Hi-C workflow

docker/bedtools/2.31.1/Dockerfile

@@ -0,0 +1,6 @@
+FROM quay.io/biocontainers/bedtools:2.31.1--hf5e1c6e_2 AS bedtools
+FROM python:3.9.19
+
+COPY --from=bedtools /usr/local/bin/ /usr/local/bin/
+
+ENTRYPOINT [ "bash" ]

docker/bowtie2/2.5.4/Dockerfile

@@ -0,0 +1,8 @@
+FROM quay.io/biocontainers/samtools:1.17--h00cdaf9_0 AS samtools
+FROM quay.io/biocontainers/bowtie2:2.5.4--he20e202_2
+
+COPY --from=samtools /usr/local/bin/ /usr/local/bin/
+COPY --from=samtools /usr/local/lib/ /usr/local/lib/
+COPY --from=samtools /usr/local/libexec/ /usr/local/libexec/
+
+ENTRYPOINT [ "bowtie2" ]

docker/juicertools/1.6.2-0/Dockerfile

@@ -0,0 +1,7 @@
+FROM nservant/hicpro:3.0.0 AS hicpro
+FROM aidenlab/juicer:1.0.13
+
+COPY --from=hicpro /HiC-Pro_3.0.0/bin/utils/hicpro2juicebox.sh /HiC-Pro_3.0.0/bin/utils/hicpro2juicebox.sh
+RUN chmod a+rwx /opt/juicer-1.6.2/CPU/common/juicer_tools.1.7.6_jcuda.0.8.jar
+
+ENTRYPOINT [ "bash" ]

tools/bwa.wdl

@@ -209,6 +209,10 @@ task bwa_mem {
             description: "Read group information for BWA to insert into the header. BWA format: '@RG\tID:foo\tSM:bar'",
             group: "common",
         }
+        skip_mate_rescue: "Skip mate rescue"
+        skip_pairing: "Skip pairing; mate rescue performed unless `skip_mate_rescue` also in use"
+        split_smallest: "For split alignment, take the alignment with the smallest coordinate as primary"
+        short_secondary: "Mark shorter split hits as secondary"
         use_all_cores: {
             description: "Use all cores? Recommended for cloud environments.",
             group: "common",
@@ -230,6 +234,10 @@ task bwa_mem {
             ""
         )
         String read_group = ""
+        Boolean skip_mate_rescue = false
+        Boolean skip_pairing = false
+        Boolean split_smallest = false
+        Boolean short_secondary = false
         Boolean use_all_cores = false
         Int ncpu = 4
         Int modify_disk_size_gb = 0
@@ -269,6 +277,10 @@ task bwa_mem {
             bwa_db/"$PREFIX" \
             ~{basename(read_one_fastq_gz)} \
             ~{basename(read_two_file)} \
+            ~{if skip_mate_rescue then "-S" else ""} \
+            ~{if skip_pairing then "-P" else ""} \
+            ~{if split_smallest then "-5" else ""} \
+            ~{if short_secondary then "-M" else ""} \
             | samtools view --no-PG --threads "$samtools_cores" -hb - \
             > ~{output_bam}