From 60040ed6bded13359814a4f396a32c1ae155a4da Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 6 Mar 2019 16:10:14 +0100
Subject: [PATCH] cutadapt: add singularity to nf files and add -resume to all
tests.sh
---
src/nf_modules/bedtools/fasta_from_bed.nf | 1 -
src/nf_modules/bowtie/tests.sh | 18 ++++++---
.../cutadapt/adaptor_removal_paired.config | 11 ++++++
.../cutadapt/adaptor_removal_single.config | 11 ++++++
src/nf_modules/cutadapt/tests.sh | 38 +++++++++++++++++--
.../cutadapt/trimming_paired.config | 11 ++++++
.../cutadapt/trimming_single.config | 11 ++++++
src/nf_modules/deeptools/tests.sh | 23 +++++++++--
src/nf_modules/htseq/tests.sh | 3 +-
src/nf_modules/kallisto/tests.sh | 9 +++--
src/nf_modules/multiqc/tests.sh | 6 ++-
src/nf_modules/music/tests.sh | 3 +-
src/nf_modules/rsem/tests.sh | 9 +++--
src/nf_modules/samblaster/tests.sh | 3 +-
src/nf_modules/samtools/tests.sh | 12 ++++--
src/nf_modules/sratoolkit/tests.sh | 3 +-
16 files changed, 141 insertions(+), 31 deletions(-)
diff --git a/src/nf_modules/bedtools/fasta_from_bed.nf b/src/nf_modules/bedtools/fasta_from_bed.nf
index 297fd9ef..5e7504dc 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.nf
+++ b/src/nf_modules/bedtools/fasta_from_bed.nf
@@ -23,7 +23,6 @@ Channel
process fasta_from_bed {
tag "${bed.baseName}"
- cpus 4
publishDir "results/fasta/", mode: 'copy'
input:
diff --git a/src/nf_modules/bowtie/tests.sh b/src/nf_modules/bowtie/tests.sh
index 65dfe80e..a3052918 100755
--- a/src/nf_modules/bowtie/tests.sh
+++ b/src/nf_modules/bowtie/tests.sh
@@ -1,35 +1,41 @@
./nextflow src/nf_modules/bowtie/indexing.nf \
-c src/nf_modules/bowtie/indexing.config \
-profile docker \
- --fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
+ --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
+ -resume
./nextflow src/nf_modules/bowtie/mapping_single.nf \
-c src/nf_modules/bowtie/mapping_single.config \
-profile docker \
--index "results/mapping/index/*.ebwt" \
- --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
+ --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+ -resume
./nextflow src/nf_modules/bowtie/mapping_paired.nf \
-c src/nf_modules/bowtie/mapping_paired.config \
-profile docker \
--index "results/mapping/index/*.ebwt" \
- --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
+ --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
+ -resume
if [ -x "$(command -v singularity)" ]; then
./nextflow src/nf_modules/bowtie/indexing.nf \
-c src/nf_modules/bowtie/indexing.config \
-profile singularity \
- --fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
+ --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
+ -resume
./nextflow src/nf_modules/bowtie/mapping_single.nf \
-c src/nf_modules/bowtie/mapping_single.config \
-profile singularity \
--index "results/mapping/index/*.ebwt" \
- --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
+ --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+ -resume
./nextflow src/nf_modules/bowtie/mapping_paired.nf \
-c src/nf_modules/bowtie/mapping_paired.config \
-profile singularity \
--index "results/mapping/index/*.ebwt" \
- --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
+ --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
+ -resume
fi
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index 335a697e..903ed680 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -5,6 +5,16 @@ profiles {
process {
withName: adaptor_removal {
container = "cutadapt:1.15"
+ cpus = 1
+ }
+ }
+ }
+ singularity {
+ singularity.enabled = true
+ process {
+ withName: adaptor_removal {
+ container = "file://bin/cutadapt:1.15.sif"
+ cpus = 1
}
}
}
@@ -15,6 +25,7 @@ profiles {
module = "cutadapt/1.14"
executor = "sge"
clusterOptions = "-m e -cwd -V"
+ cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index 335a697e..903ed680 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -5,6 +5,16 @@ profiles {
process {
withName: adaptor_removal {
container = "cutadapt:1.15"
+ cpus = 1
+ }
+ }
+ }
+ singularity {
+ singularity.enabled = true
+ process {
+ withName: adaptor_removal {
+ container = "file://bin/cutadapt:1.15.sif"
+ cpus = 1
}
}
}
@@ -15,6 +25,7 @@ profiles {
module = "cutadapt/1.14"
executor = "sge"
clusterOptions = "-m e -cwd -V"
+ cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
diff --git a/src/nf_modules/cutadapt/tests.sh b/src/nf_modules/cutadapt/tests.sh
index 75089624..77712b20 100755
--- a/src/nf_modules/cutadapt/tests.sh
+++ b/src/nf_modules/cutadapt/tests.sh
@@ -1,19 +1,49 @@
./nextflow src/nf_modules/cutadapt/adaptor_removal_paired.nf \
-c src/nf_modules/cutadapt/adaptor_removal_paired.config \
-profile docker \
- --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
+ --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
+ -resume
./nextflow src/nf_modules/cutadapt/adaptor_removal_single.nf \
-c src/nf_modules/cutadapt/adaptor_removal_single.config \
-profile docker \
- --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
+ --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+ -resume
./nextflow src/nf_modules/cutadapt/trimming_paired.nf \
-c src/nf_modules/cutadapt/trimming_paired.config \
-profile docker \
- --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
+ --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
+ -resume
./nextflow src/nf_modules/cutadapt/trimming_single.nf \
-c src/nf_modules/cutadapt/trimming_single.config \
-profile docker \
- --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
+ --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+ -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/cutadapt/adaptor_removal_paired.nf \
+ -c src/nf_modules/cutadapt/adaptor_removal_paired.config \
+ -profile docker \
+ --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
+ -resume
+
+./nextflow src/nf_modules/cutadapt/adaptor_removal_single.nf \
+ -c src/nf_modules/cutadapt/adaptor_removal_single.config \
+ -profile docker \
+ --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+ -resume
+
+./nextflow src/nf_modules/cutadapt/trimming_paired.nf \
+ -c src/nf_modules/cutadapt/trimming_paired.config \
+ -profile docker \
+ --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
+ -resume
+
+./nextflow src/nf_modules/cutadapt/trimming_single.nf \
+ -c src/nf_modules/cutadapt/trimming_single.config \
+ -profile docker \
+ --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+ -resume
+fi
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index c2f05ec2..9dce3d72 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -5,6 +5,16 @@ profiles {
process {
withName: trimming {
container = "cutadapt:1.15"
+ cpus = 1
+ }
+ }
+ }
+ singularity {
+ singularity.enabled = true
+ process {
+ withName: trimming {
+ container = "file://bin/cutadapt:1.15.sif"
+ cpus = 1
}
}
}
@@ -15,6 +25,7 @@ profiles {
module = "cutadapt/1.14"
executor = "sge"
clusterOptions = "-m e -cwd -V"
+ cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index c2f05ec2..9dce3d72 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -5,6 +5,16 @@ profiles {
process {
withName: trimming {
container = "cutadapt:1.15"
+ cpus = 1
+ }
+ }
+ }
+ singularity {
+ singularity.enabled = true
+ process {
+ withName: trimming {
+ container = "file://bin/cutadapt:1.15.sif"
+ cpus = 1
}
}
}
@@ -15,6 +25,7 @@ profiles {
module = "cutadapt/1.14"
executor = "sge"
clusterOptions = "-m e -cwd -V"
+ cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
diff --git a/src/nf_modules/deeptools/tests.sh b/src/nf_modules/deeptools/tests.sh
index 9100afcc..8c95d405 100755
--- a/src/nf_modules/deeptools/tests.sh
+++ b/src/nf_modules/deeptools/tests.sh
@@ -1,9 +1,24 @@
#!/bin/sh
-cp data/tiny_dataset/map/tiny_v2.sort.bam data/tiny_dataset/map/tiny_v2_bis.sort.bam
+cp data/tiny_dataset/map/tiny_v2.sort.bam \
+ data/tiny_dataset/map/tiny_v2_bis.sort.bam
-./nextflow src/nf_modules/deeptools/bam_to_bigwig.nf -c src/nf_modules/deeptools/bam_to_bigwig.config -profile docker --bam "data/tiny_dataset/map/tiny_v2*.sort.bam"
+./nextflow src/nf_modules/deeptools/bam_to_bigwig.nf \
+ -c src/nf_modules/deeptools/bam_to_bigwig.config \
+ -profile docker \
+ --bam "data/tiny_dataset/map/tiny_v2*.sort.bam" \
+ -resume
-./nextflow src/nf_modules/deeptools/compute_matrix.nf -c src/nf_modules/deeptools/compute_matrix.config -profile docker --bw "results/mapping/bigwig/*.bw" --bed "data/tiny_dataset/annot/tiny.bed"
+./nextflow src/nf_modules/deeptools/compute_matrix.nf \
+ -c src/nf_modules/deeptools/compute_matrix.config \
+ -profile docker \
+ --bw "results/mapping/bigwig/*.bw" \
+ --bed "data/tiny_dataset/annot/tiny.bed" \
+ -resume
-./nextflow src/nf_modules/deeptools/plot_profile.nf -c src/nf_modules/deeptools/plot_profile.config -profile docker --matrix "results/mapping/region_matrix/*.mat.gz" --title "plot title"
+./nextflow src/nf_modules/deeptools/plot_profile.nf \
+ -c src/nf_modules/deeptools/plot_profile.config \
+ -profile docker \
+ --matrix "results/mapping/region_matrix/*.mat.gz" \
+ --title "plot title" \
+ -resume
diff --git a/src/nf_modules/htseq/tests.sh b/src/nf_modules/htseq/tests.sh
index 63e4ad51..3bb59705 100755
--- a/src/nf_modules/htseq/tests.sh
+++ b/src/nf_modules/htseq/tests.sh
@@ -2,5 +2,6 @@
-c src/nf_modules/htseq/htseq.config \
-profile docker \
--gtf "data/tiny_dataset/annot/tiny.gff" \
- --bam "data/tiny_dataset/map/tiny_v2.bam"
+ --bam "data/tiny_dataset/map/tiny_v2.bam" \
+ -resume
diff --git a/src/nf_modules/kallisto/tests.sh b/src/nf_modules/kallisto/tests.sh
index cd87cf00..299c8dd5 100755
--- a/src/nf_modules/kallisto/tests.sh
+++ b/src/nf_modules/kallisto/tests.sh
@@ -1,17 +1,20 @@
./nextflow src/nf_modules/kallisto/indexing.nf \
-c src/nf_modules/kallisto/indexing.config \
-profile docker \
- --fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
+ --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
+ -resume
./nextflow src/nf_modules/kallisto/mapping_single.nf \
-c src/nf_modules/kallisto/mapping_single.config \
-profile docker \
--index "results/mapping/index/tiny_v2.index" \
- --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
+ --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+ -resume
./nextflow src/nf_modules/kallisto/mapping_paired.nf \
-c src/nf_modules/kallisto/mapping_paired.config \
-profile docker \
--index "results/mapping/index/tiny_v2.index" \
- --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
+ --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
+ -resume
diff --git a/src/nf_modules/multiqc/tests.sh b/src/nf_modules/multiqc/tests.sh
index baa1afaa..b323f300 100755
--- a/src/nf_modules/multiqc/tests.sh
+++ b/src/nf_modules/multiqc/tests.sh
@@ -1,9 +1,11 @@
./nextflow src/nf_modules/multiqc/multiqc_paired.nf \
-c src/nf_modules/multiqc/multiqc_paired.config \
-profile docker \
- --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
+ --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
+ -resume
./nextflow src/nf_modules/multiqc/multiqc_single.nf \
-c src/nf_modules/multiqc/multiqc_single.config \
-profile docker \
- --fastq "data/tiny_dataset/fastq/tiny_S.fastq"
+ --fastq "data/tiny_dataset/fastq/tiny_S.fastq" \
+ -resume
diff --git a/src/nf_modules/music/tests.sh b/src/nf_modules/music/tests.sh
index 23a62b4f..7e44e5d0 100755
--- a/src/nf_modules/music/tests.sh
+++ b/src/nf_modules/music/tests.sh
@@ -5,4 +5,5 @@ cp results/training/bams/sBNLN18.bam results/training/bams/sBNLN18_control.bam
--fasta "results/training/fasta/*.fasta" \
--bam "results/training/bams/s*.bam" \
--index "results/training/mapping/index/*" \
- --read_size 50 --frag_size 300
+ --read_size 50 --frag_size 300 \
+ -resume
diff --git a/src/nf_modules/rsem/tests.sh b/src/nf_modules/rsem/tests.sh
index bfdba62a..fdf0aa30 100755
--- a/src/nf_modules/rsem/tests.sh
+++ b/src/nf_modules/rsem/tests.sh
@@ -2,17 +2,20 @@
-c src/nf_modules/rsem/indexing.config \
-profile docker \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
- --annotation "data/tiny_dataset/annot/tiny.gff"
+ --annotation "data/tiny_dataset/annot/tiny.gff" \
+ -resume
./nextflow src/nf_modules/rsem/quantification_single.nf \
-c src/nf_modules/rsem/quantification_single.config \
-profile docker \
--index "results/mapping/index/tiny_v2.index*" \
- --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
+ --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+ -resume
./nextflow src/nf_modules/rsem/quantification_paired.nf \
-c src/nf_modules/rsem/quantification_paired.config \
-profile docker \
--index "results/mapping/index/tiny_v2.index*" \
- --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
+ --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
+ -resume
diff --git a/src/nf_modules/samblaster/tests.sh b/src/nf_modules/samblaster/tests.sh
index 536f5621..962f2b8b 100755
--- a/src/nf_modules/samblaster/tests.sh
+++ b/src/nf_modules/samblaster/tests.sh
@@ -1,4 +1,5 @@
./nextflow src/nf_modules/samblaster/dedup_sams.nf \
-c src/nf_modules/samblaster/dedup_sams.config \
-profile docker \
- --bam "data/tiny_dataset/map/tiny_v2.bam"
+ --bam "data/tiny_dataset/map/tiny_v2.bam" \
+ -resume
diff --git a/src/nf_modules/samtools/tests.sh b/src/nf_modules/samtools/tests.sh
index 96a55e51..e9bd50d0 100755
--- a/src/nf_modules/samtools/tests.sh
+++ b/src/nf_modules/samtools/tests.sh
@@ -1,20 +1,24 @@
./nextflow src/nf_modules/samtools/sort_bams.nf \
-c src/nf_modules/samtools/sort_bams.config \
-profile docker \
- --bam "data/tiny_dataset/map/tiny_v2.bam"
+ --bam "data/tiny_dataset/map/tiny_v2.bam" \
+ -resume
./nextflow src/nf_modules/samtools/index_bams.nf \
-c src/nf_modules/samtools/index_bams.config \
-profile docker \
- --bam "data/tiny_dataset/map/tiny_v2.sort.bam"
+ --bam "data/tiny_dataset/map/tiny_v2.sort.bam" \
+ -resume
./nextflow src/nf_modules/samtools/split_bams.nf \
-c src/nf_modules/samtools/split_bams.config \
-profile docker \
- --bam "data/tiny_dataset/map/tiny_v2.bam"
+ --bam "data/tiny_dataset/map/tiny_v2.bam" \
+ -resume
./nextflow src/nf_modules/samtools/filter_bams.nf \
-c src/nf_modules/samtools/filter_bams.config \
-profile docker \
--bam "data/tiny_dataset/map/tiny_v2.bam" \
- --bed "data/tiny_dataset/OLD/2genes.bed"
+ --bed "data/tiny_dataset/OLD/2genes.bed" \
+ -resume
diff --git a/src/nf_modules/sratoolkit/tests.sh b/src/nf_modules/sratoolkit/tests.sh
index 0321590e..97d8026b 100755
--- a/src/nf_modules/sratoolkit/tests.sh
+++ b/src/nf_modules/sratoolkit/tests.sh
@@ -1,4 +1,5 @@
./nextflow src/nf_modules/sratoolkit/fastqdump.nf \
-c src/nf_modules/sratoolkit/fastqdump.config \
-profile docker \
- --list_srr "src/nf_modules/sratoolkit/list-srr.txt"
+ --list_srr "src/nf_modules/sratoolkit/list-srr.txt" \
+ -resume
--
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