Added code and README.

1-generate-sv-calls/manta.nf

@@ -0,0 +1,78 @@
+#!/usr/bin/env nextflow
+
+params.reference = 'ref.fa'
+
+reference_file = file(params.reference)
+
+Channel
+    .fromSRA(file('../library_list.txt').readLines())
+    .set{reads}
+
+process bwa_index {
+    publishDir 'bwa_index'
+    module 'bwa/bwa-0.7.17'
+
+    input:
+    file reference from reference_file
+
+    output:
+    file "${reference}.*" into reference_index
+
+    """ bwa index ${reference} """
+}
+
+process samtools_faidx {
+    module 'samtools/samtools-1.9'
+
+    input:
+    file reference from reference_file
+
+    output:
+    file "${reference}.fai" into faidx
+
+    """ samtools faidx ${reference} """
+}
+
+process align {
+    cpus 16
+    module 'bwa/bwa-0.7.17:samtools/samtools-1.9'
+    publishDir 'alignments'
+
+    input:
+    file ref from reference_file
+    file index from reference_index
+    set accession, file(both_ends) from reads
+
+    output:
+    file "${accession}.bam" into aligned
+    file "${accession}.bam.bai" into aligned_index
+
+    """
+    bwa mem -t ${task.cpus} ${ref} ${both_ends} | samtools view -bh - | \
+        samtools fixmate -m - - | samtools sort - | \
+        samtools markdup -r - ${accession}.bam
+    samtools index ${accession}.bam
+    """
+}
+
+process manta {
+    cpus 16
+    module 'biocompute/biocompute-modules'
+    module 'manta/manta-1.6.0'
+    publishDir 'results'
+
+    input:
+    file 'ref.fa' from reference_file
+    file 'ref.fa.fai' from faidx
+    file bams from aligned.collect()
+    file bais from aligned_index.collect()
+
+    output:
+    file "manta*" into results
+
+    """
+    bams=""; for bam in ${bams}; do bams+="--bam \$bam "; done
+    configManta.py \$bams --referenceFasta ref.fa --runDir manta
+    manta/runWorkflow.py -j ${task.cpus}
+    """
+}

1-generate-sv-calls/smoove.nf

@@ -0,0 +1,137 @@
+#!/usr/bin/env nextflow
+
+params.reference = 'ref.fa'
+params.scratch = '/local/scratch/esrbhb'
+
+Channel
+    .fromSRA(file('../library_list.txt').readLines())
+    .set{reads}
+
+reference_file = file(params.reference)
+
+process bwa_index {
+    publishDir 'bwa_index'
+    module 'bwa/bwa-0.7.17'
+
+    input:
+    file reference from reference_file
+
+    output:
+    file "${reference}.*" into reference_index
+
+    """ bwa index ${reference} """
+}
+
+process samtools_faidx {
+    module 'samtools/samtools-1.9'
+
+    input:
+    file reference from reference_file
+
+    output:
+    file "${reference}.fai" into faidx
+
+    """ samtools faidx ${reference} """
+}
+
+process align {
+    cpus 16
+    module 'bwa/bwa-0.7.17:samtools/samtools-1.9'
+    publishDir 'alignments'
+
+    input:
+    file ref from reference_file
+    file index from reference_index
+    set accession, file(both_ends) from reads
+
+    output:
+    set accession, "${accession}.bam*" into aligned
+
+    """
+    bwa mem -R "@RG\\tID:${accession}\\tSM:${accession}\\tPL:ILLUMINA" \
+        -t ${task.cpus} ${ref} ${both_ends} | samtools view -bh - | \
+        samtools fixmate -m - - | samtools sort - | \
+        samtools markdup -r - ${accession}.bam
+    samtools index ${accession}.bam
+    """
+}
+
+aligned.into { aligned_for_smoove_call; aligned_for_smoove_genotype }
+faidx.into { faidx_for_smoove_call; faidx_for_smoove_merge;
+             faidx_for_smoove_genotype }
+
+process smoove_call {
+    container 'brentp/smoove:v0.2.3'
+    publishDir 'unmerged'
+    cpus 8
+
+    input:
+    file 'ref.fa' from reference_file
+    file 'ref.fa.fai' from faidx_for_smoove_call
+    set accession, file(bam) from aligned_for_smoove_call
+
+    output:
+    file "${accession}-smoove.genotyped.vcf.gz" into unmerged
+
+    """
+    smoove call --name ${accession} --fasta ref.fa -p ${task.cpus} \
+        --genotype ${accession}.bam
+    """
+}
+
+process smoove_merge {
+    container 'brentp/smoove:v0.2.3'
+
+    input:
+    file 'ref.fa' from reference_file
+    file 'ref.fa.fai' from faidx_for_smoove_merge
+    file all_unmerged from unmerged.collect()
+
+    output:
+    file "merged.sites.vcf.gz" into merged
+
+    """
+    smoove merge --name merged -f ref.fa ${all_unmerged}
+    """
+}
+
+merged_vcf_faidx_and_bams = merged.combine(faidx_for_smoove_genotype)
+    .combine(aligned_for_smoove_genotype)
+
+process smoove_genotype {
+    container 'brentp/smoove:v0.2.3'
+
+    input:
+    file 'ref.fa' from reference_file
+    set 'merged.sites.vcf.gz', 'ref.fa.fai', accession,
+        file(bam) from merged_vcf_faidx_and_bams
+
+    output:
+    file "${accession}-joint-smoove.genotyped.vcf.gz" into joint_genotyped
+    file "${accession}-joint-smoove.genotyped.vcf.gz.csi" into j_g_index
+
+    """
+    export TMPDIR=\$PWD
+    smoove genotype -d -x --name ${accession}-joint --fasta ref.fa \
+        --vcf merged.sites.vcf.gz ${accession}.bam
+    echo "done!"
+    """
+}
+
+process smoove_paste {
+    container 'brentp/smoove:v0.2.3'
+    publishDir 'output'
+
+    input:
+    file all_vcfs from joint_genotyped.collect()
+    file all_indexes from j_g_index.collect()
+
+    output:
+    file "pasted.smoove.square.vcf.gz" into pasted
+
+    """
+    smoove paste --name pasted ${all_vcfs}
+    """
+}
+
+

2-filter-sv-calls/filter_vcfs.sh

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+#!/bin/bash
+
+# filter manta calls
+cut -f2,4 ../sample_keys.tsv > sample2id.tsv
+bcftools filter -Oz \
+    -i 'INFO/SVTYPE="DEL" && INFO/SVLEN < -500 && INFO/SVLEN > -100000' \
+    ../1-generate-sv-calls/manta/results/manta/results/variants/diploidSV.vcf.gz \
+    | bcftools reheader -s sample2id.tsv - > manta_deletions_only.vcf.gz
+rm sample2id.tsv
+
+# filter lumpy calls
+cut -f1,4 ../sample_keys.tsv > srr2id.tsv
+bcftools filter -Oz \
+    -i 'INFO/SVTYPE="DEL" && INFO/SVLEN < -500 && INFO/SVLEN > -100000' \
+    ../1-generate-sv-calls/lumpy/output/pasted.smoove.square.vcf.gz | \
+    bcftools reheader -s srr2id.tsv - > lumpy_deletions_only.vcf.gz
+rm srr2id.tsv