Verified Commit 2150d981 authored by Laurent Modolo's avatar Laurent Modolo
Browse files

cleanup DSL1 test.sh

parent cc2d49f6
./nextflow src/nf_modules/bedtools/fasta_from_bed.nf \
-c src/nf_modules/bedtools/fasta_from_bed.config \
-profile docker \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
--bed "data/tiny_dataset/annot/tiny.bed" \
-resume
if [ -x "$(command -v singularity)" ]; then
./nextflow src/nf_modules/bedtools/fasta_from_bed.nf \
-c src/nf_modules/bedtools/fasta_from_bed.config \
-profile singularity \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
--bed "data/tiny_dataset/annot/tiny.bed" \
-resume
fi
./nextflow src/nf_modules/bowtie/indexing.nf \
-c src/nf_modules/bowtie/indexing.config \
-profile docker \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-resume
./nextflow src/nf_modules/bowtie/mapping_single.nf \
-c src/nf_modules/bowtie/mapping_single.config \
-profile docker \
--index "results/mapping/index/*.ebwt" \
--fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
-resume
./nextflow src/nf_modules/bowtie/mapping_paired.nf \
-c src/nf_modules/bowtie/mapping_paired.config \
-profile docker \
--index "results/mapping/index/*.ebwt" \
--fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
-resume
if [ -x "$(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" \
-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" \
-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" \
-resume
fi
./nextflow src/nf_modules/bowtie2/indexing.nf \
-c src/nf_modules/bowtie2/indexing.config \
-profile docker \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-resume
./nextflow src/nf_modules/bowtie2/mapping_single.nf \
-c src/nf_modules/bowtie2/mapping_single.config \
-profile docker \
--index "data/tiny_dataset/fasta/*.bt2" \
--fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
-resume
./nextflow src/nf_modules/bowtie2/mapping_paired.nf \
-c src/nf_modules/bowtie2/mapping_paired.config \
-profile docker \
--index "data/tiny_dataset/fasta/*.bt2" \
--fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
-resume
if [ -x "$(command -v singularity)" ]; then
./nextflow src/nf_modules/bowtie2/indexing.nf \
-c src/nf_modules/bowtie2/indexing.config \
-profile singularity \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-resume
./nextflow src/nf_modules/bowtie2/mapping_single.nf \
-c src/nf_modules/bowtie2/mapping_single.config \
-profile singularity \
--index "data/tiny_dataset/fasta/*.bt2" \
--fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
-resume
./nextflow src/nf_modules/bowtie2/mapping_paired.nf \
-c src/nf_modules/bowtie2/mapping_paired.config \
-profile singularity \
--index "data/tiny_dataset/fasta/*.bt2" \
--fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
-resume
fi
./nextflow src/nf_modules/bwa/indexing.nf \
-c src/nf_modules/bwa/indexing.config \
-profile docker \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-resume
# ./nextflow src/nf_modules/bwa/mapping_single.nf \
# -c src/nf_modules/bwa/mapping_single.config \
# -profile docker \
# --index "results/mapping/index/tiny_v2.index" \
# --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
./nextflow src/nf_modules/bwa/mapping_paired.nf \
-c src/nf_modules/bwa/mapping_paired.config \
-profile docker \
--index "results/mapping/index/tiny_v2.*" \
--fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
-resume
if [ -x "$(command -v singularity)" ]; then
./nextflow src/nf_modules/bwa/indexing.nf \
-c src/nf_modules/bwa/indexing.config \
-profile singularity \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-resume
# ./nextflow src/nf_modules/bwa/mapping_single.nf \
# -c src/nf_modules/bwa/mapping_single.config \
# -profile singularity \
# --index "results/mapping/index/tiny_v2.index" \
# --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
./nextflow src/nf_modules/bwa/mapping_paired.nf \
-c src/nf_modules/bwa/mapping_paired.config \
-profile singularity \
--index "results/mapping/index/tiny_v2.*" \
--fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
-resume
fi
./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
if [ -x "$(command -v singularity)" ]; then
./nextflow src/nf_modules/cutadapt/adaptor_removal_paired.nf \
-c src/nf_modules/cutadapt/adaptor_removal_paired.config \
-profile docker \
--fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
-resume
./nextflow src/nf_modules/cutadapt/adaptor_removal_single.nf \
-c src/nf_modules/cutadapt/adaptor_removal_single.config \
-profile docker \
--fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
-resume
./nextflow src/nf_modules/cutadapt/trimming_paired.nf \
-c src/nf_modules/cutadapt/trimming_paired.config \
-profile docker \
--fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
-resume
./nextflow src/nf_modules/cutadapt/trimming_single.nf \
-c src/nf_modules/cutadapt/trimming_single.config \
-profile docker \
--fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
-resume
fi
#!/bin/sh
cp data/tiny_dataset/map/tiny_v2.sort.bam \
data/tiny_dataset/map/tiny_v2_bis.sort.bam
./nextflow src/nf_modules/deeptools/bam_to_bigwig.nf \
-c src/nf_modules/deeptools/bam_to_bigwig.config \
-profile docker \
--bam "data/tiny_dataset/map/tiny_v2*.sort.bam" \
-resume
./nextflow src/nf_modules/deeptools/compute_matrix.nf \
-c src/nf_modules/deeptools/compute_matrix.config \
-profile docker \
--bw "results/mapping/bigwig/*.bw" \
--bed "data/tiny_dataset/annot/tiny.bed" \
-resume
./nextflow src/nf_modules/deeptools/plot_profile.nf \
-c src/nf_modules/deeptools/plot_profile.config \
-profile docker \
--matrix "results/mapping/region_matrix/*.mat.gz" \
--title "plot title" \
-resume
if [ -x "$(command -v singularity)" ]; then
./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" \
-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" \
-resume
fi
./nextflow src/nf_modules/fastp/fastp_paired.nf \
-c src/nf_modules/fastp/fastp_paired.config \
-profile docker \
--fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
-resume
./nextflow src/nf_modules/fastp/fastp_single.nf \
-c src/nf_modules/fastp/fastp_single.config \
-profile docker \
--fastq "data/tiny_dataset/fastq/tiny_S.fastq" \
-resume
if [ -x "$(command -v singularity)" ]; then
./nextflow src/nf_modules/fastp/fastp_paired.nf \
-c src/nf_modules/fastp/fastp_paired.config \
-profile singularity \
--fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
-resume
./nextflow src/nf_modules/fastp/fastp_single.nf \
-c src/nf_modules/fastp/fastp_single.config \
-profile singularity \
--fastq "data/tiny_dataset/fastq/tiny_S.fastq" \
-resume
fi
./nextflow src/nf_modules/fastqc/fastqc_paired.nf \
-c src/nf_modules/fastqc/fastqc_paired.config \
-profile docker \
--fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
-resume
./nextflow src/nf_modules/fastqc/fastqc_single.nf \
-c src/nf_modules/fastqc/fastqc_single.config \
-profile docker \
--fastq "data/tiny_dataset/fastq/tiny_S.fastq" \
-resume
if [ -x "$(command -v singularity)" ]; then
./nextflow src/nf_modules/fastqc/fastqc_paired.nf \
-c src/nf_modules/fastqc/fastqc_paired.config \
-profile singularity \
--fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
-resume
./nextflow src/nf_modules/fastqc/fastqc_single.nf \
-c src/nf_modules/fastqc/fastqc_single.config \
-profile singularity \
--fastq "data/tiny_dataset/fastq/tiny_S.fastq" \
-resume
fi
./nextflow src/nf_modules/hisat2/indexing.nf \
-c src/nf_modules/hisat2/indexing.config \
-profile docker \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-resume
./nextflow src/nf_modules/hisat2/mapping_paired.nf \
-c src/nf_modules/hisat2/mapping_paired.config \
-profile docker \
--index "results/mapping/index/tiny_v2.index*" \
--fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
-resume
./nextflow src/nf_modules/hisat2/mapping_single.nf \
-c src/nf_modules/hisat2/mapping_single.config \
-profile docker \
--index "results/mapping/index/tiny_v2.index*" \
--fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
-resume
if [ -x "$(command -v singularity)" ]; then
./nextflow src/nf_modules/hisat2/indexing.nf \
-c src/nf_modules/hisat2/indexing.config \
-profile singularity \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-resume
./nextflow src/nf_modules/hisat2/mapping_paired.nf \
-c src/nf_modules/hisat2/mapping_paired.config \
-profile singularity \
--index "results/mapping/index/tiny_v2.index*" \
--fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
./nextflow src/nf_modules/hisat2/mapping_single.nf \
-c src/nf_modules/hisat2/mapping_single.config \
-profile singularity \
--index "results/mapping/index/tiny_v2.index*" \
--fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
fi
./nextflow src/nf_modules/htseq/htseq.nf \
-c src/nf_modules/htseq/htseq.config \
-profile docker \
--gtf "data/tiny_dataset/annot/tiny.gff" \
--bam "data/tiny_dataset/map/tiny_v2.bam" \
-resume
if [ -x "$(command -v singularity)" ]; then
./nextflow src/nf_modules/htseq/htseq.nf \
-c src/nf_modules/htseq/htseq.config \
-profile singularity \
--gtf "data/tiny_dataset/annot/tiny.gff" \
--bam "data/tiny_dataset/map/tiny_v2.bam" \
-resume
fi
./nextflow src/nf_modules/kallisto/indexing.nf \
-c src/nf_modules/kallisto/indexing.config \
-profile docker \
--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" \
-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" \
-resume
if [ -x "$(command -v singularity)" ]; then
./nextflow src/nf_modules/kallisto/indexing.nf \
-c src/nf_modules/kallisto/indexing.config \
-profile singularity \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-resume
./nextflow src/nf_modules/kallisto/mapping_single.nf \
-c src/nf_modules/kallisto/mapping_single.config \
-profile singularity \
--index "results/mapping/index/tiny_v2.index" \
--fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
-resume
./nextflow src/nf_modules/kallisto/mapping_paired.nf \
-c src/nf_modules/kallisto/mapping_paired.config \
-profile singularity \
--index "results/mapping/index/tiny_v2.index" \
--fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
-resume
fi
cp data/tiny_dataset/map/tiny_v2.bam data/tiny_dataset/map/tiny_v2_control.bam
./nextflow src/nf_modules/macs2/peak_calling.nf \
-c src/nf_modules/macs2/peak_calling.config \
-profile docker \
-resume \
--bam "data/tiny_dataset/map/tiny_v2*.bam" \
--genome_size 129984 \
--control_tag "control"
if [ -x "$(command -v singularity)" ]; then
./nextflow src/nf_modules/macs2/peak_calling.nf \
-c src/nf_modules/macs2/peak_calling.config \
-profile singularity \
-resume \
--bam "data/tiny_dataset/map/tiny_v2*.bam" \
--genome_size 129984 \
--control_tag "control"
fi
./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" \
-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" \
-resume
if [ -x "$(command -v singularity)" ]; then
./nextflow src/nf_modules/multiqc/multiqc_paired.nf \
-c src/nf_modules/multiqc/multiqc_paired.config \
-profile singularity \
--fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
-resume
./nextflow src/nf_modules/multiqc/multiqc_single.nf \
-c src/nf_modules/multiqc/multiqc_single.config \
-profile singularity \
--fastq "data/tiny_dataset/fastq/tiny_S.fastq" \
-resume
fi
cp data/tiny_dataset/map/tiny_v2.sort.bam data/tiny_dataset/map/tiny_v2_control.sort.bam
./nextflow src/nf_modules/music/peak_calling_single.nf \
-c src/nf_modules/music/peak_calling_single.config \
-profile docker \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
--bam "data/tiny_dataset/map/*.sort.bam" \
--index "data/tiny_dataset/map/*.sort.bam.bai*" \
--read_size 50 --frag_size 300 \
-resume
if [ -x "$(command -v singularity)" ]; then
./nextflow src/nf_modules/music/peak_calling_single.nf \
-c src/nf_modules/music/peak_calling_single.config \
-profile singularity \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
--bam "data/tiny_dataset/map/*.sort.bam" \
--index "data/tiny_dataset/map/*.sort.bam.bai*" \
--read_size 50 --frag_size 300 \
-resume
fi
./nextflow src/nf_modules/rsem/indexing.nf \
-c src/nf_modules/rsem/indexing.config \
-profile docker \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
--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*_R1.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" \
-resume
if [ -x "$(command -v singularity)" ]; then
./nextflow src/nf_modules/rsem/indexing.nf \
-c src/nf_modules/rsem/indexing.config \
-profile docker \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
--annotation "data/tiny_dataset/annot/tiny.gff" \
-resume
./nextflow src/nf_modules/rsem/quantification_single.nf \
-c src/nf_modules/rsem/quantification_single.config \
-profile docker \
--index "results/mapping/index/tiny_v2.index*" \
--fastq "data/tiny_dataset/fastq/tiny*_R1.fastq" \
-resume
./nextflow src/nf_modules/rsem/quantification_paired.nf \
-c src/nf_modules/rsem/quantification_paired.config \
-profile docker \
--index "results/mapping/index/tiny_v2.index*" \
--fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
-resume
fi
./nextflow src/nf_modules/sambamba/sort_bams.nf \
-c src/nf_modules/sambamba/sort_bams.config \
-profile docker \
--bam "data/tiny_dataset/map/tiny_v2.bam" \
-resume
./nextflow src/nf_modules/sambamba/index_bams.nf \
-c src/nf_modules/sambamba/index_bams.config \
-profile docker \
--bam "data/tiny_dataset/map/tiny_v2.sort.bam" \
-resume
./nextflow src/nf_modules/sambamba/split_bams.nf \
-c src/nf_modules/sambamba/split_bams.config \
-profile docker \
--bam "data/tiny_dataset/map/tiny_v2.bam" \
-resume
if [ -x "$(command -v singularity)" ]; then
./nextflow src/nf_modules/sambamba/sort_bams.nf \
-c src/nf_modules/sambamba/sort_bams.config \
-profile singularity \
--bam "data/tiny_dataset/map/tiny_v2.bam" \
-resume
./nextflow src/nf_modules/sambamba/index_bams.nf \
-c src/nf_modules/sambamba/index_bams.config \
-profile singularity \
--bam "data/tiny_dataset/map/tiny_v2.sort.bam" \
-resume
./nextflow src/nf_modules/sambamba/split_bams.nf \
-c src/nf_modules/sambamba/split_bams.config \
-profile singularity \
--bam "data/tiny_dataset/map/tiny_v2.bam" \
-resume
fi
./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" \
-resume
if [ -x "$(command -v singularity)" ]; then
./nextflow src/nf_modules/samblaster/dedup_sams.nf \
-c src/nf_modules/samblaster/dedup_sams.config \
-profile docker \
--bam "data/tiny_dataset/map/tiny_v2.bam" \
-resume
fi
./nextflow src/nf_modules/samtools/sort_bams.nf \
-c src/nf_modules/samtools/sort_bams.config \
-profile docker \
--bam "data/tiny_dataset/map/tiny_v2.bam" \
-resume
./nextflow src/nf_modules/samtools/index_bams.nf \
-c src/nf_modules/samtools/index_bams.config \
-profile docker \
--bam "data/tiny_dataset/map/tiny_v2.sort.bam" \
-resume
./nextflow src/nf_modules/samtools/split_bams.nf \
-c src/nf_modules/samtools/split_bams.config \
-profile docker \
--bam "data/tiny_dataset/map/tiny_v2.bam" \
-resume
./nextflow src/nf_modules/samtools/filter_bams.nf \
-c src/nf_modules/samtools/filter_bams.config \
-profile docker \
--bam "data/tiny_dataset/map/tiny_v2.bam" \
--bed "data/tiny_dataset/OLD/2genes.bed" \
-resume
if [ -x "$(command -v singularity)" ]; then
./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" \
-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" \
-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" \
-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" \
-resume
fi