fix for singularity/docker standalone

SFGLab · Jul 24, 2024 · bbf9e70 · bbf9e70
1 parent 4d572a1
commit bbf9e70
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Showing 3 changed files with 8 additions and 8 deletions.
diff --git 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
@@ -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
@@ -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