diff --git a/Dockerfile b/Dockerfile index e30ff84..97763d9 100644 --- a/Dockerfile +++ b/Dockerfile @@ -81,6 +81,6 @@ RUN pip3 install plumbum RUN curl -s https://get.nextflow.io | bash && mv nextflow /opt/ -RUN wget https://github.com/SFGLab/nf-hichip/archive/refs/tags/1.4.tar.gz && tar -xvzf 1.4.tar.gz && mv nf-hichip-1.4/* . && rm 1.4.tar.gz && rm -r nf-hichip-1.4 +RUN wget https://github.com/SFGLab/nf-hichip/archive/refs/tags/1.5.tar.gz && tar -xvzf 1.4.tar.gz && mv nf-hichip-1.5/* . && rm 1.5.tar.gz && rm -r nf-hichip-1.5 RUN /opt/nextflow diff --git a/main.nf b/main.nf index 4169613..fd422c5 100644 --- a/main.nf +++ b/main.nf @@ -1,9 +1,9 @@ // Authors: Mateusz Chiliński (nextflow version) & Zofia Tojek (original version) -params.ref = "/app/hichip-nf-pipeline/ref/Homo_sapiens_assembly38.fasta" +params.ref = "/app/ref/Homo_sapiens_assembly38.fasta" params.outdir = "results" -params.design = "/app/hichip-nf-pipeline/design_high.csv" -params.chrom_sizes = "/app/hichip-nf-pipeline/hg38.chrom.sizes" +params.design = "/app/design_high.csv" +params.chrom_sizes = "/app/hg38.chrom.sizes" params.threads = 4 params.mem = 16 params.mapq = 30 @@ -181,7 +181,7 @@ process RunMapsSingleReplicate { export BWA_INDEX=${params.ref} export MAPQ=${params.mapq} export THREADS=${params.threads} - /app/hichip-nf-pipeline/tasks/run_maps.sh > ${sample}_maps.txt + /app/tasks/run_maps.sh > ${sample}_maps.txt mv MAPS_output/${sample}_current/${sample}.5k.2.sig3Dinteractions.bedpe . """ } diff --git a/main_chipseq.nf b/main_chipseq.nf index 568d3c3..b58d916 100644 --- a/main_chipseq.nf +++ b/main_chipseq.nf @@ -1,9 +1,9 @@ // Authors: Mateusz Chiliński (nextflow version) & Zofia Tojek (original version) -params.ref = "/app/hichip-nf-pipeline/ref/Homo_sapiens_assembly38.fasta" +params.ref = "/app/ref/Homo_sapiens_assembly38.fasta" params.outdir = "results" -params.design = "/app/hichip-nf-pipeline/design_high.csv" -params.chrom_sizes = "/app/hichip-nf-pipeline/hg38.chrom.sizes" +params.design = "/app/design_high.csv" +params.chrom_sizes = "/app/hg38.chrom.sizes" params.threads = 4 params.mem = 16 params.mapq = 30