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Unverified Commit 60040ed6 authored by Laurent Modolo's avatar Laurent Modolo
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cutadapt: add singularity to nf files and add -resume to all tests.sh

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with 141 additions and 31 deletions
...@@ -23,7 +23,6 @@ Channel ...@@ -23,7 +23,6 @@ Channel
process fasta_from_bed { process fasta_from_bed {
tag "${bed.baseName}" tag "${bed.baseName}"
cpus 4
publishDir "results/fasta/", mode: 'copy' publishDir "results/fasta/", mode: 'copy'
input: input:
......
./nextflow src/nf_modules/bowtie/indexing.nf \ ./nextflow src/nf_modules/bowtie/indexing.nf \
-c src/nf_modules/bowtie/indexing.config \ -c src/nf_modules/bowtie/indexing.config \
-profile docker \ -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 \ ./nextflow src/nf_modules/bowtie/mapping_single.nf \
-c src/nf_modules/bowtie/mapping_single.config \ -c src/nf_modules/bowtie/mapping_single.config \
-profile docker \ -profile docker \
--index "results/mapping/index/*.ebwt" \ --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 \ ./nextflow src/nf_modules/bowtie/mapping_paired.nf \
-c src/nf_modules/bowtie/mapping_paired.config \ -c src/nf_modules/bowtie/mapping_paired.config \
-profile docker \ -profile docker \
--index "results/mapping/index/*.ebwt" \ --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 "$(command -v singularity)" ]; then if [ -x "$(command -v singularity)" ]; then
./nextflow src/nf_modules/bowtie/indexing.nf \ ./nextflow src/nf_modules/bowtie/indexing.nf \
-c src/nf_modules/bowtie/indexing.config \ -c src/nf_modules/bowtie/indexing.config \
-profile singularity \ -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 \ ./nextflow src/nf_modules/bowtie/mapping_single.nf \
-c src/nf_modules/bowtie/mapping_single.config \ -c src/nf_modules/bowtie/mapping_single.config \
-profile singularity \ -profile singularity \
--index "results/mapping/index/*.ebwt" \ --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 \ ./nextflow src/nf_modules/bowtie/mapping_paired.nf \
-c src/nf_modules/bowtie/mapping_paired.config \ -c src/nf_modules/bowtie/mapping_paired.config \
-profile singularity \ -profile singularity \
--index "results/mapping/index/*.ebwt" \ --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 fi
...@@ -5,6 +5,16 @@ profiles { ...@@ -5,6 +5,16 @@ profiles {
process { process {
withName: adaptor_removal { withName: adaptor_removal {
container = "cutadapt:1.15" 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 { ...@@ -15,6 +25,7 @@ profiles {
module = "cutadapt/1.14" module = "cutadapt/1.14"
executor = "sge" executor = "sge"
clusterOptions = "-m e -cwd -V" clusterOptions = "-m e -cwd -V"
cpus = 1
memory = "20GB" memory = "20GB"
time = "12h" time = "12h"
queue = 'monointeldeb128' queue = 'monointeldeb128'
......
...@@ -5,6 +5,16 @@ profiles { ...@@ -5,6 +5,16 @@ profiles {
process { process {
withName: adaptor_removal { withName: adaptor_removal {
container = "cutadapt:1.15" 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 { ...@@ -15,6 +25,7 @@ profiles {
module = "cutadapt/1.14" module = "cutadapt/1.14"
executor = "sge" executor = "sge"
clusterOptions = "-m e -cwd -V" clusterOptions = "-m e -cwd -V"
cpus = 1
memory = "20GB" memory = "20GB"
time = "12h" time = "12h"
queue = 'monointeldeb128' queue = 'monointeldeb128'
......
./nextflow src/nf_modules/cutadapt/adaptor_removal_paired.nf \ ./nextflow src/nf_modules/cutadapt/adaptor_removal_paired.nf \
-c src/nf_modules/cutadapt/adaptor_removal_paired.config \ -c src/nf_modules/cutadapt/adaptor_removal_paired.config \
-profile docker \ -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 \ ./nextflow src/nf_modules/cutadapt/adaptor_removal_single.nf \
-c src/nf_modules/cutadapt/adaptor_removal_single.config \ -c src/nf_modules/cutadapt/adaptor_removal_single.config \
-profile docker \ -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 \ ./nextflow src/nf_modules/cutadapt/trimming_paired.nf \
-c src/nf_modules/cutadapt/trimming_paired.config \ -c src/nf_modules/cutadapt/trimming_paired.config \
-profile docker \ -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 \ ./nextflow src/nf_modules/cutadapt/trimming_single.nf \
-c src/nf_modules/cutadapt/trimming_single.config \ -c src/nf_modules/cutadapt/trimming_single.config \
-profile docker \ -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
...@@ -5,6 +5,16 @@ profiles { ...@@ -5,6 +5,16 @@ profiles {
process { process {
withName: trimming { withName: trimming {
container = "cutadapt:1.15" 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 { ...@@ -15,6 +25,7 @@ profiles {
module = "cutadapt/1.14" module = "cutadapt/1.14"
executor = "sge" executor = "sge"
clusterOptions = "-m e -cwd -V" clusterOptions = "-m e -cwd -V"
cpus = 1
memory = "20GB" memory = "20GB"
time = "12h" time = "12h"
queue = 'monointeldeb128' queue = 'monointeldeb128'
......
...@@ -5,6 +5,16 @@ profiles { ...@@ -5,6 +5,16 @@ profiles {
process { process {
withName: trimming { withName: trimming {
container = "cutadapt:1.15" 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 { ...@@ -15,6 +25,7 @@ profiles {
module = "cutadapt/1.14" module = "cutadapt/1.14"
executor = "sge" executor = "sge"
clusterOptions = "-m e -cwd -V" clusterOptions = "-m e -cwd -V"
cpus = 1
memory = "20GB" memory = "20GB"
time = "12h" time = "12h"
queue = 'monointeldeb128' queue = 'monointeldeb128'
......
#!/bin/sh #!/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
...@@ -2,5 +2,6 @@ ...@@ -2,5 +2,6 @@
-c src/nf_modules/htseq/htseq.config \ -c src/nf_modules/htseq/htseq.config \
-profile docker \ -profile docker \
--gtf "data/tiny_dataset/annot/tiny.gff" \ --gtf "data/tiny_dataset/annot/tiny.gff" \
--bam "data/tiny_dataset/map/tiny_v2.bam" --bam "data/tiny_dataset/map/tiny_v2.bam" \
-resume
./nextflow src/nf_modules/kallisto/indexing.nf \ ./nextflow src/nf_modules/kallisto/indexing.nf \
-c src/nf_modules/kallisto/indexing.config \ -c src/nf_modules/kallisto/indexing.config \
-profile docker \ -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 \ ./nextflow src/nf_modules/kallisto/mapping_single.nf \
-c src/nf_modules/kallisto/mapping_single.config \ -c src/nf_modules/kallisto/mapping_single.config \
-profile docker \ -profile docker \
--index "results/mapping/index/tiny_v2.index" \ --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 \ ./nextflow src/nf_modules/kallisto/mapping_paired.nf \
-c src/nf_modules/kallisto/mapping_paired.config \ -c src/nf_modules/kallisto/mapping_paired.config \
-profile docker \ -profile docker \
--index "results/mapping/index/tiny_v2.index" \ --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
./nextflow src/nf_modules/multiqc/multiqc_paired.nf \ ./nextflow src/nf_modules/multiqc/multiqc_paired.nf \
-c src/nf_modules/multiqc/multiqc_paired.config \ -c src/nf_modules/multiqc/multiqc_paired.config \
-profile docker \ -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 \ ./nextflow src/nf_modules/multiqc/multiqc_single.nf \
-c src/nf_modules/multiqc/multiqc_single.config \ -c src/nf_modules/multiqc/multiqc_single.config \
-profile docker \ -profile docker \
--fastq "data/tiny_dataset/fastq/tiny_S.fastq" --fastq "data/tiny_dataset/fastq/tiny_S.fastq" \
-resume
...@@ -5,4 +5,5 @@ cp results/training/bams/sBNLN18.bam results/training/bams/sBNLN18_control.bam ...@@ -5,4 +5,5 @@ cp results/training/bams/sBNLN18.bam results/training/bams/sBNLN18_control.bam
--fasta "results/training/fasta/*.fasta" \ --fasta "results/training/fasta/*.fasta" \
--bam "results/training/bams/s*.bam" \ --bam "results/training/bams/s*.bam" \
--index "results/training/mapping/index/*" \ --index "results/training/mapping/index/*" \
--read_size 50 --frag_size 300 --read_size 50 --frag_size 300 \
-resume
...@@ -2,17 +2,20 @@ ...@@ -2,17 +2,20 @@
-c src/nf_modules/rsem/indexing.config \ -c src/nf_modules/rsem/indexing.config \
-profile docker \ -profile docker \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \ --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 \ ./nextflow src/nf_modules/rsem/quantification_single.nf \
-c src/nf_modules/rsem/quantification_single.config \ -c src/nf_modules/rsem/quantification_single.config \
-profile docker \ -profile docker \
--index "results/mapping/index/tiny_v2.index*" \ --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 \ ./nextflow src/nf_modules/rsem/quantification_paired.nf \
-c src/nf_modules/rsem/quantification_paired.config \ -c src/nf_modules/rsem/quantification_paired.config \
-profile docker \ -profile docker \
--index "results/mapping/index/tiny_v2.index*" \ --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
./nextflow src/nf_modules/samblaster/dedup_sams.nf \ ./nextflow src/nf_modules/samblaster/dedup_sams.nf \
-c src/nf_modules/samblaster/dedup_sams.config \ -c src/nf_modules/samblaster/dedup_sams.config \
-profile docker \ -profile docker \
--bam "data/tiny_dataset/map/tiny_v2.bam" --bam "data/tiny_dataset/map/tiny_v2.bam" \
-resume
./nextflow src/nf_modules/samtools/sort_bams.nf \ ./nextflow src/nf_modules/samtools/sort_bams.nf \
-c src/nf_modules/samtools/sort_bams.config \ -c src/nf_modules/samtools/sort_bams.config \
-profile docker \ -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 \ ./nextflow src/nf_modules/samtools/index_bams.nf \
-c src/nf_modules/samtools/index_bams.config \ -c src/nf_modules/samtools/index_bams.config \
-profile docker \ -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 \ ./nextflow src/nf_modules/samtools/split_bams.nf \
-c src/nf_modules/samtools/split_bams.config \ -c src/nf_modules/samtools/split_bams.config \
-profile docker \ -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 \ ./nextflow src/nf_modules/samtools/filter_bams.nf \
-c src/nf_modules/samtools/filter_bams.config \ -c src/nf_modules/samtools/filter_bams.config \
-profile docker \ -profile docker \
--bam "data/tiny_dataset/map/tiny_v2.bam" \ --bam "data/tiny_dataset/map/tiny_v2.bam" \
--bed "data/tiny_dataset/OLD/2genes.bed" --bed "data/tiny_dataset/OLD/2genes.bed" \
-resume
./nextflow src/nf_modules/sratoolkit/fastqdump.nf \ ./nextflow src/nf_modules/sratoolkit/fastqdump.nf \
-c src/nf_modules/sratoolkit/fastqdump.config \ -c src/nf_modules/sratoolkit/fastqdump.config \
-profile docker \ -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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