .set { bam_files }
-
-process split_bam {
- tag "$file_id"
-
- input:
- set file_id, file(bam) from bam_files
-
- output:
- set file_id, "*_forward.bam*" into forward_bam_files
- set file_id, "*_reverse.bam*" into reverse_bam_files
- script:
-"""
-samtools view -hb -F 0x10 ${bam} > ${file_id}_forward.bam &
-samtools view -hb -f 0x10 ${bam} > ${file_id}_reverse.bam
-"""
-}
-
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
deleted file mode 100644
index 4287e92f..00000000
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ /dev/null
@@ -1,56 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: fastq_dump {
- container = "lbmc/sratoolkit:2.8.2"
- cpus = 1
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: split_bam {
- container = "lbmc/sratoolkit:2.8.2"
- cpus = 1
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: fastq_dump {
- container = "lbmc/sratoolkit:2.8.2"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "20GB"
- time = "12h"
- queue = "monointeldeb128"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: fastq_dump {
- container = "lbmc/sratoolkit:2.8.2"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/sratoolkit/fastqdump.nf b/src/nf_modules/sratoolkit/fastqdump.nf
deleted file mode 100644
index 6ba77271..00000000
--- a/src/nf_modules/sratoolkit/fastqdump.nf
+++ /dev/null
@@ -1,48 +0,0 @@
-/*
-* sra-tools :
-
-*/
-
-/* fastq-dump
-* Imputs : srr list
-* Outputs : fastq files
-*/
-
-params.list_srr = "$baseDir/data/SRR/*.txt"
-
-log.info "downloading list srr : ${params.list_srr}"
-
-Channel
- .fromPath( params.list_srr )
- .ifEmpty { error "Cannot find any bam files matching: ${params.list_srr}" }
- .splitCsv()
- .map { it -> it[0]}
- .set { SRR }
-
-//run is the column name containing SRR ids
-
-process fastq_dump {
- tag "$file_id"
- publishDir "results/download/fastq/${file_id}/", mode: 'copy'
-
- input:
- val file_id from SRR
-
- output:
- set file_id, "*.fastq" into fastq
-
- script:
-"""
-HOME=\$(pwd) # ensure that fastq dump tmp file are in the right place
-#for test only 10000 reads are downloading with the option -N 10000 -X 20000
-fastq-dump --split-files --defline-seq '@\$ac_\$si/\$ri' --defline-qual "+" -N 10000 -X 20000 ${file_id}
-if [ -f ${file_id}_1.fastq ]
-then
- mv ${file_id}_1.fastq ${file_id}_R1.fastq
-fi
-if [ -f ${file_id}_2.fastq ]
-then
- mv ${file_id}_2.fastq ${file_id}_R2.fastq
-fi
-"""
-}
diff --git a/src/nf_modules/star/indexing.config b/src/nf_modules/star/indexing.config
deleted file mode 100644
index 503c1b8c..00000000
--- a/src/nf_modules/star/indexing.config
+++ /dev/null
@@ -1,56 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: index_fasta {
- container = "lbmc/star:2.7.3a"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: index_fasta {
- container = "lbmc/star:2.7.3a"
- cpus = 4
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: index_fasta {
- container = "lbmc/star:2.7.3a"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "20GB"
- time = "12h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: index_fasta {
- container = "lbmc/star:2.7.3a"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/star/indexing.nf b/src/nf_modules/star/indexing.nf
deleted file mode 100644
index 0f340b2d..00000000
--- a/src/nf_modules/star/indexing.nf
+++ /dev/null
@@ -1,36 +0,0 @@
-params.fasta = "$baseDir/data/bam/*.fasta"
-params.annotation = "$baseDir/data/bam/*.gtf"
-
-log.info "fasta files : ${params.fasta}"
-
-Channel
- .fromPath( params.fasta )
- .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
- .set { fasta_file }
-Channel
- .fromPath( params.annotation )
- .ifEmpty { error "Cannot find any annotation files matching: ${params.annotation}" }
- .set { annotation_file }
-
-process index_fasta {
- tag "$fasta.baseName"
- publishDir "results/mapping/index/", mode: 'copy'
-
- input:
- file fasta from fasta_file
- file annotation from annotation_file
-
- output:
- file "*" into index_files
-
- script:
-"""
-STAR --runThreadN ${task.cpus} --runMode genomeGenerate \
---genomeDir ./ \
---genomeFastaFiles ${fasta} \
---sjdbGTFfile ${annotation} \
---genomeSAindexNbases 3 # min(14, log2(GenomeLength)/2 - 1)
-"""
-}
-
-
diff --git a/src/nf_modules/star/mapping_paired.config b/src/nf_modules/star/mapping_paired.config
deleted file mode 100644
index d9d43b94..00000000
--- a/src/nf_modules/star/mapping_paired.config
+++ /dev/null
@@ -1,56 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: mapping_fastq {
- container = "lbmc/star:2.7.3a"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: mapping_fastq {
- container = "lbmc/star:2.7.3a"
- cpus = 4
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: mapping_fastq {
- container = "lbmc/star:2.7.3a"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: mapping_fastq {
- container = "lbmc/star:2.7.3a"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/star/mapping_paired.nf b/src/nf_modules/star/mapping_paired.nf
deleted file mode 100644
index 9ea90175..00000000
--- a/src/nf_modules/star/mapping_paired.nf
+++ /dev/null
@@ -1,40 +0,0 @@
-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"
- 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 "*.out" into mapping_report
-
- script:
-"""
-mkdir -p index
-mv ${index} index/
-STAR --runThreadN ${task.cpus} \
---genomeDir index/ \
---readFilesIn ${reads[0]} ${reads[1]} \
---outFileNamePrefix ${pair_id} \
---outSAMmapqUnique 0 \
---outSAMtype BAM SortedByCoordinate
-"""
-}
-
diff --git a/src/nf_modules/star/mapping_single.config b/src/nf_modules/star/mapping_single.config
deleted file mode 100644
index d9d43b94..00000000
--- a/src/nf_modules/star/mapping_single.config
+++ /dev/null
@@ -1,56 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: mapping_fastq {
- container = "lbmc/star:2.7.3a"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: mapping_fastq {
- container = "lbmc/star:2.7.3a"
- cpus = 4
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: mapping_fastq {
- container = "lbmc/star:2.7.3a"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: mapping_fastq {
- container = "lbmc/star:2.7.3a"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/star/mapping_single.nf b/src/nf_modules/star/mapping_single.nf
deleted file mode 100644
index 9d3d51b3..00000000
--- a/src/nf_modules/star/mapping_single.nf
+++ /dev/null
@@ -1,39 +0,0 @@
-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"
- 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 "*.out" into mapping_report
-
- script:
-"""
-mkdir -p index
-mv ${index} index/
-STAR --runThreadN ${task.cpus} \
---genomeDir index/ \
---readFilesIn ${reads} \
---outFileNamePrefix ${file_id} \
---outSAMmapqUnique 0 \
---outSAMtype BAM SortedByCoordinate
-"""
-}
diff --git a/src/nf_modules/subread/subread.config b/src/nf_modules/subread/subread.config
deleted file mode 100644
index 2d09601a..00000000
--- a/src/nf_modules/subread/subread.config
+++ /dev/null
@@ -1,75 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: sort_bam {
- container = "lbmc/samtools:1.7"
- cpus = 1
- }
- withName: counting {
- container = "lbmc/subread:1.6.4"
- cpus = 1
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: sort_bam {
- container = "lbmc/samtools:1.7"
- cpus = 1
- }
- withName: counting {
- container = "lbmc/subread:1.6.4"
- cpus = 1
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withName: sort_bam {
- container = "lbmc/subread:1.6.4"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "20GB"
- time = "12h"
- queue = "monointeldeb128"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: sort_bam {
- container = "lbmc/samtools:1.7"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- withName: counting {
- container = "lbmc/subread:1.6.4"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
diff --git a/src/nf_modules/subread/subread.nf b/src/nf_modules/subread/subread.nf
deleted file mode 100644
index f0b53e39..00000000
--- a/src/nf_modules/subread/subread.nf
+++ /dev/null
@@ -1,52 +0,0 @@
-params.bam = "$baseDir/data/bam/*.bam"
-params.gtf = "$baseDir/data/annotation/*.gtf"
-
-log.info "bam files : ${params.bam}"
-log.info "gtf files : ${params.gtf}"
-
-Channel
- .fromPath( params.bam )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.bam}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
- .set { bam_files }
-Channel
- .fromPath( params.gtf )
- .ifEmpty { error "Cannot find any gtf file matching: ${params.gtf}" }
- .set { gtf_file }
-
-process sort_bam {
- tag "$file_id"
- cpus 4
-
- input:
- set file_id, file(bam) from bam_files
-
- output:
- set file_id, "*_sorted.sam" into sorted_bam_files
-
- script:
-"""
-# sort bam by name
-samtools sort -@ ${task.cpus} -n -O SAM -o ${file_id}_sorted.sam ${bam}
-"""
-}
-
-process counting {
- tag "$file_id"
- publishDir "results/quantification/", mode: 'copy'
-
- input:
- set file_id, file(bam) from sorted_bam_files
- file gtf from gtf_file
-
- output:
- file "*.count" into count_files
-
- script:
-"""
-featureCounts ${bam} -a ${gtf} -p \
- -o ${file_id}.count \
- -R BAM
-"""
-}
-
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
deleted file mode 100644
index f8f533f4..00000000
--- a/src/nf_modules/urqt/trimming_paired.config
+++ /dev/null
@@ -1,58 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withLabel: urqt {
- cpus = 4
- container = "lbmc/urqt:d62c1f8"
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withLabel: urqt {
- cpus = 4
- container = "lbmc/urqt:d62c1f8"
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withLabel: urqt {
- container = "lbmc/urqt:d62c1f8"
- executor = "sge"
- clusterOptions = "-cwd -V"
- memory = "5GB"
- cpus = 32
- time = "12h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withLabel: urqt {
- container = "lbmc/urqt:d62c1f8"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
-
diff --git a/src/nf_modules/urqt/trimming_paired.nf b/src/nf_modules/urqt/trimming_paired.nf
deleted file mode 100644
index 0b28219c..00000000
--- a/src/nf_modules/urqt/trimming_paired.nf
+++ /dev/null
@@ -1,27 +0,0 @@
-log.info "fastq files : ${params.fastq}"
-
-Channel
- .fromFilePairs( params.fastq )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
- .set { fastq_files }
-
-process trimming {
- tag "${reads}"
- publishDir "results/fastq/trimming/", mode: 'copy'
- label "urqt"
-
- input:
- set pair_id, file(reads) from fastq_files
-
- output:
- set pair_id, "*_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 ${pair_id}_trim_R1.fastq.gz --outpair ${pair_id}_trim_R2.fastq.gz \
-> ${pair_id}_trimming_report.txt
-"""
-}
-
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
deleted file mode 100644
index e1843f17..00000000
--- a/src/nf_modules/urqt/trimming_single.config
+++ /dev/null
@@ -1,58 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withLabel: urqt {
- container = "lbmc/urqt:d62c1f8"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withLabel: urqt {
- container = "lbmc/urqt:d62c1f8"
- cpus = 4
- }
- }
- }
- psmn{
- singularity.enabled = true
- singularity.cacheDir = "/.singularity_psmn/"
- singularity.runOptions = "--bind /Xnfs,/scratch"
- process{
- withLabel: urqt {
- container = "lbmc/urqt:d62c1f8"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 32
- memory = "5GB"
- time = "12h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withLabel: urqt {
- container = "lbmc/urqt:d62c1f8"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
- cpus = 1
- queue = "huge"
- }
- }
- }
-}
-
diff --git a/src/nf_modules/urqt/trimming_single.nf b/src/nf_modules/urqt/trimming_single.nf
deleted file mode 100644
index 42bc7c2c..00000000
--- a/src/nf_modules/urqt/trimming_single.nf
+++ /dev/null
@@ -1,30 +0,0 @@
-params.fastq = "$baseDir/data/fastq/*.fastq"
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
- .fromPath( params.fastq )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
- .set { fastq_files }
-
-process trimming {
- tag "$file_id"
- echo true
- label "urqt"
-
- input:
- set file_id, file(reads) from fastq_files
-
- output:
- set file_id, "*_trim.fastq.gz" into fastq_files_trim
-
- script:
- """
- UrQt --t 20 --m ${task.cpus} --gz \
- --in ${reads} \
- --out ${file_id}_trim.fastq.gz \
- > ${file_id}_trimming_report.txt
- """
-}
-
--
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